Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
The amendment filed on June 8, 2026 has been entered.
Election/Restrictions
Applicant's election with traverse of Group I in the reply filed on June 8, 2026 is acknowledged. Applicant has elected the following species:
SEQ ID NO: 16 for the thioredoxin (TRX) and SEQ ID NO: 15 as the thioredoxin binding domain (TBD), wherein the elected species has the structure of SEQ ID NO: 16--SEQ ID NO: 2--SEQ ID NO: 3--SEQ ID NO: 4--SEQ ID NO: 5--SEQ ID NO: 6--SEQ ID NO: 7--SEQ ID NO: 8--SEQ ID NO: 9--SEQ ID NO: 10--SEQ ID NO: 15--SEQ ID NO: 12, the TRX-Taq-TBD construct corresponding to SEQ ID NO: 35 (designated pATG7346 in the specification). Applicant also elects SEQ ID NO:1 as element (a) and substitution of all or a portion of SEQ ID NO:11 with the heterologous TBD of SEQ ID NO:15.
The traversal is on the ground(s) that there would be no serious burden to search and/or examine Groups I and II together. This is not found persuasive because as discussed in the Requirement for Restriction/Election mailed on April 8, 2026, there would be a serious search and/or examination burden because Groups I and II have a different classification, requires a different field of search, and raises different examination issues, such as issues under 35 USC 101, 112, and art issues for the product of Group I that is not required for Group II.
The requirement is still deemed proper and is therefore made FINAL.
Status of Claims
Claims 1, 13, 42, 70, 78, 86, 94, 103, and 111 are pending.
Claim 94 is withdrawn.
Claims 1, 13, 42, 70, 78, 86, 103, and 111 are under examination.
Claim for Domestic Priority
Applicants' claim for domestic priority under 35 USC 119(e) to US provisional application 63/488,416 filed 03/03/2023 and 63/488,035 filed 03/02/2023, is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on May 21, 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Objections
Claim 70 is objected for lack of a conjunction between elements (a) and (b).
Appropriate correction is required.
For examination purposes, claim 70 has been interpreted as “(a)…12;” or “(b)….”.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 13 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 13 recites the phrase “genetic fusion”. The metes and bounds of the phrase in the context of the above claims are not clear. Claim 13 is directed to a chimeric polypeptide comprising DNA polymerase domain, TBD, and TRX. Therefore, it is unclear how the chimera is a genetic fusion. Clarification is requested.
Claim 70 and claim 78 depending therefrom are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 70 recites the phrase “DNA polymerase domain corresponding to SEQ ID NO:1 and comprising… (a) segments having at least 40% sequence identity to one of SEQ ID NOS: 3, 5, 7, 9, 11….(b) (i) segments having at least 40% sequence identity to one of SEQ ID NOS:.. (ii) wherein all or a portion of the sequences in SEQ ID NO:1.. are substituted for a heterologous sequence..”. The metes and bounds of the phrase in the context of the above claims are not clear. It is unclear how the DNA polymerase can comprise the amino acid sequence of SEQ ID NO:1 and also have segments having at least 40% sequence identity to any one of SEQ ID NO:.2-12 or all or portions of SEQ ID NO:3, 5, 7, 9, 11 substituted with TBD, TRX, or TBD/TRX. A polypeptide either has the amino acid sequence of a given sequence identifier or it does not. Clarification is requested.
Claim 78 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 78 recites the phrase “DNA polymerase of claim 70, comprising a sequence having at least 60% sequence identity to one of….”. The metes and bounds of the phrase in the context of the above claims are not clear. Claim 70 stipulates that the DNA polymerase has the amino acid sequence of SEQ ID NO:1. Therefore, it is unclear how the DNA polymerase can comprise SEQ ID NO:15, 16, and 17. A polypeptide either has the amino acid sequence of a given sequence identifier or it does not. Clarification is requested.
Claim 78 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 78 recites the phrases “(SEQ ID NO:.)”. The metes and bounds of the limitations in the context of the above claims are not clear. The usage parentheses renders the claims indefinite because it is unclear whether the limitation(s) enclosed in the parentheses are part of the claimed invention or is a representative sequence for the recited DNA polymerase, TRX, and TBD. See MPEP § 2173.05(d).
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 78 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 78 recites the phrase “DNA polymerase of claim 70, comprising a sequence having at least 60% sequence identity to one of….”. Claim 70 stipulates that the DNA polymerase has the amino acid sequence of SEQ ID NO:1. Therefore, claim 78 fails to further limit claim 70.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 13, 42, 70, 78, 86, 103, and 111 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.'' Claims 1, 3, 42, 86, and 111 encompass a DNA polymerase system comprising (a) any DNA polymerase domain, (b) any thioredoxin binding domain (TBD), and (c) any thioredoxin domain (TRX), wherein the system has reduced stutter proclivity. Claim 70 encompasses any DNA polymerase comprising (a) segments having at least 40% sequence identity to SEQ ID NO:2, 4, 6, 8, 10, or 12 and (b)(i) segments having at least 40% sequence identity to SEQ ID NO:3, 5, 7, 9, or 11, or (ii) wherein all or any portion of SEQ DI NO:3, 5, 7, 9, or 11 are substituted with any TBD, TRX, or TBD/TRX. Claim 78 encompasses any DNA polymerase having at least 60% sequence identity to a sequence comprising SEQ ID NO: 16--SEQ ID NO: 2--SEQ ID NO: 3--SEQ ID NO: 4--SEQ ID NO: 5--SEQ ID NO: 6--SEQ ID NO: 7--SEQ ID NO: 8--SEQ ID NO: 9--SEQ ID NO: 10--SEQ ID NO: 15--SEQ ID NO: 12. Claim 103 encompasses any thioredoxin having the properties of (a)-b). Therefore, the claims are drawn to a polypeptide comprising (a) a genus of DNA polymerase domains having unknown structure, (b) genus of thioredoxin binding domains (TBD) having unknown structure, and (c) genus of thioredoxin domains (TRX) having unknown structure, wherein the polypeptide has DNA polymerase activity and/or DNA polymerase activity and reduced stutter proclivity.
MPEP 2163 I. states that to “satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention.
MPEP 2163. II.A.3.(a) sates that “Possession may be shown in many ways. For example, possession may be shown by describing an actual reduction to practice of the claimed invention. Possession may also be shown by a clear depiction of the invention in detailed drawings or in structural chemical formulas which permit a person skilled in the art to clearly recognize that inventor had possession of the claimed invention. An adequate written description of the invention may be shown by any description of sufficient, relevant, identifying characteristics so long as a person skilled in the art would recognize that the inventor had possession of the claimed invention.
According to MPEP 2163.II.A.3.(a).ii), “Satisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’"
The recitations of “DNA polymerase”, “thioredoxin binding domain”, “thioredoxin domain”, and “reduced stutter proclivity” fail to provide a sufficient description of the claimed genus as it merely describes the functional features of the genus without providing any definition of the structural features of the species within the genus. The specification does not specifically define any of the species that fall within the genus. The specification does not define any structural features commonly possessed by members of the genus that distinguish them from others. One skilled in the art therefore cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus.
DNA polymerase, TBD, and TRX were known in the art, see Davidson (Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase. Nucleic Acids Res. 2003 Aug 15;31(16):4702-9. – form PTO-1449). Davidson discloses insertion of a specific T3 TBD into a specific Taq DNA polymerase. However, the prior art and the specification do not disclose the combination of genus of DNA polymerase, TBD, and TRX, wherein the DNA polymerase continues to have enzymatic activity and/or “reduced stutter proclivity”.
The specification is limited to specific fusion proteins comprising different combination of a Taq DNA polymerase of SEQ ID NO:1 and specific variants thereof, specific TBD, and specific TRX , such as the fusion protein comprising the amino acid sequence of SEQ ID NO:35, wherein the fusion protein has DNA polymerase activity and reduced stutter proclivity. While MPEP 2163 acknowledges that in certain situations “one species adequately supports a genus,” it also acknowledges that “[f]or inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus.” In view of the widely variant species encompassed by the genus, the examples described in the specification is not enough and does not constitute a representative number of species to describe the whole genus. Therefore, the specification fails to describe a representative species of the claimed genus.
Further, the claimed invention requires a defined set of DNA polymerase, TBD, and TRX, wherein a fusion protein comprising said DNA polymerase, TBD, and TRX results in a fusion protein having DNA polymerase activity and reduced stutter proclivity. Although the specification discloses exemplary DNA polymerase, TBD, and TRX, a “laundry list” disclosure of every possible moiety does not necessarily constitute a written description of every species in a genus because it would not “reasonably lead” those skilled in the art to any particular species, see Fujikawa v. Wattanasin, 93 F.3d 1559, 1571, 39 USPQ2d 1895, 1905 (Fed. Cir. 1996) or MPEP 2163. While the exemplary DNA polymerase, TBD, and TRX were known in the art, this knowledge alone would not allow one level of skill in the art to immediately envisage the claimed genus. Therefore, the level of skill and knowledge in the art is such that one of ordinary skill would not be able to identify without further testing which combination of DNA polymerase, TBD, and TRX results in a fusion protein comprising said DNA polymerase, TBD, and TRX having DNA polymerase activity and reduced stutter proclivity.
Regarding claims 70, 78, and 103, one of skill in the art could identify all of the polypeptides having 40% sequence identity to SEQ ID NO:2-12, having 60% sequence identity to SEQ ID NO:35 (claim 78(k)), or having 70% sequence identity to amino acids 29-37, 60-77, and 89-98 of SEQ ID NO:16. However, there is no teaching regarding which 60% of the amino acids can vary from SEQ ID NO:2-12 and result in a polypeptide having DNA polymerase activity, which 30% of the amino acids can vary from SEQ ID NO:35 and result in a polypeptide having DNA polymerase activity, and which 70% of amino acids 29-37, 60-77, and 89-98 of SEQ ID NO:16 and result in a polypeptide having the function of a thioredoxin.
Fransceus (J Ind Microbiol Biotechnol. 2017 May;44(4-5):687-695. – form PTO-892) reviews protein engineering techniques, such as random mutagenesis and recombination, directed evolution and iterative or combinatory saturation “hotspots”. Fransceus states that “a recurring problem, however, is choosing which amino acid positions should be targeted. Answering this question is not an easy feat and requires substantial insight in the relationship between an enzyme’s sequence or structure and its properties.” Sanavia (Computational and Structural Biotechnology Journal, Volume 18, 2020, Pages 1968-1979. – form PTO-892) discloses challenges in the prediction of protein stability in the occurrence of multiple mutations. “Multiple-point mutations are common variations of the protein sequence that may be needed in protein engineering when a single-point mutation is not enough to yield the desired stability change. Dealing with multiple-site variations adds another level of complexity beyond the prediction of the effect of a single variant on protein stability, since it requires the learning of many types of combinatorial effects”.
An important consideration is that structure is not necessarily a reliable indicator of function. In the instant case, there is no disclosure relating similarity of structure to conservation of function. Conservation of structure is not necessarily a surrogate for conservation of function.
Given this lack of description of the representative species encompassed by the genus of the claims, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that applicants were in possession of the inventions of claims 1, 13, 42, 70, 78, 86, 103, and 111.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 42, 70, 78, 86, and 103 is/are rejected under 35 U.S.C. 102(a)(1) and/or as being anticipated by Davidson (Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase. Nucleic Acids Res. 2003 Aug 15;31(16):4702-9. – form PTO-1449).
Regarding claim 1, Davidson discloses composition comprising (a) a DNA polymerase, (b) thioredoxin binding domain (TBD), and (c) a thioredoxin (TRX), which reads on a DNA polymerase system (abstract, page 4703 “Generation of ybrid Taq DNA polTBD”, and pages 4703-4704 “Processivity”, “PCR conditions”, “Base substitution fidelity”, Figure 1 at page 4705, and Table 1 at page 4705). Davidson teaches that insertion of the T3 DNA polymerase TBD into the thermostable Taq DNA polymerase converts the Taq DNA polymerase from a low processive to a highly processive enzyme (abstract).
Regarding claim 42, Davidson discloses a composition comprising a DNA polymerase domain conjugated to a thioredoxin binding domain (Figure 1 at page 4705).
Regarding claim 70, the phrase “DNA polymerase domain corresponding to SEQ ID NO:1 and comprising: (a)..(b)..” is indefinite, see the 112(b) rejection above. MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.''. Therefore, claim 70(a) has been broadly interpreted to encompass a DNA polymerase mutant of SEQ ID NO:1 and comprising segments having at least 40% sequence identity to SEQ ID NO:2. Regarding claim 70(a), the Taq DNA polymerase disclosed by Davidson comprises SEQ ID NO:2 of the instant application (see the sequence alignment below). Regarding claim 70(b), Davidson discloses substitution of all portion of SEQ ID NO:11 (HPFNLN) with a heterologous T3 TBD (Figure 1).
Regarding claim 78, the Taq DNA polymerase disclosed by Davidson has at least 60% sequence identity to SEQ ID NO: 16--SEQ ID NO: 2--SEQ ID NO: 3--SEQ ID NO: 4--SEQ ID NO: 5--SEQ ID NO: 6--SEQ ID NO: 7--SEQ ID NO: 8--SEQ ID NO: 9--SEQ ID NO: 10--SEQ ID NO: 15--SEQ ID NO: 12, the TRX-Taq-TBD construct corresponding to SEQ ID NO: 35 of the instant application (see the sequence alignment below).
Regarding claim 86, Davidson discloses a reaction mixture comprising the Taq DNA polymerase and amplification reagents sufficient to amply a DNA target sequence (page 4704 “PCR conditions” and “Base substitution fidelity”).
Regarding claim 103(c), Davidson discloses that that the thioredoxin binding to T3 thioredoxin binding domain is an E. coli thioredoxin (abstract and page 4702 right column). E. coli thioredoxin has 100% sequence identity to SEQ ID NO:16 of the instant application (see the sequence alignment below). The T3 TBD of Davidson has 100% sequence identity to the T3 TBD of SEQ ID NO:15 of the instant application (Figure 1).
Therefore, the reference of Davidson anticipates claims 1, 42, 70, 78, 86, and 103.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 13, 70, 78, and 111 is/are rejected under 35 U.S.C. 103 as being unpatentable over Davidson (Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase. Nucleic Acids Res. 2003 Aug 15;31(16):4702-9. – form PTO-1449) and LaVallie (Thioredoxin as a fusion partner for production of soluble recombinant proteins in Escherichia coli. Methods Enzymol. 2000;326:322-40 – form PTO-892).
Regarding claims 13 and 70, Davidson discloses composition comprising a chimeric DNA polymerase comprising Taq DNA polymerase and thioredoxin binding domain (TBD), wherein HPPFNLN segment (identical to the HPPFNLN of SEQ ID NO:11 of the instant application) of the Taq DNA polymerase is substituted with T3 TBD (identical to the T3 TBD of SEQ ID NO:15 of the instant application) (Figure 1). Davidson teaches that chimeric DNA polymerase converts the Taq DNA polymerase from a low processive to a highly processive enzyme (abstract, page 4703 “Generation of ybrid Taq DNA polTBD”, and pages 4703-4704 “Processivity”, “PCR conditions”, “Base substitution fidelity”, Figure 1 at page 4705, and Table 1 at page 4705).
Regarding claim 78, the Taq DNA polymerase disclosed by Davidson has at least 60% sequence identity to SEQ ID NO: 16--SEQ ID NO: 2--SEQ ID NO: 3--SEQ ID NO: 4--SEQ ID NO: 5--SEQ ID NO: 6--SEQ ID NO: 7--SEQ ID NO: 8--SEQ ID NO: 9--SEQ ID NO: 10--SEQ ID NO: 15--SEQ ID NO: 12, the TRX-Taq-TBD construct corresponding to SEQ ID NO: 35 of the instant application (see the sequence alignment below). SEQ ID NO:1 of the instant application comprises the segments of SEQ ID NO:2-12 of the instant application.
Davidson does not disclose fusing the E. coli thioredoxin of SEQ ID NO:16 to the N-terminus of the chimeric DNA polymerase, wherein the resulting chimer DNA polymerase has reduced stutter proclivity.
Davidson discloses that the thioredoxin (TRX) binding to T3 TBD is an E. coli thioredoxin (abstract and page 4702 right column). E. coli TRX has 100% sequence identity to the TRX of SEQ ID NO:16 of the instant application (see the sequence alignment below). Davidson discloses that the presence of thioredoxin stimulates the activity of the chimeric DNA polymerase (page 4705, 2nd full paragraph).
Regarding claims 13, 78, and 111, LaVallie discloses using E. coli TRX as a fusion partner for production of soluble recombinant proteins in E. coli (page 323).
Regarding the property of having reduced stutter proclivity, the specification of the instant application discloses that the addition of thioredoxin to TBD-modified Taq DNA polymerase or TRX-TBD-modified Taq results in reduced stutter proclivity (Example 1). Therefore, fusing E. coli thioredoxin to the chimeric DNA polymerase of Davidson inherently results in reduced stutter proclivity and reduced stutter proclivity is necessarily present and would flow naturally from following the suggestion of the prior art. MPEP 2112 II states that “[t]here is no requirement that a person of ordinary skill in the art would have recognized the inherent disclosure at the relevant time, but only that the subject matter is in fact inherent in the prior art reference.”
Therefore, in combining the teachings of the above references, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to modify the chimeric DNA polymerase of Davidson by fusing E. coli TRX to the N-terminus or C-terminus of the chimeric DNA polymerase and express the fusion construct in E. coli and obtain the fusion construct, which comprises multiple polypeptides comprising (a) DNA polymerase domain, TBD, and TRX and (b) DNA polymerase domain and TBD. One having ordinary skill in the art would have been motivated to do so as an alternative to supplying TRX to the reaction system comprising the chimeric DNA polymerase of Davidson and/or facilitate soluble expression of said DNA polymerase. One of ordinary skill in the art would have had a reasonable expectation of success since Davidson teaches a chimeric DNA polymerase, wherein the segment SEQ ID NO:2 of Taq polymerase is replaced with T3 TBD of SEQ ID NO:15, Davidson teaches supplying TRX to a reaction system comprising said chimeric DNA polymerase, and LaVallie teaches fusing TRX to recombinant proteins.
Therefore, the above references render claims 13, 70, 78, and 111 prima facie obvious.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 42, 70, 78, and 103 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Claim interpretation
Regarding claim 42, the claim is directed to a naturally occurring Taq DNA polymerase and naturally occurring T3 thioredoxin binding domain, which were known in the art, see Davidson (Insertion of the T3 DNA polymerase thioredoxin binding domain enhances the processivity and fidelity of Taq DNA polymerase. Nucleic Acids Res. 2003 Aug 15;31(16):4702-9. – form PTO-1449)
Regarding claim 70, the claim is directed to a naturally occurring Taq DNA polymerase comprising SEQ ID NO:2 of the instant application (see the sequence alignment below).
Regarding claim 78, the claim is directed to a naturally occurring Taq DNA polymerase, which has at least 60% sequence identity to SEQ ID NO: 16--SEQ ID NO: 2--SEQ ID NO: 3--SEQ ID NO: 4--SEQ ID NO: 5--SEQ ID NO: 6--SEQ ID NO: 7--SEQ ID NO: 8--SEQ ID NO: 9--SEQ ID NO: 10--SEQ ID NO: 15--SEQ ID NO: 12, the TRX-Taq-TBD construct corresponding to SEQ ID NO: 35 of the instant application (see the sequence alignment below).
Regarding claim 103(c), the claim is directed to a naturally occurring E. coli thioredoxin, which was known in the art, see Davidson (abstract and page 4702 right column and see the sequence alignment below).
Therefore, claims 42, 70, 78, and 103 are directed to (A) Taq DNA polymerase, a nature-based product, (B) T3 TBD, a natured based product, or (c) E. coli TRX, a nature based product.
Step 1: This part of the eligibility analysis evaluates whether the claim falls within any statutory category (see MPEP 2106.03). Since the claims are directed to a composition/system comprising the nature-base products, the claims are directed to a composition of matter, which is one of the statutory categories of invention. (Step 1: YES)
Step 2A Prong 1: This part of the eligibility analysis evaluates whether the claim recites a judicial exception (see MPEP 2106.04). The Taq DNA polymerase, T3 TBD, and E. coli TRX are not considered to have markedly different characteristics from what occurs in nature, a naturally occurring Taq DNA polymerase, T3 TBD, and E. coli TRX and are considered to be a law of nature exception. There is no indication in the specification that placing Taq DNA polymerase, T3 TBD, or E. coli TRX into a composition or conjugating/fusing Taq DNA polymerase to T3 TBD result in the Taq DNA polymerase, T3 TBD, and E. coli TRX having any characteristics (structural, functional, or otherwise) that are different from the naturally occurring Taq DNA polymerase, T3 TBD, and E. coli TRX. Because there is no difference in characteristics (structural, functional, or otherwise) between the Taq DNA polymerase, T3 TBD, or E. coli TRX comprised in the claimed composition/system and the naturally Taq DNA polymerase, T3 TBD, and E. coli TRX, respectively, the claimed composition/system comprising Taq DNA polymerase, T3 TBD, or E. coli TRX is directed to a judicial exception.
Step 2A Prong 2: This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application (see MPEP 2106.04(d)). This evaluation is performed by (a) identifying whether there are any additional recited elements in the claim beyond the judicial exception and (b) evaluating those additional elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. There is no indication in the specification that placing Taq DNA polymerase, T3 TBD, or E. coli TRX in a composition/system result in a transformation of the Taq DNA polymerase, T3 TBD, and E. coli TRX (Step2 A: YES)
Step 2B: This part of the eligibility analysis evaluates whether the claim as a whole amounts to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim (see MPEP § 2106.05). The claim only recites the laws of nature and do not include any additional elements that could add significantly more to the judicial exceptions. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the Taq DNA polymerase, T3 TBD, or E. coli TRX comprised in the composition is not markedly different from its naturally occurring counterpart because it conveys the same structural and functional information. Thus, Taq DNA polymerase, T3 TBD, and E. coli TRX does not meaningfully limit the claims, and the claims as a whole do not amount to significantly more than each “product of nature by itself (Step 2B: NO).
As such, the claims do not qualify as eligible subject matter.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 13, 42, 86, and 103 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 and 131 of copending Application No. 19/319,451 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the instant application and the claims of the reference application are directed to chimeric DNA polymerase.
Regarding claims 1 and 3 of the instant application, claims 1 and 10 of the reference application recites a DNA polymerase system comprising (a) a DNA polymerase domain, (b) thioredoxin binding domain (TBD), and (C) a thioredoxin domain (TRX), wherein the system has reduced stutter proclivity.
Regarding claim 42 of the instant application, claim 12 of the reference application recites that the DNA polymerase domain is conjugated to TBD.
Regarding claim 86 of the instant application, claim 131 of the reference application recites a reaction mixture comprising the DNA polymerase system and amplification reagents sufficient to amplify a DNA target sequence.
Regarding claim 103 of the instant application, claim 1 of the reference application recites a TRX having a non-cysteine amino acid at a position corresponding to 35 of SEQ ID NO:16. The specification of the reference application discloses that TRX of SEQ ID NO:200 (which does not have a Cys residue at the position corresponding to 35 of SEQ ID NO:16) has a 3D fold threshold of 0.8 or greater to a TRX database model 6N7W (page 14).
Therefore, the conflicting claims are not patentably distinct from each other
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Claims 1, 13, 42, 70, 78, 86, 94, 103, and 111 are pending.
Claim 94 is withdrawn.
Claims 1, 13, 42, 70, 78, 86, 103, and 111 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YONG D PAK whose telephone number is (571)272-0935. The examiner can normally be reached M-Th: 5:30 am - 3:30 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert Mondesi can be reached on 408-918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YONG D PAK/Primary Examiner, Art Unit 1652
Sequence alignment of the Taq DNA polymerase SEQ ID NO:1 of the instant application (“Qy”) and Taq DNA polymerase (“Db”)
DPO1_THEAQ
ID DPO1_THEAQ Reviewed; 832 AA.
AC P19821;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1991, sequence version 1.
DT 10-JUN-2026, entry version 158.
DE RecName: Full=DNA polymerase I, thermostable;
DE EC=2.7.7.7 {ECO:0000250|UniProtKB:P52026};
DE AltName: Full=Taq polymerase 1;
GN Name=polA; Synonyms=pol1;
OS Thermus aquaticus.
OC Bacteria; Thermotogati; Deinococcota; Deinococci; Thermales; Thermaceae;
OC Thermus.
OX NCBI_TaxID=271;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2649500; DOI=10.1016/s0021-9258(18)83367-1;
RA Lawyer F.C., Stoffel S., Saiki R.K., Myambo K., Drummond R., Gelfand D.H.;
RT "Isolation, characterization, and expression in Escherichia coli of the DNA
RT polymerase gene from Thermus aquaticus.";
RL J. Biol. Chem. 264:6427-6437(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=ATCC 25104 / DSM 625 / JCM 10724 / NBRC 103206 / NCIMB 11243 / YT-1;
RX PubMed=7896728; DOI=10.1093/oxfordjournals.jbchem.a124622;
RA Ishino Y., Ueno T., Miyagi M., Uemori T., Imamura M., Tsunasawa S.,
RA Kato I.;
RT "Overproduction of Thermus aquaticus DNA polymerase and its structural
RT analysis by ion-spray mass spectrometry.";
RL J. Biochem. 116:1019-1024(1994).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RX PubMed=7637814; DOI=10.1038/376612a0;
RA Kim Y., Eom S.H., Wang J., Lee D.-S., Suh S.W., Steitz T.A.;
RT "Crystal structure of Thermus aquaticus DNA polymerase.";
RL Nature 376:612-616(1995).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
RX PubMed=7568114; DOI=10.1073/pnas.92.20.9264;
RA Korolev S., Nayal M., Barnes W.M., di Cera E., Waksman G.;
RT "Crystal structure of the large fragment of Thermus aquaticus DNA
RT polymerase I at 2.5-A resolution: structural basis for thermostability.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:9264-9268(1995).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RX PubMed=8717047; DOI=10.1038/382278a0;
RA Eom S.H., Wang J., Steitz T.A.;
RT "Structure of Taq polymerase with DNA at the polymerase active site.";
RL Nature 382:278-281(1996).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 295-832.
RX PubMed=9857206; DOI=10.1093/emboj/17.24.7514;
RA Li Y., Korolev S., Waksman G.;
RT "Crystal structures of open and closed forms of binary and ternary
RT complexes of the large fragment of Thermus aquaticus DNA polymerase I:
RT structural basis for nucleotide incorporation.";
RL EMBO J. 17:7514-7525(1998).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
RX PubMed=9605316; DOI=10.1002/pro.5560070505;
RA Li Y., Kong Y., Korolev S., Waksman G.;
RT "Crystal structures of the Klenow fragment of Thermus aquaticus DNA
RT polymerase I complexed with deoxyribonucleoside triphosphates.";
RL Protein Sci. 7:1116-1123(1998).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 293-831.
RX PubMed=10449720; DOI=10.1073/pnas.96.17.9491;
RA Li Y., Mitaxov V., Waksman G.;
RT "Structure-based design of Taq DNA polymerases with improved properties of
RT dideoxynucleotide incorporation.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:9491-9496(1999).
CC -!- FUNCTION: In addition to polymerase activity, this DNA polymerase
CC exhibits 5'-3' exonuclease activity (By similarity). Unlikely to have
CC 3'-5' exonuclease activity due to absence of a 3'-5' exonuclease domain
CC (Probable). {ECO:0000250|UniProtKB:P52026, ECO:0000305|PubMed:7637814}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) +
CC diphosphate; Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, Rhea:RHEA-
CC COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, ChEBI:CHEBI:173112;
CC EC=2.7.7.7; Evidence={ECO:0000250|UniProtKB:P52026};
CC -!- BIOTECHNOLOGY: Used in the PCR method because of its high
CC thermostability. Has a relatively high error rate probably related to
CC the lack of exonuclease proofreading functionality. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-A family. {ECO:0000305}.
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DR EMBL; J04639; AAA27507.1; -; Genomic_DNA.
DR EMBL; D32013; BAA06775.1; -; Genomic_DNA.
DR PIR; A33530; A33530.
DR PIR; JX0359; JX0359.
DR PDB; 1BGX; X-ray; 2.30 A; T=1-832.
DR PDB; 1JXE; X-ray; 2.85 A; A=293-832.
DR PDB; 1KTQ; X-ray; 2.50 A; A=290-832.
DR PDB; 1QSS; X-ray; 2.30 A; A=293-831.
DR PDB; 1QSY; X-ray; 2.30 A; A=293-831.
DR PDB; 1QTM; X-ray; 2.30 A; A=293-831.
DR PDB; 1TAQ; X-ray; 2.40 A; A=1-832.
DR PDB; 1TAU; X-ray; 3.00 A; A=1-832.
DR PDB; 2KTQ; X-ray; 2.30 A; A=295-832.
DR PDB; 3KTQ; X-ray; 2.30 A; A=293-832.
DR PDB; 3LWL; X-ray; 2.25 A; A=293-832.
DR PDB; 3LWM; X-ray; 2.19 A; A=293-832.
DR PDB; 3M8R; X-ray; 2.00 A; A=293-832.
DR PDB; 3M8S; X-ray; 2.20 A; A=293-832.
DR PDB; 3OJS; X-ray; 1.90 A; A=293-832.
DR PDB; 3OJU; X-ray; 2.00 A; A=293-832.
DR PDB; 3PO4; X-ray; 1.80 A; A=293-832.
DR PDB; 3PO5; X-ray; 2.39 A; A=293-832.
DR PDB; 3PY8; X-ray; 1.74 A; A=293-832.
DR PDB; 3RR7; X-ray; 1.95 A; A=293-832.
DR PDB; 3RR8; X-ray; 2.40 A; A=293-832.
DR PDB; 3RRG; X-ray; 2.30 A; A=293-832.
DR PDB; 3RRH; X-ray; 1.80 A; A=293-832.
DR PDB; 3RTV; X-ray; 1.90 A; A=293-832.
DR PDB; 3SV3; X-ray; 2.10 A; A=293-832.
DR PDB; 3SV4; X-ray; 1.99 A; A=293-832.
DR PDB; 3SYZ; X-ray; 1.95 A; A=293-832.
DR PDB; 3SZ2; X-ray; 2.15 A; A=293-832.
DR PDB; 3T3F; X-ray; 1.90 A; A=293-832.
DR PDB; 4BWJ; X-ray; 1.55 A; A=293-832.
DR PDB; 4BWM; X-ray; 1.75 A; A=293-832.
DR PDB; 4C8K; X-ray; 2.17 A; A=293-832.
DR PDB; 4C8L; X-ray; 1.70 A; A=293-832.
DR PDB; 4C8M; X-ray; 1.57 A; A=293-832.
DR PDB; 4C8N; X-ray; 1.88 A; A=293-832.
DR PDB; 4C8O; X-ray; 1.75 A; A=293-832.
DR PDB; 4CCH; X-ray; 2.55 A; A=293-832.
DR PDB; 4DF4; X-ray; 2.20 A; A=293-832.
DR PDB; 4DF8; X-ray; 2.00 A; A=293-832.
DR PDB; 4DFJ; X-ray; 1.90 A; A=293-832.
DR PDB; 4DFK; X-ray; 1.65 A; A=293-832.
DR PDB; 4DFM; X-ray; 1.89 A; A=293-832.
DR PDB; 4DFP; X-ray; 2.00 A; A=293-832.
DR PDB; 4DLE; X-ray; 2.44 A; A=293-832.
DR PDB; 4DLG; X-ray; 1.89 A; A=293-832.
DR PDB; 4ELT; X-ray; 2.20 A; A=293-832.
DR PDB; 4ELU; X-ray; 1.80 A; A=293-832.
DR PDB; 4ELV; X-ray; 1.90 A; A=293-832.
DR PDB; 4KTQ; X-ray; 2.50 A; A=294-832.
DR PDB; 4N56; X-ray; 2.20 A; A=281-832.
DR PDB; 4N5S; X-ray; 1.67 A; A=281-832.
DR PDB; 4XIU; X-ray; 2.50 A; A=294-832.
DR PDB; 5E41; X-ray; 1.80 A; A=293-832.
DR PDB; 5KTQ; X-ray; 2.50 A; A=290-832.
DR PDB; 5NKL; X-ray; 1.70 A; A=293-832.
DR PDB; 5O7T; X-ray; 1.80 A; A=293-832.
DR PDB; 5OXJ; X-ray; 2.00 A; A=293-832.
DR PDB; 5SZT; X-ray; 1.80 A; A=293-832.
DR PDB; 5W6K; X-ray; 2.34 A; A=293-832.
DR PDB; 5W6Q; X-ray; 2.66 A; A/C/G=293-832.
DR PDB; 5YTC; X-ray; 2.28 A; A=294-832.
DR PDB; 5YTD; X-ray; 2.00 A; A=294-832.
DR PDB; 5YTE; X-ray; 2.21 A; A=294-832.
DR PDB; 5YTF; X-ray; 1.98 A; A=294-832.
DR PDB; 5YTG; X-ray; 2.07 A; A=294-832.
DR PDB; 5YTH; X-ray; 2.53 A; A=294-832.
DR PDB; 5Z3N; X-ray; 1.91 A; A=294-832.
DR PDB; 6FBC; X-ray; 1.54 A; A=293-832.
DR PDB; 6FBD; X-ray; 2.10 A; A=293-832.
DR PDB; 6FBE; X-ray; 1.59 A; A=293-832.
DR PDB; 6FBF; X-ray; 2.00 A; A=293-832.
DR PDB; 6FBG; X-ray; 1.70 A; A=293-832.
DR PDB; 6FBH; X-ray; 1.80 A; A=293-832.
DR PDB; 6FBI; X-ray; 1.90 A; A=293-832.
DR PDB; 6Q4U; X-ray; 2.00 A; A=293-832.
DR PDB; 6Q4V; X-ray; 2.01 A; A=293-832.
DR PDB; 7OWF; X-ray; 1.91 A; A=293-832.
DR PDB; 8XK7; X-ray; 2.00 A; A=294-832.
DR PDBsum; 1BGX; -.
DR PDBsum; 1JXE; -.
DR PDBsum; 1KTQ; -.
DR PDBsum; 1QSS; -.
DR PDBsum; 1QSY; -.
DR PDBsum; 1QTM; -.
DR PDBsum; 1TAQ; -.
DR PDBsum; 1TAU; -.
DR PDBsum; 2KTQ; -.
DR PDBsum; 3KTQ; -.
DR PDBsum; 3LWL; -.
DR PDBsum; 3LWM; -.
DR PDBsum; 3M8R; -.
DR PDBsum; 3M8S; -.
DR PDBsum; 3OJS; -.
DR PDBsum; 3OJU; -.
DR PDBsum; 3PO4; -.
DR PDBsum; 3PO5; -.
DR PDBsum; 3PY8; -.
DR PDBsum; 3RR7; -.
DR PDBsum; 3RR8; -.
DR PDBsum; 3RRG; -.
DR PDBsum; 3RRH; -.
DR PDBsum; 3RTV; -.
DR PDBsum; 3SV3; -.
DR PDBsum; 3SV4; -.
DR PDBsum; 3SYZ; -.
DR PDBsum; 3SZ2; -.
DR PDBsum; 3T3F; -.
DR PDBsum; 4BWJ; -.
DR PDBsum; 4BWM; -.
Query Match 99.7%; Score 4249; Length 832;
Best Local Similarity 100.0%;
Matches 830; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 RGMLPLFEPKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2 RGMLPLFEPKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDA 61
Qy 61 VIVVFDAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 62 VIVVFDAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDV 121
Qy 121 LASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWAD 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 122 LASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWAD 181
Qy 181 YRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 182 YRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKL 241
Qy 241 SWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERLEFGSLLHEFGLLESPKALEEAPWPP 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 242 SWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERLEFGSLLHEFGLLESPKALEEAPWPP 301
Qy 301 PEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLAL 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 302 PEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLAL 361
Qy 361 REGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLE 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 362 REGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLE 421
Qy 421 GEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHP 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 422 GEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHP 481
Qy 481 FNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKL 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 482 FNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKL 541
Qy 541 KSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAE 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 542 KSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAE 601
Qy 601 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 602 EGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRA 661
Qy 661 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 662 AKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVE 721
Qy 721 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLL 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 722 TLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLL 781
Qy 781 QVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAK 830
||||||||||||||||||||||||||||||||||||||||||||||||||
Db 782 QVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAK 831
Sequence alignment of SEQ ID NO:2 of the instant application (“Qy”) and Taq DNA polymerase (“Db”)
DPO1_THEAQ
ID DPO1_THEAQ Reviewed; 832 AA.
AC P19821;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1991, sequence version 1.
DT 10-JUN-2026, entry version 158.
DE RecName: Full=DNA polymerase I, thermostable;
DE EC=2.7.7.7 {ECO:0000250|UniProtKB:P52026};
DE AltName: Full=Taq polymerase 1;
GN Name=polA; Synonyms=pol1;
OS Thermus aquaticus.
OC Bacteria; Thermotogati; Deinococcota; Deinococci; Thermales; Thermaceae;
OC Thermus.
OX NCBI_TaxID=271;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2649500; DOI=10.1016/s0021-9258(18)83367-1;
RA Lawyer F.C., Stoffel S., Saiki R.K., Myambo K., Drummond R., Gelfand D.H.;
RT "Isolation, characterization, and expression in Escherichia coli of the DNA
RT polymerase gene from Thermus aquaticus.";
RL J. Biol. Chem. 264:6427-6437(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=ATCC 25104 / DSM 625 / JCM 10724 / NBRC 103206 / NCIMB 11243 / YT-1;
RX PubMed=7896728; DOI=10.1093/oxfordjournals.jbchem.a124622;
RA Ishino Y., Ueno T., Miyagi M., Uemori T., Imamura M., Tsunasawa S.,
RA Kato I.;
RT "Overproduction of Thermus aquaticus DNA polymerase and its structural
RT analysis by ion-spray mass spectrometry.";
RL J. Biochem. 116:1019-1024(1994).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RX PubMed=7637814; DOI=10.1038/376612a0;
RA Kim Y., Eom S.H., Wang J., Lee D.-S., Suh S.W., Steitz T.A.;
RT "Crystal structure of Thermus aquaticus DNA polymerase.";
RL Nature 376:612-616(1995).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
RX PubMed=7568114; DOI=10.1073/pnas.92.20.9264;
RA Korolev S., Nayal M., Barnes W.M., di Cera E., Waksman G.;
RT "Crystal structure of the large fragment of Thermus aquaticus DNA
RT polymerase I at 2.5-A resolution: structural basis for thermostability.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:9264-9268(1995).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RX PubMed=8717047; DOI=10.1038/382278a0;
RA Eom S.H., Wang J., Steitz T.A.;
RT "Structure of Taq polymerase with DNA at the polymerase active site.";
RL Nature 382:278-281(1996).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 295-832.
RX PubMed=9857206; DOI=10.1093/emboj/17.24.7514;
RA Li Y., Korolev S., Waksman G.;
RT "Crystal structures of open and closed forms of binary and ternary
RT complexes of the large fragment of Thermus aquaticus DNA polymerase I:
RT structural basis for nucleotide incorporation.";
RL EMBO J. 17:7514-7525(1998).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
RX PubMed=9605316; DOI=10.1002/pro.5560070505;
RA Li Y., Kong Y., Korolev S., Waksman G.;
RT "Crystal structures of the Klenow fragment of Thermus aquaticus DNA
RT polymerase I complexed with deoxyribonucleoside triphosphates.";
RL Protein Sci. 7:1116-1123(1998).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 293-831.
RX PubMed=10449720; DOI=10.1073/pnas.96.17.9491;
RA Li Y., Mitaxov V., Waksman G.;
RT "Structure-based design of Taq DNA polymerases with improved properties of
RT dideoxynucleotide incorporation.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:9491-9496(1999).
CC -!- FUNCTION: In addition to polymerase activity, this DNA polymerase
CC exhibits 5'-3' exonuclease activity (By similarity). Unlikely to have
CC 3'-5' exonuclease activity due to absence of a 3'-5' exonuclease domain
CC (Probable). {ECO:0000250|UniProtKB:P52026, ECO:0000305|PubMed:7637814}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) +
CC diphosphate; Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, Rhea:RHEA-
CC COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, ChEBI:CHEBI:173112;
CC EC=2.7.7.7; Evidence={ECO:0000250|UniProtKB:P52026};
CC -!- BIOTECHNOLOGY: Used in the PCR method because of its high
CC thermostability. Has a relatively high error rate probably related to
CC the lack of exonuclease proofreading functionality. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-A family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; J04639; AAA27507.1; -; Genomic_DNA.
DR EMBL; D32013; BAA06775.1; -; Genomic_DNA.
DR PIR; A33530; A33530.
DR PIR; JX0359; JX0359.
DR PDB; 1BGX; X-ray; 2.30 A; T=1-832.
DR PDB; 1JXE; X-ray; 2.85 A; A=293-832.
DR PDB; 1KTQ; X-ray; 2.50 A; A=290-832.
DR PDB; 1QSS; X-ray; 2.30 A; A=293-831.
DR PDB; 1QSY; X-ray; 2.30 A; A=293-831.
DR PDB; 1QTM; X-ray; 2.30 A; A=293-831.
DR PDB; 1TAQ; X-ray; 2.40 A; A=1-832.
DR PDB; 1TAU; X-ray; 3.00 A; A=1-832.
DR PDB; 2KTQ; X-ray; 2.30 A; A=295-832.
DR PDB; 3KTQ; X-ray; 2.30 A; A=293-832.
DR PDB; 3LWL; X-ray; 2.25 A; A=293-832.
DR PDB; 3LWM; X-ray; 2.19 A; A=293-832.
DR PDB; 3M8R; X-ray; 2.00 A; A=293-832.
DR PDB; 3M8S; X-ray; 2.20 A; A=293-832.
DR PDB; 3OJS; X-ray; 1.90 A; A=293-832.
DR PDB; 3OJU; X-ray; 2.00 A; A=293-832.
DR PDB; 3PO4; X-ray; 1.80 A; A=293-832.
DR PDB; 3PO5; X-ray; 2.39 A; A=293-832.
DR PDB; 3PY8; X-ray; 1.74 A; A=293-832.
DR PDB; 3RR7; X-ray; 1.95 A; A=293-832.
DR PDB; 3RR8; X-ray; 2.40 A; A=293-832.
DR PDB; 3RRG; X-ray; 2.30 A; A=293-832.
DR PDB; 3RRH; X-ray; 1.80 A; A=293-832.
DR PDB; 3RTV; X-ray; 1.90 A; A=293-832.
DR PDB; 3SV3; X-ray; 2.10 A; A=293-832.
DR PDB; 3SV4; X-ray; 1.99 A; A=293-832.
DR PDB; 3SYZ; X-ray; 1.95 A; A=293-832.
DR PDB; 3SZ2; X-ray; 2.15 A; A=293-832.
DR PDB; 3T3F; X-ray; 1.90 A; A=293-832.
DR PDB; 4BWJ; X-ray; 1.55 A; A=293-832.
DR PDB; 4BWM; X-ray; 1.75 A; A=293-832.
DR PDB; 4C8K; X-ray; 2.17 A; A=293-832.
DR PDB; 4C8L; X-ray; 1.70 A; A=293-832.
DR PDB; 4C8M; X-ray; 1.57 A; A=293-832.
DR PDB; 4C8N; X-ray; 1.88 A; A=293-832.
DR PDB; 4C8O; X-ray; 1.75 A; A=293-832.
DR PDB; 4CCH; X-ray; 2.55 A; A=293-832.
DR PDB; 4DF4; X-ray; 2.20 A; A=293-832.
DR PDB; 4DF8; X-ray; 2.00 A; A=293-832.
DR PDB; 4DFJ; X-ray; 1.90 A; A=293-832.
DR PDB; 4DFK; X-ray; 1.65 A; A=293-832.
DR PDB; 4DFM; X-ray; 1.89 A; A=293-832.
DR PDB; 4DFP; X-ray; 2.00 A; A=293-832.
DR PDB; 4DLE; X-ray; 2.44 A; A=293-832.
DR PDB; 4DLG; X-ray; 1.89 A; A=293-832.
DR PDB; 4ELT; X-ray; 2.20 A; A=293-832.
DR PDB; 4ELU; X-ray; 1.80 A; A=293-832.
DR PDB; 4ELV; X-ray; 1.90 A; A=293-832.
DR PDB; 4KTQ; X-ray; 2.50 A; A=294-832.
DR PDB; 4N56; X-ray; 2.20 A; A=281-832.
DR PDB; 4N5S; X-ray; 1.67 A; A=281-832.
DR PDB; 4XIU; X-ray; 2.50 A; A=294-832.
DR PDB; 5E41; X-ray; 1.80 A; A=293-832.
DR PDB; 5KTQ; X-ray; 2.50 A; A=290-832.
DR PDB; 5NKL; X-ray; 1.70 A; A=293-832.
DR PDB; 5O7T; X-ray; 1.80 A; A=293-832.
DR PDB; 5OXJ; X-ray; 2.00 A; A=293-832.
DR PDB; 5SZT; X-ray; 1.80 A; A=293-832.
DR PDB; 5W6K; X-ray; 2.34 A; A=293-832.
DR PDB; 5W6Q; X-ray; 2.66 A; A/C/G=293-832.
DR PDB; 5YTC; X-ray; 2.28 A; A=294-832.
DR PDB; 5YTD; X-ray; 2.00 A; A=294-832.
DR PDB; 5YTE; X-ray; 2.21 A; A=294-832.
DR PDB; 5YTF; X-ray; 1.98 A; A=294-832.
DR PDB; 5YTG; X-ray; 2.07 A; A=294-832.
DR PDB; 5YTH; X-ray; 2.53 A; A=294-832.
DR PDB; 5Z3N; X-ray; 1.91 A; A=294-832.
DR PDB; 6FBC; X-ray; 1.54 A; A=293-832.
DR PDB; 6FBD; X-ray; 2.10 A; A=293-832.
DR PDB; 6FBE; X-ray; 1.59 A; A=293-832.
DR PDB; 6FBF; X-ray; 2.00 A; A=293-832.
DR PDB; 6FBG; X-ray; 1.70 A; A=293-832.
DR PDB; 6FBH; X-ray; 1.80 A; A=293-832.
DR PDB; 6FBI; X-ray; 1.90 A; A=293-832.
DR PDB; 6Q4U; X-ray; 2.00 A; A=293-832.
DR PDB; 6Q4V; X-ray; 2.01 A; A=293-832.
DR PDB; 7OWF; X-ray; 1.91 A; A=293-832.
DR PDB; 8XK7; X-ray; 2.00 A; A=294-832.
DR PDBsum; 1BGX; -.
DR PDBsum; 1JXE; -.
DR PDBsum; 1KTQ; -.
DR PDBsum; 1QSS; -.
DR PDBsum; 1QSY; -.
DR PDBsum; 1QTM; -.
DR PDBsum; 1TAQ; -.
DR PDBsum; 1TAU; -.
DR PDBsum; 2KTQ; -.
DR PDBsum; 3KTQ; -.
DR PDBsum; 3LWL; -.
DR PDBsum; 3LWM; -.
DR PDBsum; 3M8R; -.
DR PDBsum; 3M8S; -.
DR PDBsum; 3OJS; -.
DR PDBsum; 3OJU; -.
DR PDBsum; 3PO4; -.
DR PDBsum; 3PO5; -.
DR PDBsum; 3PY8; -.
DR PDBsum; 3RR7; -.
DR PDBsum; 3RR8; -.
DR PDBsum; 3RRG; -.
DR PDBsum; 3RRH; -.
DR PDBsum; 3RTV; -.
DR PDBsum; 3SV3; -.
DR PDBsum; 3SV4; -.
DR PDBsum; 3SYZ; -.
DR PDBsum; 3SZ2; -.
DR PDBsum; 3T3F; -.
DR PDBsum; 4BWJ; -.
DR PDBsum; 4BWM; -.
Query Match 100.0%; Score 167; Length 832;
Best Local Similarity 100.0%;
Matches 31; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 RGMLPLFEPKGRVLLVDGHHLAYRTFHALKG 31
|||||||||||||||||||||||||||||||
Db 2 RGMLPLFEPKGRVLLVDGHHLAYRTFHALKG 32
Sequence alignment of SEQ ID NO:35 of the instant application (“Qy”) and Taq DNA polymerase (“Db”)
DPO1_THEAQ
ID DPO1_THEAQ Reviewed; 832 AA.
AC P19821;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1991, sequence version 1.
DT 10-JUN-2026, entry version 158.
DE RecName: Full=DNA polymerase I, thermostable;
DE EC=2.7.7.7 {ECO:0000250|UniProtKB:P52026};
DE AltName: Full=Taq polymerase 1;
GN Name=polA; Synonyms=pol1;
OS Thermus aquaticus.
OC Bacteria; Thermotogati; Deinococcota; Deinococci; Thermales; Thermaceae;
OC Thermus.
OX NCBI_TaxID=271;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2649500; DOI=10.1016/s0021-9258(18)83367-1;
RA Lawyer F.C., Stoffel S., Saiki R.K., Myambo K., Drummond R., Gelfand D.H.;
RT "Isolation, characterization, and expression in Escherichia coli of the DNA
RT polymerase gene from Thermus aquaticus.";
RL J. Biol. Chem. 264:6427-6437(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC STRAIN=ATCC 25104 / DSM 625 / JCM 10724 / NBRC 103206 / NCIMB 11243 / YT-1;
RX PubMed=7896728; DOI=10.1093/oxfordjournals.jbchem.a124622;
RA Ishino Y., Ueno T., Miyagi M., Uemori T., Imamura M., Tsunasawa S.,
RA Kato I.;
RT "Overproduction of Thermus aquaticus DNA polymerase and its structural
RT analysis by ion-spray mass spectrometry.";
RL J. Biochem. 116:1019-1024(1994).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
RX PubMed=7637814; DOI=10.1038/376612a0;
RA Kim Y., Eom S.H., Wang J., Lee D.-S., Suh S.W., Steitz T.A.;
RT "Crystal structure of Thermus aquaticus DNA polymerase.";
RL Nature 376:612-616(1995).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
RX PubMed=7568114; DOI=10.1073/pnas.92.20.9264;
RA Korolev S., Nayal M., Barnes W.M., di Cera E., Waksman G.;
RT "Crystal structure of the large fragment of Thermus aquaticus DNA
RT polymerase I at 2.5-A resolution: structural basis for thermostability.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:9264-9268(1995).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RX PubMed=8717047; DOI=10.1038/382278a0;
RA Eom S.H., Wang J., Steitz T.A.;
RT "Structure of Taq polymerase with DNA at the polymerase active site.";
RL Nature 382:278-281(1996).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 295-832.
RX PubMed=9857206; DOI=10.1093/emboj/17.24.7514;
RA Li Y., Korolev S., Waksman G.;
RT "Crystal structures of open and closed forms of binary and ternary
RT complexes of the large fragment of Thermus aquaticus DNA polymerase I:
RT structural basis for nucleotide incorporation.";
RL EMBO J. 17:7514-7525(1998).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
RX PubMed=9605316; DOI=10.1002/pro.5560070505;
RA Li Y., Kong Y., Korolev S., Waksman G.;
RT "Crystal structures of the Klenow fragment of Thermus aquaticus DNA
RT polymerase I complexed with deoxyribonucleoside triphosphates.";
RL Protein Sci. 7:1116-1123(1998).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 293-831.
RX PubMed=10449720; DOI=10.1073/pnas.96.17.9491;
RA Li Y., Mitaxov V., Waksman G.;
RT "Structure-based design of Taq DNA polymerases with improved properties of
RT dideoxynucleotide incorporation.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:9491-9496(1999).
CC -!- FUNCTION: In addition to polymerase activity, this DNA polymerase
CC exhibits 5'-3' exonuclease activity (By similarity). Unlikely to have
CC 3'-5' exonuclease activity due to absence of a 3'-5' exonuclease domain
CC (Probable). {ECO:0000250|UniProtKB:P52026, ECO:0000305|PubMed:7637814}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) +
CC diphosphate; Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339, Rhea:RHEA-
CC COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560, ChEBI:CHEBI:173112;
CC EC=2.7.7.7; Evidence={ECO:0000250|UniProtKB:P52026};
CC -!- BIOTECHNOLOGY: Used in the PCR method because of its high
CC thermostability. Has a relatively high error rate probably related to
CC the lack of exonuclease proofreading functionality. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-A family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; J04639; AAA27507.1; -; Genomic_DNA.
DR EMBL; D32013; BAA06775.1; -; Genomic_DNA.
DR PIR; A33530; A33530.
DR PIR; JX0359; JX0359.
DR PDB; 1BGX; X-ray; 2.30 A; T=1-832.
DR PDB; 1JXE; X-ray; 2.85 A; A=293-832.
DR PDB; 1KTQ; X-ray; 2.50 A; A=290-832.
DR PDB; 1QSS; X-ray; 2.30 A; A=293-831.
DR PDB; 1QSY; X-ray; 2.30 A; A=293-831.
DR PDB; 1QTM; X-ray; 2.30 A; A=293-831.
DR PDB; 1TAQ; X-ray; 2.40 A; A=1-832.
DR PDB; 1TAU; X-ray; 3.00 A; A=1-832.
DR PDB; 2KTQ; X-ray; 2.30 A; A=295-832.
DR PDB; 3KTQ; X-ray; 2.30 A; A=293-832.
DR PDB; 3LWL; X-ray; 2.25 A; A=293-832.
DR PDB; 3LWM; X-ray; 2.19 A; A=293-832.
DR PDB; 3M8R; X-ray; 2.00 A; A=293-832.
DR PDB; 3M8S; X-ray; 2.20 A; A=293-832.
DR PDB; 3OJS; X-ray; 1.90 A; A=293-832.
DR PDB; 3OJU; X-ray; 2.00 A; A=293-832.
DR PDB; 3PO4; X-ray; 1.80 A; A=293-832.
DR PDB; 3PO5; X-ray; 2.39 A; A=293-832.
DR PDB; 3PY8; X-ray; 1.74 A; A=293-832.
DR PDB; 3RR7; X-ray; 1.95 A; A=293-832.
DR PDB; 3RR8; X-ray; 2.40 A; A=293-832.
DR PDB; 3RRG; X-ray; 2.30 A; A=293-832.
DR PDB; 3RRH; X-ray; 1.80 A; A=293-832.
DR PDB; 3RTV; X-ray; 1.90 A; A=293-832.
DR PDB; 3SV3; X-ray; 2.10 A; A=293-832.
DR PDB; 3SV4; X-ray; 1.99 A; A=293-832.
DR PDB; 3SYZ; X-ray; 1.95 A; A=293-832.
DR PDB; 3SZ2; X-ray; 2.15 A; A=293-832.
DR PDB; 3T3F; X-ray; 1.90 A; A=293-832.
DR PDB; 4BWJ; X-ray; 1.55 A; A=293-832.
DR PDB; 4BWM; X-ray; 1.75 A; A=293-832.
DR PDB; 4C8K; X-ray; 2.17 A; A=293-832.
DR PDB; 4C8L; X-ray; 1.70 A; A=293-832.
DR PDB; 4C8M; X-ray; 1.57 A; A=293-832.
DR PDB; 4C8N; X-ray; 1.88 A; A=293-832.
DR PDB; 4C8O; X-ray; 1.75 A; A=293-832.
DR PDB; 4CCH; X-ray; 2.55 A; A=293-832.
DR PDB; 4DF4; X-ray; 2.20 A; A=293-832.
DR PDB; 4DF8; X-ray; 2.00 A; A=293-832.
DR PDB; 4DFJ; X-ray; 1.90 A; A=293-832.
DR PDB; 4DFK; X-ray; 1.65 A; A=293-832.
DR PDB; 4DFM; X-ray; 1.89 A; A=293-832.
DR PDB; 4DFP; X-ray; 2.00 A; A=293-832.
DR PDB; 4DLE; X-ray; 2.44 A; A=293-832.
DR PDB; 4DLG; X-ray; 1.89 A; A=293-832.
DR PDB; 4ELT; X-ray; 2.20 A; A=293-832.
DR PDB; 4ELU; X-ray; 1.80 A; A=293-832.
DR PDB; 4ELV; X-ray; 1.90 A; A=293-832.
DR PDB; 4KTQ; X-ray; 2.50 A; A=294-832.
DR PDB; 4N56; X-ray; 2.20 A; A=281-832.
DR PDB; 4N5S; X-ray; 1.67 A; A=281-832.
DR PDB; 4XIU; X-ray; 2.50 A; A=294-832.
DR PDB; 5E41; X-ray; 1.80 A; A=293-832.
DR PDB; 5KTQ; X-ray; 2.50 A; A=290-832.
DR PDB; 5NKL; X-ray; 1.70 A; A=293-832.
DR PDB; 5O7T; X-ray; 1.80 A; A=293-832.
DR PDB; 5OXJ; X-ray; 2.00 A; A=293-832.
DR PDB; 5SZT; X-ray; 1.80 A; A=293-832.
DR PDB; 5W6K; X-ray; 2.34 A; A=293-832.
DR PDB; 5W6Q; X-ray; 2.66 A; A/C/G=293-832.
DR PDB; 5YTC; X-ray; 2.28 A; A=294-832.
DR PDB; 5YTD; X-ray; 2.00 A; A=294-832.
DR PDB; 5YTE; X-ray; 2.21 A; A=294-832.
DR PDB; 5YTF; X-ray; 1.98 A; A=294-832.
DR PDB; 5YTG; X-ray; 2.07 A; A=294-832.
DR PDB; 5YTH; X-ray; 2.53 A; A=294-832.
DR PDB; 5Z3N; X-ray; 1.91 A; A=294-832.
DR PDB; 6FBC; X-ray; 1.54 A; A=293-832.
DR PDB; 6FBD; X-ray; 2.10 A; A=293-832.
DR PDB; 6FBE; X-ray; 1.59 A; A=293-832.
DR PDB; 6FBF; X-ray; 2.00 A; A=293-832.
DR PDB; 6FBG; X-ray; 1.70 A; A=293-832.
DR PDB; 6FBH; X-ray; 1.80 A; A=293-832.
DR PDB; 6FBI; X-ray; 1.90 A; A=293-832.
DR PDB; 6Q4U; X-ray; 2.00 A; A=293-832.
DR PDB; 6Q4V; X-ray; 2.01 A; A=293-832.
DR PDB; 7OWF; X-ray; 1.91 A; A=293-832.
DR PDB; 8XK7; X-ray; 2.00 A; A=294-832.
DR PDBsum; 1BGX; -.
DR PDBsum; 1JXE; -.
DR PDBsum; 1KTQ; -.
DR PDBsum; 1QSS; -.
DR PDBsum; 1QSY; -.
DR PDBsum; 1QTM; -.
DR PDBsum; 1TAQ; -.
DR PDBsum; 1TAU; -.
DR PDBsum; 2KTQ; -.
DR PDBsum; 3KTQ; -.
DR PDBsum; 3LWL; -.
DR PDBsum; 3LWM; -.
DR PDBsum; 3M8R; -.
DR PDBsum; 3M8S; -.
DR PDBsum; 3OJS; -.
DR PDBsum; 3OJU; -.
DR PDBsum; 3PO4; -.
DR PDBsum; 3PO5; -.
DR PDBsum; 3PY8; -.
DR PDBsum; 3RR7; -.
DR PDBsum; 3RR8; -.
DR PDBsum; 3RRG; -.
DR PDBsum; 3RRH; -.
DR PDBsum; 3RTV; -.
DR PDBsum; 3SV3; -.
DR PDBsum; 3SV4; -.
DR PDBsum; 3SYZ; -.
DR PDBsum; 3SZ2; -.
DR PDBsum; 3T3F; -.
DR PDBsum; 4BWJ; -.
DR PDBsum; 4BWM; -.
Query Match 75.6%; Score 4182; Length 832;
Best Local Similarity 92.0%;
Matches 828; Conservative 1; Mismatches 1; Indels 70; Gaps 2;
Qy 170 RGMLPLFEPKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDA 229
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2 RGMLPLFEPKGRVLLVDGHHLAYRTFHALKGLTTSRGEPVQAVYGFAKSLLKALKEDGDA 61
Qy 230 VIVVFDAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDV 289
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 62 VIVVFDAKAPSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDV 121
Qy 290 LASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWAD 349
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 122 LASLAKKAEKEGYEVRILTADKDLYQLLSDRIHVLHPEGYLITPAWLWEKYGLRPDQWAD 181
Qy 350 YRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKL 409
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 182 YRALTGDESDNLPGVKGIGEKTARKLLEEWGSLEALLKNLDRLKPAIREKILAHMDDLKL 241
Qy 410 SWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERLEFGSLLHEFGLLESPKALEEAPWPP 469
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 242 SWDLAKVRTDLPLEVDFAKRREPDRERLRAFLERLEFGSLLHEFGLLESPKALEEAPWPP 301
Qy 470 PEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLAL 529
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 302 PEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLAL 361
Qy 530 REGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLE 589
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 362 REGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLE 421
Qy 590 GEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGGS 649
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 422 GEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAG-- 479
Qy 650 WYQPKGGTEMFCHPRTGKPLPKYPRIKIPKVGGIFKKPKNKAQREGREPCELDTREYVAG 709
||
Db 480 ------------HP---------------------------------------------- 481
Qy 710 APYTPVEHVVFNPSSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEK 769
|| :||||||||||||||||||||||||||||||||||||||||||||||
Db 482 ----------FNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEK 531
Qy 770 ILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLG 829
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 532 ILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLG 591
Qy 830 QRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPR 889
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 592 QRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPR 651
Qy 890 EAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTL 949
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 652 EAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTL 711
Qy 950 EEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPR 1009
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 712 EEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPR 771
Qy 1010 LEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAK 1069
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 772 LEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAK 831
Sequence alignment of the thioredoxin of SEQ ID NO:16 of the instant application (“Qy”) and E. coli thioredoxin (“Db”)
THIO_ECOLI
ID THIO_ECOLI Reviewed; 109 AA.
AC P0AA25; P00274; P76750; Q2M889; Q47674; Q8XAT2;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 10-JUN-2026, entry version 174.
DE RecName: Full=Thioredoxin 1;
DE Short=Trx-1;
GN Name=trxA; Synonyms=fipA, tsnC; OrderedLocusNames=b3781, JW5856;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC Enterobacterales; Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6098320; DOI=10.1007/bf01116889;
RA Hoeoeg J.-O., von Bahr-Lindstroem H., Josephson S., Wallace B.J.,
RA Kushner S.R., Joernvall H., Holmgren A.;
RT "Nucleotide sequence of the thioredoxin gene from Escherichia coli.";
RL Biosci. Rep. 4:917-923(1984).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6099324; DOI=10.1016/0378-1119(84)90015-5;
RA Wallace B.J., Kushner S.R.;
RT "Genetic and physical analysis of the thioredoxin (trxA) gene of
RT Escherichia coli K-12.";
RL Gene 32:399-408(1984).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3891733; DOI=10.1128/jb.163.1.311-316.1985;
RA Lim C.-J., Geraghty D., Fuchs J.A.;
RT "Cloning and nucleotide sequence of the trxA gene of Escherichia coli K-
RT 12.";
RL J. Bacteriol. 163:311-316(1985).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Wallace B.J., Zownir O., Kushner S.R.;
RT "Physical analysis of the thioredoxin gene from Escherichia coli K-12.";
RL (In) Holmgren A. (eds.);
RL Thioredoxin and glutaredoxin systems, structure and function, pp.11-19,
RL Raven Press, New York (1986).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1379743; DOI=10.1126/science.1379743;
RA Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.;
RT "Analysis of the Escherichia coli genome: DNA sequence of the region from
RT 84.5 to 86.5 minutes.";
RL Science 257:771-778(1992).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [8]
RP PROTEIN SEQUENCE OF 2-109.
RC STRAIN=B;
RX PubMed=4883076; DOI=10.1111/j.1432-1033.1968.tb00470.x;
RA Holmgren A.;
RT "Thioredoxin. 6. The amino acid sequence of the protein from Escherichia
RT coli B.";
RL Eur. J. Biochem. 6:475-484(1968).
RN [9]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [10]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-70, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA Grishin N.V., Zhao Y.;
RT "Lysine acetylation is a highly abundant and evolutionarily conserved
RT modification in Escherichia coli.";
RL Mol. Cell. Proteomics 8:215-225(2009).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
RX PubMed=1094461; DOI=10.1073/pnas.72.6.2305;
RA Holmgren A., Soederberg B.-O., Eklund H., Braenden C.-I.;
RT "Three-dimensional structure of Escherichia coli thioredoxin-S2 to 2.8-A
RT resolution.";
RL Proc. Natl. Acad. Sci. U.S.A. 72:2305-2309(1975).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS).
RX PubMed=4616096; DOI=10.1016/0022-2836(74)90262-9;
RA Soederberg B.-O., Holmgren A., Braenden C.-I.;
RT "Structure of oxidized thioredoxin to 4 with 5-A resolution.";
RL J. Mol. Biol. 90:143-152(1974).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS).
RX PubMed=2181145; DOI=10.1016/0022-2836(90)90313-b;
RA Katti S.K., le Master D.M., Eklund H.;
RT "Crystal structure of thioredoxin from Escherichia coli at 1.68-A
RT resolution.";
RL J. Mol. Biol. 212:167-184(1990).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT GLU-37.
RX PubMed=8098620; DOI=10.1021/bi00070a017;
RA Nikkola M., Gleason F.K., Fuchs J.A., Eklund H.;
RT "Crystal structure analysis of a mutant Escherichia coli thioredoxin in
RT which lysine 36 is replaced by glutamic acid.";
RL Biochemistry 32:5093-5098(1993).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), AND DISULFIDE BOND.
RX PubMed=10489448; DOI=10.1107/s0907444999008756;
RA Schultz L.W., Chivers P.T., Raines R.T.;
RT "The CXXC motif: crystal structure of an active-site variant of Escherichia
RT coli thioredoxin.";
RL Acta Crystallogr. D 55:1533-1538(1999).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (2.95 ANGSTROMS) IN COMPLEX WITH TRXB.
RX PubMed=10947986; DOI=10.1126/science.289.5482.1190;
RA Lennon B.W., Williams C.H. Jr., Ludwig M.L.;
RT "Twists in catalysis: alternating conformations of Escherichia coli
RT thioredoxin reductase.";
RL Science 289:1190-1194(2000).
RN [17]
RP STRUCTURE BY NMR.
RX PubMed=2193685; DOI=10.1021/bi00469a016;
RA Dyson H.J., Gippert G.P., Case D.A., Holmgren A., Wright P.E.;
RT "Three-dimensional solution structure of the reduced form of Escherichia
RT coli thioredoxin determined by nuclear magnetic resonance spectroscopy.";
RL Biochemistry 29:4129-4136(1990).
RN [18]
RP STRUCTURE BY NMR.
RX PubMed=7812718; DOI=10.1016/s0969-2126(94)00086-7;
RA Jeng M.F., Campbell A.P., Begley T., Holmgren A., Case D.A., Wright P.E.,
RA Dyson H.J.;
RT "High-resolution solution structures of oxidized and reduced Escherichia
RT coli thioredoxin.";
RL Structure 2:853-868(1994).
CC -!- FUNCTION: Participates in various redox reactions through the
CC reversible oxidation of its active center dithiol to a disulfide and
CC catalyzes dithiol-disulfide exchange reactions.
CC -!- SUBUNIT: Monomer. Interacts with bacteriophage T3 DNA polymerase.
CC {ECO:0000269|PubMed:10947986}.
CC -!- INTERACTION:
CC P0AA25; P0A9P4: trxB; NbExp=2; IntAct=EBI-368542, EBI-1029826;
CC P0AA25; P00581: 5; Xeno; NbExp=2; IntAct=EBI-368542, EBI-8664634;
CC P0AA25; O22160: At2g44920; Xeno; NbExp=2; IntAct=EBI-368542, EBI-2895776;
CC P0AA25; Q9SCY2: FKBP13; Xeno; NbExp=2; IntAct=EBI-368542, EBI-2895757;
CC P0AA25; Q9LXX5: PPD6; Xeno; NbExp=2; IntAct=EBI-368542, EBI-2895738;
CC P0AA25; Q9LU86: PRXQ; Xeno; NbExp=2; IntAct=EBI-368542, EBI-540311;
CC P0AA25; P23321: PSBO1; Xeno; NbExp=2; IntAct=EBI-368542, EBI-449414;
CC P0AA25; Q9S841: PSBO2; Xeno; NbExp=2; IntAct=EBI-368542, EBI-449424;
CC P0AA25; P81760: TL17; Xeno; NbExp=2; IntAct=EBI-368542, EBI-449573;
CC P0AA25; P82281: TL29; Xeno; NbExp=2; IntAct=EBI-368542, EBI-2895799;
CC P0AA25; Q39249: VDE1; Xeno; NbExp=2; IntAct=EBI-368542, EBI-2895666;
CC -!- SIMILARITY: Belongs to the thioredoxin family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA24534.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAA67582.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; M26133; AAA24693.1; -; Genomic_DNA.
DR EMBL; K02845; AAA24534.1; ALT_INIT; Genomic_DNA.
DR EMBL; M10424; AAA24533.1; -; Genomic_DNA.
DR EMBL; M54881; AAA24696.1; -; Genomic_DNA.
DR EMBL; M12779; AAA24694.1; -; Genomic_DNA.
DR EMBL; M87049; AAA67582.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76786.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE77517.1; -; Genomic_DNA.
DR PIR; A91519; TXEC.
DR RefSeq; NP_418228.2; NC_000913.3.
DR RefSeq; WP_001280776.1; NZ_CP009789.1.
DR PDB; 1F6M; X-ray; 2.95 A; C/D/G/H=2-109.
DR PDB; 1KEB; X-ray; 1.80 A; A/B=2-109.
DR PDB; 1M7T; NMR; -; A=32-108.
DR PDB; 1OAZ; X-ray; 2.78 A; A/B=2-109.
DR PDB; 1SKR; X-ray; 2.40 A; B=2-109.
DR PDB; 1SKS; X-ray; 2.30 A; B=2-109.
DR PDB; 1SKW; X-ray; 2.30 A; B=2-109.
DR PDB; 1SL0; X-ray; 3.20 A; B/D=2-109.
DR PDB; 1SL1; X-ray; 2.20 A; B=2-109.
DR PDB; 1SL2; X-ray; 2.30 A; B=2-109.
DR PDB; 1SRX; X-ray; 2.80 A; A=2-109.
DR PDB; 1T7P; X-ray; 2.20 A; B=2-109.
DR PDB; 1T8E; X-ray; 2.54 A; B=2-109.
DR PDB; 1THO; X-ray; 2.30 A; A=2-109.
DR PDB; 1TK0; X-ray; 2.30 A; B=2-109.
DR PDB; 1TK5; X-ray; 2.20 A; B=2-109.
DR PDB; 1TK8; X-ray; 2.50 A; B=2-109.
DR PDB; 1TKD; X-ray; 2.49 A; B=2-109.
DR PDB; 1TXX; X-ray; 2.20 A; A=2-109.
DR PDB; 1X9M; X-ray; 2.10 A; B=2-109.
DR PDB; 1X9S; X-ray; 2.70 A; B=2-109.
DR PDB; 1X9W; X-ray; 2.30 A; B=2-109.
DR PDB; 1XOA; NMR; -; A=2-109.
DR PDB; 1XOB; NMR; -; A=2-109.
DR PDB; 1ZCP; X-ray; 2.30 A; A/B/C/D=2-109.
DR PDB; 1ZYQ; X-ray; 2.70 A; B=2-109.
DR PDB; 1ZZY; X-ray; 2.50 A; A/B=2-109.
DR PDB; 2AJQ; X-ray; 2.60 A; B/I=2-109.
DR PDB; 2BTO; X-ray; 2.50 A; T=2-109.
DR PDB; 2EIO; X-ray; 2.60 A; A/B/C/D=2-109.
DR PDB; 2EIQ; X-ray; 1.90 A; A/B=2-109.
DR PDB; 2EIR; X-ray; 2.50 A; A/B/C/D=2-109.
DR PDB; 2FCH; X-ray; 2.60 A; A/B/C/D/E/F/G=2-109.
DR PDB; 2FD3; X-ray; 2.45 A; A/B=2-109.
DR PDB; 2H6X; X-ray; 2.60 A; A/B=2-109.
DR PDB; 2H6Y; X-ray; 2.40 A; A/B=2-109.
DR PDB; 2H6Z; X-ray; 2.25 A; A/B=2-109.
DR PDB; 2H70; X-ray; 2.70 A; A/B=2-109.
DR PDB; 2H71; X-ray; 2.20 A; A/B=2-109.
DR PDB; 2H72; X-ray; 2.25 A; A/B=2-109.
DR PDB; 2H73; X-ray; 2.45 A; A/B=2-109.
DR PDB; 2H74; X-ray; 2.40 A; A/B=4-109.
DR PDB; 2H75; X-ray; 2.20 A; A/B=2-109.
DR PDB; 2H76; X-ray; 2.25 A; A/B=2-109.
DR PDB; 2O8V; X-ray; 3.00 A; B=2-109.
DR PDB; 2TIR; X-ray; 2.00 A; A=2-109.
DR PDB; 2TRX; X-ray; 1.68 A; A/B=2-109.
DR PDB; 3DYR; X-ray; 2.00 A; A/B=2-109.
DR PDB; 4HU7; X-ray; 1.40 A; A/B=2-109.
DR PDB; 4HU9; X-ray; 1.55 A; A=2-109.
DR PDB; 4HUA; X-ray; 1.10 A; A=2-109.
DR PDB; 4X43; X-ray; 1.65 A; A/B/C=2-109.
DR PDB; 5HR0; X-ray; 1.31 A; A/B=1-109.
DR PDB; 5HR1; X-ray; 2.14 A; A/B/C/D/E/F/G=1-107.
DR PDB; 5HR2; X-ray; 1.20 A; A=1-109.
DR PDB; 5HR3; X-ray; 1.10 A; A/B=1-109.
DR PDB; 5XOC; X-ray; 2.40 A; B=2-109.
DR PDB; 6GD1; X-ray; 2.01 A; A/B=1-109.
DR PDB; 6GDG; EM; 4.11 A; A=2-109.
DR PDB; 6H1Y; X-ray; 2.99 A; A/B=2-14, A/B=24-109.
DR PDB; 6H7J; X-ray; 2.80 A; E/F=2-109.
DR PDB; 6H7L; X-ray; 2.70 A; E/F=2-109.
DR PDB; 6H7M; X-ray; 2.76 A; E/F=2-109.
DR PDB; 6H7N; X-ray; 2.50 A; E/F=2-109.
DR PDB; 6H7O; X-ray; 2.80 A; E/F=2-109.
DR PDB; 6IBL; X-ray; 2.70 A; A/B=2-109.
DR PDB; 6LUR; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-109.
DR PDB; 6N7W; EM; 4.50 A; I=1-109.
DR PDB; 6P7E; X-ray; 3.00 A; E/F/G/H=1-109.
DR PDB; 6Y4Y; X-ray; 1.75 A; A/B/C/D=1-109.
DR PDB; 6Y4Z; X-ray; 1.90 A; A/B/C/D=1-109.
DR PDB; 6YEV; X-ray; 2.94 A; E/F/G=1-109.
DR PDB; 7SCD; X-ray; 2.90 A; A=1-108.
DR PDB; 7SCE; X-ray; 2.75 A; A=1-108.
DR PDB; 8KGZ; X-ray; 2.21 A; A/B=1-109.
DR PDB; 8S2N; X-ray; 2.11 A; C=2-109.
DR PDB; 9JFS; EM; 2.67 A; E=1-109.
DR PDB; 9JG3; EM; 3.20 A; E=1-109.
DR PDBsum; 1F6M; -.
DR PDBsum; 1KEB; -.
DR PDBsum; 1M7T; -.
DR PDBsum; 1OAZ; -.
DR PDBsum; 1SKR; -.
DR PDBsum; 1SKS; -.
DR PDBsum; 1SKW; -.
DR PDBsum; 1SL0; -.
DR PDBsum; 1SL1; -.
DR PDBsum; 1SL2; -.
DR PDBsum; 1SRX; -.
DR PDBsum; 1T7P; -.
DR PDBsum; 1T8E; -.
DR PDBsum; 1THO; -.
DR PDBsum; 1TK0; -.
DR PDBsum; 1TK5; -.
DR PDBsum; 1TK8; -.
DR PDBsum; 1TKD; -.
DR PDBsum; 1TXX; -.
DR PDBsum; 1X9M; -.
DR PDBsum; 1X9S; -.
DR PDBsum; 1X9W; -.
DR PDBsum; 1XOA; -.
DR PDBsum; 1XOB; -.
DR PDBsum; 1ZCP; -.
DR PDBsum; 1ZYQ; -.
DR PDBsum; 1ZZY; -.
DR PDBsum; 2AJQ; -.
DR PDBsum; 2BTO; -.
DR PDBsum; 2EIO; -.
DR PDBsum; 2EIQ; -.
DR PDBsum; 2EIR; -.
DR PDBsum; 2FCH; -.
DR PDBsum; 2FD3; -.
DR PDBsum; 2H6X; -.
DR PDBsum; 2H6Y; -.
DR PDBsum; 2H6Z; -.
DR PDBsum; 2H70; -.
DR PDBsum; 2H71; -.
DR PDBsum; 2H72; -.
DR PDBsum; 2H73; -.
DR PDBsum; 2H74; -.
DR PDBsum; 2H75; -.
DR PDBsum; 2H76; -.
DR PDBsum; 2O8V; -.
DR PDBsum; 2TIR; -.
DR PDBsum; 2TRX; -.
DR PDBsum; 3DYR; -.
DR PDBsum; 4HU7; -.
DR PDBsum; 4HU9; -.
DR PDBsum; 4HUA; -.
DR PDBsum; 4X43; -.
DR PDBsum; 5HR0; -.
DR PDBsum; 5HR1; -.
DR PDBsum; 5HR2; -.
DR PDBsum; 5HR3; -.
DR PDBsum; 5XOC; -.
DR PDBsum; 6GD1; -.
DR PDBsum; 6GDG; -.
DR PDBsum; 6H1Y; -.
DR PDBsum; 6H7J; -.
DR PDBsum; 6H7L; -.
DR PDBsum; 6H7M; -.
DR PDBsum; 6H7N; -.
DR PDBsum; 6H7O; -.
DR PDBsum; 6IBL; -.
DR PDBsum; 6LUR; -.
DR PDBsum; 6N7W; -.
DR PDBsum; 6P7E; -.
DR PDBsum; 6Y4Y; -.
DR PDBsum; 6Y4Z; -.
DR PDBsum; 6YEV; -.
DR PDBsum; 7SCD; -.
DR PDBsum; 7SCE; -.
DR PDBsum; 8KGZ; -.
DR PDBsum; 8S2N; -.
DR PDBsum; 9JFS; -.
DR PDBsum; 9JG3; -.
DR AlphaFoldDB; P0AA25; -.
DR BMRB; P0AA25; -.
DR SASBDB; P0AA25; -.
DR SMR; P0AA25; -.
DR BioGRID; 4263316; 306.
DR BioGRID; 852588; 9.
DR DIP; DIP-31856N; -.
DR FunCoup; P0AA25; 803.
DR IntAct; P0AA25; 99.
DR MINT; P0AA25; -.
DR STRING; 511145.b3781; -.
DR CarbonylDB; P0AA25; -.
DR iPTMnet; P0AA25; -.
DR jPOST; P0AA25; -.
DR PaxDb; 511145-b3781; -.
DR EnsemblBacteria; AAC76786; AAC76786; b3781.
DR GeneID; 67174651; -.
DR GeneID; 93778163; -.
DR GeneID; 948289; -.
DR KEGG; ecj:JW5856; -.
DR KEGG; eco:b3781; -.
DR KEGG; ecoc:C3026_20470; -.
DR PATRIC; fig|511145.12.peg.3896; -.
DR EchoBASE; EB1024; -.
DR eggNOG; COG3118; Bacteria.
DR HOGENOM; CLU_090389_10_2_6; -.
DR InParanoid; P0AA25; -.
DR OMA; HIHYVTD; -.
DR OrthoDB; 9790390at2; -.
DR PhylomeDB; P0AA25; -.
DR BioCyc; EcoCyc:RED-THIOREDOXIN-MONOMER; -.
DR BioCyc; MetaCyc:RED-THIOREDOXIN-MONOMER; -.
DR EvolutionaryTrace; P0AA25; -.
DR PRO; PR:P0AA25; -.
DR Proteomes; UP000000625; Chromosome.
DR AbasyAtlas; P0AA25; -.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0030337; F:DNA polymerase processivity factor activity; IDA:FlyBase.
DR GO; GO:0015035; F:protein-disulfide reductase activity; IDA:EcoCyc.
DR GO; GO:0045454; P:cell redox homeostasis; IMP:EcoCyc.
DR CDD; cd02947; TRX_family; 1.
DR FunFam; 3.40.30.10:FF:000001; Thioredoxin; 1.
DR Gene3D; 3.40.30.10; Glutaredoxin; 1.
DR InterPro; IPR005746; Thioredoxin.
DR InterPro; IPR036249; Thioredoxin-like_sf.
DR InterPro; IPR017937; Thioredoxin_CS.
DR InterPro; IPR013766; Thioredoxin_domain.
DR NCBIfam; NF006898; PRK09381.1; 1.
DR NCBIfam; TIGR01068; thioredoxin; 1.
DR PANTHER; PTHR45663; GEO12009P1; 1.
DR PANTHER; PTHR45663:SF11; GEO12009P1; 1.
DR Pfam; PF00085; Thioredoxin; 1.
DR PIRSF; PIRSF000077; Thioredoxin; 1.
DR PRINTS; PR00421; THIOREDOXIN.
DR SUPFAM; SSF52833; Thioredoxin-like; 1.
DR PROSITE; PS00194; THIOREDOXIN_1; 1.
DR PROSITE; PS51352; THIOREDOXIN_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; Disulfide bond;
KW Electron transport; Host-virus interaction; Redox-active center;
KW Reference proteome; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:4883076"
FT CHAIN 2..109
FT /note="Thioredoxin 1"
FT /id="PRO_0000120096"
FT DOMAIN 2..109
FT /note="Thioredoxin"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00691"
FT ACT_SITE 33
FT /note="Nucleophile"
FT ACT_SITE 36
FT /note="Nucleophile"
FT SITE 27
FT /note="Deprotonates C-terminal active site Cys"
FT SITE 34
FT /note="Contributes to redox potential value"
FT SITE 35
FT /note="Contributes to redox potential value"
FT MOD_RES 70
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT DISULFID 33..36
FT /note="Redox-active"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00691,
FT ECO:0000269|PubMed:10489448"
FT CONFLICT 72..73
FT /note="GI -> IG (in Ref. 8; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 88
FT /note="A -> AS (in Ref. 5; AAA24696)"
FT /evidence="ECO:0000305"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:4HUA"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:4HUA"
FT HELIX 14..18
FT /evidence="ECO:0007829|PDB:4HUA"
FT STRAND 22..29
FT /evidence="ECO:0007829|PDB:4HUA"
FT HELIX 34..49
FT /evidence="ECO:0007829|PDB:4HUA"
FT TURN 50..53
FT /evidence="ECO:0007829|PDB:4HUA"
FT STRAND 55..60
FT /evidence="ECO:0007829|PDB:4HUA"
FT TURN 61..63
FT /evidence="ECO:0007829|PDB:4HUA"
FT HELIX 65..70
FT /evidence="ECO:0007829|PDB:4HUA"
FT STRAND 75..83
FT /evidence="ECO:0007829|PDB:4HUA"
FT STRAND 86..93
FT /evidence="ECO:0007829|PDB:4HUA"
FT HELIX 97..106
FT /evidence="ECO:0007829|PDB:4HUA"
SQ SEQUENCE 109 AA; 11807 MW; EF5933EA29668EE9 CRC64;
Query Match 100.0%; Score 563; Length 109;
Best Local Similarity 100.0%;
Matches 108; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNI 60
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Db 2 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNI 61
Qy 61 DQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA 108
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Db 62 DQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA 109
Prosecution Insights