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
This application is a 371 of PCT/EP2021/068279.
The amendment filed on June 9, 2026 has been entered.
Election/Restrictions
Applicant elected with traverse of Group I with a species election of (1) SEQ ID NO:1 (MaPylRS) as the parent enzyme (parent aaRS), (2) V168C+M129L as the amino acid modification, (3) pyrrolysyl-tRNA synthetase activity, specifically aminoacylation of non-canonical amino acids, and (4) NƐ-((2-azidoethoxy)carbonyl)-L-lysine (AzK) as the lysine derivative in the reply filed on September 29, 2025.
Claims 2, 17-18, 20, 23-24, and 31 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on September 29, 2005.
Status of Claims
Claims 1-5, 10-13, 17-18, 20-21, and 23-31 are pending.
Claims 2, 17-18, 20, 23-24, and 31 are withdrawn.
Claims 1, 3-5, 10-13, 21, and 25-30 are under examination.
Response to Amendments/Arguments
Claim Rejections - 35 USC § 112(b)
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.
Withdrawn Rejections
Applicant’s arguments, see page 8 of the Remarks, filed June 9, 2026, with respect to claims 1 and 4 and claims 3, 5-13, and 21 depending therefrom have been fully considered and are persuasive. Claims 1 and 4 have been amended to remove the recitation of a broad range within a narrow range. Claims 6-9 have been cancelled. Therefore, the rejection of claims 1 and 4 and claims 3, 5-13, and 21 depending therefrom under 35 U.S.C. 112(b) has been withdrawn.
Applicant’s arguments, see page 8 of the Remarks, filed June 9, 2026, with respect to claims 1, 3-4, 7, and 9-13 and claims 5-6, 8-9, and 21 depending therefrom have been fully considered and are persuasive. Claims 1, 3-4, and 10-13 have been amended to remove the recitation of “e.g”. Claims 6-9 have been cancelled. Therefore, the rejection of claims 1, 3-4, 7, and 9-13 and claims 5-6, 8-9, and 21 depending therefrom under 35 U.S.C. 112(b) has been withdrawn.
Applicant’s arguments, see page 8 of the Remarks, filed June 9, 2026, with respect to claims 7, 9, and 10 have been fully considered and are persuasive. Claims 1 and 9 have been cancelled. Claim 10 has been amended to delete “preferably”. Therefore, the rejection of claims 7, 9, and 10 under 35 U.S.C. 112(b) has been withdrawn.
Applicant’s arguments, see page 9 of the Remarks, filed June 9, 2026, with respect to claim 7 have been fully considered and are persuasive. Claim 7 has been cancelled. Therefore, the rejection of claim 7 under 35 U.S.C. 112(b) has been withdrawn.
Applicant’s arguments, see page 9 of the Remarks, filed June 9, 2026, with respect to claims 8-9 have been fully considered and are persuasive. Claims 8-9 have been cancelled. Therefore, the rejection of claims 8-9 under 35 U.S.C. 112(b) has been withdrawn.
Applicant’s arguments, see page 9 of the Remarks, filed June 9, 2026, with respect to claim 8 have been fully considered and are persuasive. Claim 8 has been cancelled. Therefore, the rejection of claim 8 under 35 U.S.C. 112(b) has been withdrawn.
New Rejection
Claim 29 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 29 recites the limitation "A variant of a parent aminoacyl-tRNA synthetase comprising or consisting of SEQ ID NO:2 and having amino acyl-tRNA synthetase activity". The metes and bounds of the limitation in the context of the claim are not clear. It is unclear if (1) the variant comprises or consists of SEQ ID NO:2 or (2) if the parent comprises or consist of SEQ ID NO:2. Clarification is requested.
For examination purposes, claim 29 has been broadly interpreted to comprise both interpretations.
Claim Rejections - 35 USC § 112(a)
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.
Withdrawn Rejections
Applicant’s arguments, see pages 9-12 of the Remarks, filed June 9, 2026, with respect to claims 1, 3-4, 6-13, and 21 have been fully considered and are persuasive. Claim 1 has been amended to recite an aminoacyl-tRNA synthetase variant has at lsat 85% sequence identity to SEQ ID NO:1. Claims 6-9 have been cancelled. Therefore, the rejection of claims 1, 3-4, 6-13, and 21 under 35 U.S.C. 112(a) (written description) has been withdrawn.
Applicant’s arguments, see pages 12-13 of the Remarks, filed June 9, 2026, with respect to claims 1, 3-4, 6-13, and 21 have been fully considered and are persuasive. Claim 1 has been amended to recite an aminoacyl-tRNA synthetase variant has at least 85% sequence identity to SEQ ID NO:1. Claims 6-9 have been cancelled. Therefore, the rejection of claims 1, 3-4, 6-13, and 21 under 35 U.S.C. 112(a) (enablement) has been withdrawn.
New Rejections
Claim 29 is 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.'' In this case, the claim has been broadly interpreted to encompass any variant of a parent aminoacyl-tRNA synthetase having the amino acid sequence of SEQ ID NO:2, wherein the variant has any number of amino acid modifications. Therefore, the claims are drawn to a genus of polypeptides having unknown structure but having aminoacyl-tRNA synthetase activity.
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 recitation of “aminoacyl-tRNA synthetase” fails to provide a sufficient description of the genus of the polypeptides 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.
Methanomethylophilus alvus PylRS (MaPylRS) having the amino acid sequence of SEQ ID NO:1 of the instant application was known in the art, see Borrel (Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette. Archaea. 2014 Jan 27;2014:374146 – cited previously on form PTO-892 Section 2 at page 2 “CP004049.1” and see the sequence alignment below). However, neither the prior art nor the instant specification disclose any variants of SEQ ID NO:2 but having aminoacyl-tRNA synthetase activity.
Fransceus (J Ind Microbiol Biotechnol. 2017 May;44(4-5):687-695. – cited previously on 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. – cited previously on 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”.
The specification is limited to description of the aminoacyl-tRNA synthetase having the amino acid sequence of SEQ ID NO:2, which is the variant of SEQ ID NO:1 consisting of V168C+M129L amino acid substitutions, wherein the aminoacyl-tRNA synthetase has pyrrolysyl-tRNA synthetase activity and incorporates the lysine derivate, Azk. 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 example described above is not enough and does not constitute a representative number of species to describe the whole genus of polypeptides having unknown structure but having aminoacyl-tRNA synthetase. Therefore, the specification fails to describe a representative species of the claimed genus.
Further, one of skill in the art could identify variants of SEQ ID NO:2. However, there is no teaching regarding which amino acids can vary from SEQ ID NO:2 and result in polypeptide having aminoacyl-tRNA synthetase activity. 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. Since the claimed invention is that of an enzyme, and there is no disclosure of the domains responsible for having aminoacyl-tRNA synthetase activity, the absence of information may be persuasive that those of skill in the art would not take the disclosure as generic.
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 claim 29.
Claim 29 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the aminoacyl-tRNA synthetase having the amino acid sequence of SEQ ID NO:2, which is the variant of SEQ ID NO:1 consisting of V168C+M129L amino acid substitutions, does not reasonably provide enablement for polypeptides having unknown structure but having aminoacyl-tRNA synthetase. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988). They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.
The breadth of the claims.
MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.'' In this case, the claim has been broadly interpreted to encompass any variant of a parent aminoacyl-tRNA synthetase having the amino acid sequence of SEQ ID NO:2, wherein the variant has any number of amino acid modifications. Therefore, the claims are drawn to any polypeptide having unknown structure but having aminoacyl-tRNA synthetase activity.
The claims are not commensurate with the enablement provided by the disclosure with regard to the extremely large number of polypeptides having aminoacyl-tRNA synthetase activity. In the instant case, the specification is limited to the aminoacyl-tRNA synthetase having the amino acid sequence of SEQ ID NO:2, which is the variant of SEQ ID NO:1 consisting of V168C+M129L amino acid substitutions, wherein the aminoacyl-tRNA synthetase has pyrrolysyl-tRNA synthetase activity and incorporates the lysine derivate, Azk.
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification.
While enzyme isolation techniques, recombinant and mutagenesis techniques were known in the art at the time of the invention, e.g. mutagenesis, and it is routine in the art to screen for variants comprising multiple substitutions or multiple modifications as encompassed by the instant claims, the specific amino acid positions within the protein's sequence where amino acid modifications can be made with a reasonable expectation of success in obtaining the desired activity/utility are limited in any protein and the result of such modifications is unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g. multiple substitutions.
In the absence of: (a) rational and predictable scheme for making any polypeptide having unknown structure but having aminoacyl-tRNA synthetase activity, and (b) a correlation between structure and the function of having aminoacyl-tRNA synthetase activity, the specification provides insufficient guidance as to which of the essentially infinite possible choices is likely to be successful. One of skill in the art would have to test these infinite possible polypeptides to determine which polypeptides have aminoacyl-tRNA synthetase activity. While enablement is not precluded by the necessity for routine screening, if a large amount of screening is required, as is the case herein, the specification must provide a reasonable amount of guidance which respect to the direction in which the experimentation should proceed so that a reasonable number of species can be selected for testing. In view of the fact that such guidance has not been provided in the instant specification, it would require undue experimentation to enable the full scope of the claims.
The state of prior art, the relative skill of those in the art, and predictability or unpredictability of the art.
Since the amino acid sequence of the mutant determines its structural and functional properties, predictability of which changes can be tolerated in a protein's amino acid sequence and obtain the desired activity requires a knowledge of and guidance with regard to which amino acids in the protein's sequence, if any, are tolerant of modification and which are conserved (i.e. expectedly intolerant to modification), and detailed knowledge of the ways in which the proteins' structure relates to its function. In the instant case, neither the specification or the art provide a correlation between structure and activity such that one of skill in the art can envision the structure of any polypeptides having aminoacyl-tRNA synthetase activity or predict said function of a polypeptide from its primary structure. In addition, the art does not provide any teaching or guidance as to (1) which amino acids within the polypeptide of SEQ ID NO:2 that can be modified and which ones are conserved such that one of skill in the art can make the recited polypeptides having aminoacyl-tRNA synthetase activity, (2) which segments of the polypeptide of SEQ ID NO:2 hat are essential for polypeptides having aminoacyl-tRNA synthetase activity, and (3) the general tolerance of the polypeptide of SEQ ID NO:2 to structural modifications and the extent of such tolerance. The art clearly teaches that changes in a protein's amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are required for that activity is highly unpredictable. At the time of the invention there was a high level of unpredictability associated with altering a polypeptide sequence with an expectation that the polypeptide will maintain the desired activity. For example, Studer (Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochem. J. (2013) 449, 581–594. – cited previously on form PTO-892) teach that (1) protein engineers are frequently surprised by the range of effects caused by single mutations that they hoped would change only one specific and simple property in enzymes, (2) the often surprising results obtained by experiments where single mutations are made reveal how little is known about the rules of protein stability, and (3) the difficulties in designing de novo stable proteins with specific functions.
Methanomethylophilus alvus PylRS (MaPylRS) having the amino acid sequence of SEQ ID NO:1 of the instant application was known in the art, see Borrel (Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette. Archaea. 2014 Jan 27;2014:374146 – cited previously on form PTO-892 Section 2 at page 2 “CP004049.1” and see the sequence alignment below). However, neither the prior art nor the instant specification disclose any variants of SEQ ID NO:2 but having aminoacyl-tRNA synthetase activity.
Fransceus (J Ind Microbiol Biotechnol. 2017 May;44(4-5):687-695. – cited previously on 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. – cited previously on 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”.
The amount of direction or guidance presented and the existence of working examples.
The specification is limited to the aminoacyl-tRNA synthetase having the amino acid sequence of SEQ ID NO:2, which is the variant of SEQ ID NO:1 consisting of V168C+M129L amino acid substitutions, wherein the aminoacyl-tRNA synthetase has pyrrolysyl-tRNA synthetase activity and incorporates the lysine derivate, Azk. However, the speciation fails to provide any information as to (1) specific substrates associated with polypeptides having unknown structure or (2) structural elements required in a polypeptide having aminoacyl-tRNA synthetase activity. No correlation between structure and function of having aminoacyl-tRNA synthetase activity has been presented. There is no information or guidance as to which amino acid residues in the polypeptide of SEQ ID NO:2 that can be modified and which ones are to be conserved to create a polypeptide having aminoacyl-tRNA synthetase activity.
Thus, in view of the overly broad scope of the claims, the lack of guidance and working examples provided in the specification, the high level of unpredictability of the prior art in regard to structural changes and their effect on function and the lack of knowledge about a correlation between structure and function, an undue experimentation would be necessary one having ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of polypeptides having the desired biological characteristics recited in the claims are unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
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 (i.e., changing from AIA to pre-AIA ) 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.
Withdrawn Rejection
Applicant’s arguments, see pages 13-14 of the Remarks, filed June 9, 2026, with respect to claims 1, 3-13, and 21 have been fully considered and are persuasive. Claims 6-9 have been cancelled. Applicant’s argument that the reference of Tugel was not publicly available has been found persuasive (a two-year restriction on the use of the Tugel reference and the actual publicly available date is October 16, 2021). Therefore, the rejection of claims 1, 3-13, and 21 under 35 U.S.C. 102(a)(1) has been withdrawn.
New Rejection
Claim(s) 29 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by M9SC49 (UniProtKB/TrEMBL Database. May 8, 2019 - form PTO-892).
MPEP 2113 states that the “patentability of a product does not depend on its method of production.". In the instant case, the structure of the claimed variant implied is the same whether the variant is obtained from any recombinant engineering of SEQ ID NO:2 or is obtained from any source (including wild type polypeptides), as long as the resulting product has the structural limitations recited in the claims (polypeptide having at least one amino acid difference compared to SEQ ID NO:2 and having aminoacyl-tRNA synthetase activity).
Regarding claim 29, M9SC49 discloses a pyrrolysyl-tRNA synthetase having at least one amino acid difference compared to SEQ ID NO:2 (pages 1-2 and see the sequence alignment below).
Therefore, the reference of M9SC49 anticipates claim 29.
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.
Withdrawn Rejection
Applicant’s arguments, see pages 15-16 of the Remarks, filed June 9, 2026, with respect to claims 1, 3-4, 6-13, and 21 have been fully considered and are persuasive. Claims 6-9 have been cancelled. Applicant’s argument that the reference of Sakamoto does not disclose an aminoacyl-tRNA synthetase that catalyzes AzK has been found persuasive. Therefore, the rejection of claims 1, 3-13, and 21 under 35 U.S.C. 103 as being unpatentable over Sakamoto (WO 2020/045656 – cited previously on form PTO-892 and English Translation of WO 2020/045656 retrieved on May 22, 2025 – cited previously on form PTO-892. The English Translation of WO 2020/045656 is used for specific passages of Sakamoto) and evidenced by Fladischer (Non-canonical amino acids as building blocks: New translation systems for non-canonical amino acids. Dissertation. Pages 1-334. Technischen Universaitat Graz. February 2018 – form PTO-892) has been withdrawn.
Maintained Rejection
Claim(s) 1, 3-4, 10-13, 21, 25-28, and 30 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fladischer (Non-canonical amino acids as building blocks: New translation systems for non-canonical amino acids. Dissertation. Technischen Universaitat Graz. Pages 1-334. February 2018 – cited previously on form PTO-892).
Regarding claims 1, 3, and 11, Fladischer disclsoes a Methanomethylophilus alvus aminoacyl-tRNA synthetase (MaPylRS) having pyrrolysyl-tRNA synthetase activity (abstract and page 191 and Supporting Figure 2 at page 222). The MaPylRS of Fladischer has 100% sequence identity to the MaPylRS of SEQ ID NO:1 of the instant application, as evidenced by reference 22 at page 191 (Borrel. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics. 2014 Aug 13;15:679 – cited previously on form PTO-892, page 19 “Data access” “CP004049 and see the sequence alignment below).
Regarding claim 21, Fladischer discloses a composition comprising MaPylRS (bottom of page 195).
Regarding claim 30, Fladischer discloses a composition comprising MaPylRS, Azk (Azide K) and its cognate tRNA (pages 196-197).
Fladischer does not disclose a MaPylRS variant having M129L + V168C amino acid substitutions.
Regarding claims 1, 3-4, 10, 12-13, and 25-28, Fladischer discloses that AzideK (NƐ-((2-azidoethoxy)carbonyl)-L-lysine) is barely accepted as a substrate by MaPylRS but MmPylRS accepts Azide K very well (bottom of page 196 through top of page 197). Fladischer discloses that the ability of PylRS to accommodate different Lysine derivatives is correlated with the size and plasticity of the active site (middle of page 200). Fladischer discloses that in MmPylRS, residues lining the active site, N346, Y306, Y384, W417, C348, V401 and L309, were shown to be important for substrate recognition (middle of page 200). Fladischer discloses that in MaPylRS, M129, A223, and V168 occupies in the active sites correlating to L309, V401, and C348, respectively, of MmPylRS (middle of page 200). One having ordinary skill in the art would have recognized to mutate M129, A223, and V168 in the substrate recognition site of MaPylRS to M129L, A223V, and V168C in order to mimic the residues in the substrate recognitions site of MmPylRS since MmPylRS accepts Azide K very well. The resulting MaPylRS variant would have at least 85-99% sequence identity to SEQ ID NO:1 or 2 of the instant application.
Therefore, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to make a MaPylRS variant having M129L + V168C +A233V amino acid substitutions. One having ordinary skill in the art would have been motivated to do so in order to endow MaPylRS to accept Azide K as a substrate by changing the substrate recognition site to have the same residues as MmPylRS which accepts Azide K very well. One having ordinary skill in the art would have has a reasonable expectation of success since Fladischer discloses MaPylRS having pyrrolysyl-tRNA synthetase activity, identifies that M129, A223, and V168 of MaPylRS occupies in the active sites, which correlates to L309, V401, and C348, respectively, of MmPylRS, which has accepted Azide K very well.
Therefore, the above references render claims 1, 3-4, 10-13, 21, 25-28, and 30 prima facie obvious.
Applicant's arguments filed June 9, 2026 have been fully considered but they are not persuasive.
Applicant argues that the claims are not obvious because (1) MmaPyIRS comprises M129, A223 and V168 that are different from L309, V401 and C348 residues lining the active sites (N646, Y306, Y384, W417, C348, V401 and L309) of MmPylRS that are important for substrate recognition and interaction MmaPylRS, (2) Fladischer does not specifically teach what residues in Mm PylRS are important for Azide K being accepted as a substrate, and (3) the MaPylRS of Fladischer has only 22% sequence identity to SEQ ID NO:1 or 2 of the instant application.
This is not found persuasive.
(1) Although M129, A223 and V168 of MaPylRS are different from L309, V401 and C348 residues of MmPylRS, Fladischer discloses that in MaPylRS, M129, A223, and V168 occupies in the active sites correlating to L309, V401, and C348, respectively, of MmPylRS (middle of page 200).
(2) MPEP 2143.02. II. states that “[o]bviousness does not require absolute predictability, but at least some degree of predictability is required.”. In the instant case, Fladischer discloses that AzideK (NƐ-((2-azidoethoxy)carbonyl)-L-lysine) is barely accepted as a substrate by MaPylRS but MmPylRS accepts Azide K very well (bottom of page 196 through top of page 197). Fladischer discloses that in MmPylRS, residues lining the active site, N346, Y306, Y384, W417, C348, V401 and L309, were shown to be important for substrate recognition (middle of page 200). Fladischer discloses that in MaPylRS, M129, A223, and V168 occupies in the active sites correlating to L309, V401, and C348, respectively, of MmPylRS (middle of page 200). Fladischer discloses that the ability of PylRS to accommodate different Lysine derivatives is correlated with the size and plasticity of the active site (middle of page 200). Therefore, one having ordinary skill in the art would have had a reasonable expectation of success of arriving at the claimed invention because Fladischer identifies that M129, A223, and V168 of MaPylRS occupies in the active sites, which correlates to L309, V401, and C348, respectively, of MmPylRS, which acceps Azide K very well.
(3) In the sequence alignment provided by Applicant at page 18 of the Remarks filed on June 9, 2026, Applicant states that SEQ ID NO:3 is the amino acid sequence of MaPylRS. However, “SEQ ID NO:3” does not correlate to the MaPylRS amino acid sequence disclosed in Supporting Figure 2 at page 222. Fladischer disclsoes a Methanomethylophilus alvus aminoacyl-tRNA synthetase (MaPylRS) having pyrrolysyl-tRNA synthetase activity (abstract and page 191 and Supporting Figure 2 at page 222). The MaPylRS of Fladischer has 100% sequence identity to the MaPylRS of SEQ ID NO:1 of the instant application, as evidenced by reference 22 at page 191 (Borrel. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics. 2014 Aug 13;15:679 – cited previously on form PTO-892, page 19 “Data access” “CP004049 and see the sequence alignment below).
Hence the rejection is maintained.
Duplicate Claims, Objection
Claim 29 (interpreting claim 29 as a variant comprises or consists of SEQ ID NO:2, see the 112(b) rejection above) is objected to under 37 CFR 1.75 as being a substantial duplicate of claim 5. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Conclusion
Claims 1-5, 10-13, 17-18, 20-21, and 23-31 are pending.
Claims 2, 17-18, 20, 23-24, and 31 are withdrawn.
Claims 1, 3-4, 10-13, 21, and 25-30 are rejected.
Claim 5 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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 between the MaPylRS of SEQ ID NO:1 of the instant application (“Qy”) and the MaPylRS of Tugel/ Fladischer (“Db”)
M9SC49_METAX
ID M9SC49_METAX Unreviewed; 275 AA.
AC M9SC49;
DT 26-JUN-2013, integrated into UniProtKB/TrEMBL.
DT 26-JUN-2013, sequence version 1.
DT 05-FEB-2025, entry version 50.
DE SubName: Full=Pyrrolysyl-tRNA synthetase {ECO:0000313|EMBL:AGI85861.1};
DE EC=6.1.1.26 {ECO:0000313|EMBL:AGI85861.1};
GN ORFNames=MMALV_11280 {ECO:0000313|EMBL:AGI85861.1};
OS Methanomethylophilus alvi (strain Mx1201).
OC Archaea; Methanobacteriati; Thermoplasmatota; Thermoplasmata;
OC Methanomassiliicoccales; Methanomethylophilaceae; Methanomethylophilus.
OX NCBI_TaxID=1236689 {ECO:0000313|EMBL:AGI85861.1, ECO:0000313|Proteomes:UP000012672};
RN [1] {ECO:0000313|EMBL:AGI85861.1, ECO:0000313|Proteomes:UP000012672}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Mx1201 {ECO:0000313|EMBL:AGI85861.1,
RC ECO:0000313|Proteomes:UP000012672};
RX PubMed=23209209; DOI=10.1128/JB.01867-12;
RA Borrel G., Harris H.M., Tottey W., Mihajlovski A., Parisot N.,
RA Peyretaillade E., Peyret P., Gribaldo S., O'Toole P.W., Brugere J.F.;
RT "Genome sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a
RT methanogenic archaeon from the human gut belonging to a seventh order of
RT methanogens.";
RL J. Bacteriol. 194:6944-6945(2012).
RN [2] {ECO:0007829|PDB:6EZD}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS).
RA Fladischer P., Blamauer J., Pavkov-Keller T., Schweiger K., Darnhofer B.,
RA Birner-Gruenberger R., Gruber K., Wiltschi B.;
RT "A new archaeal pyrrolysyl-tRNA synthetase/amber suppressor tRNA pair for
RT orthogonal protein translation.";
RL Submitted (NOV-2017) to the PDB data bank.
RN [3] {ECO:0007829|PDB:6JP2}
RP X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS).
RX PubMed=32182048; DOI=10.1021/acssynbio.9b00288;
RA Seki E., Yanagisawa T., Kuratani M., Sakamoto K., Yokoyama S.;
RT "Fully Productive Cell-Free Genetic Code Expansion by Structure-Based
RT Engineering of <i>Methanomethylophilus alvus</i> Pyrrolysyl-tRNA
RT Synthetase.";
RL ACS Synth. Biol. 9:718-732(2020).
RN [4] {ECO:0007829|PDB:7U0R}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH MG(2+).
RX PubMed=37264106; DOI=10.1038/s41557-023-01224-y;
RA Fricke R., Swenson C.V., Roe L.T., Hamlish N.X., Shah B., Zhang Z.,
RA Ficaretta E., Ad O., Smaga S., Gee C.L., Chatterjee A., Schepartz A.;
RT "Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase
RT enzymes to include non-alpha-amino acids in vitro and in vivo.";
RL Nat. Chem. 15:960-971(2023).
RN [5] {ECO:0007829|PDB:8C49}
RP X-RAY CRYSTALLOGRAPHY (1.82 ANGSTROMS) IN COMPLEX WITH MG(2+).
RX PubMed=37051694; DOI=10.1002/pro.4640;
RA Taylor C.J., Hardy F.J., Burke A.J., Bednar R.M., Mehl R.A., Green A.P.,
RA Lovelock S.L.;
RT "Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of
RT functional histidine analogues.";
RL Protein Sci. 32:e4640-e4640(2023).
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; CP004049; AGI85861.1; -; Genomic_DNA.
DR RefSeq; WP_015505008.1; NC_020913.1.
DR PDB; 6EZD; X-ray; 2.40 A; A/B/C/D=1-275.
DR PDB; 6JP2; X-ray; 2.27 A; A/B/C/D=1-275.
DR PDB; 7U0R; X-ray; 1.80 A; A/B=1-275.
DR PDB; 8C49; X-ray; 1.82 A; A/B=1-275.
DR PDBsum; 6EZD; -.
DR PDBsum; 6JP2; -.
DR AlphaFoldDB; M9SC49; -.
DR SMR; M9SC49; -.
DR STRING; 1236689.MMALV_11280; -.
DR GeneID; 41321903; -.
DR KEGG; max:MMALV_11280; -.
DR eggNOG; arCOG00413; Archaea.
DR HOGENOM; CLU_1010485_0_0_2; -.
DR InParanoid; M9SC49; -.
DR OrthoDB; 52632at2157; -.
DR Proteomes; UP000012672; Chromosome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043767; F:pyrrolysyl-tRNA synthetase activity; IEA:UniProtKB-EC.
DR Gene3D; 3.30.930.10; Bira Bifunctional Protein, Domain 2; 1.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR041616; PheRS_beta_core.
DR InterPro; IPR023877; Pyrrolysyl-tRNA_ligase_C.
DR NCBIfam; TIGR02367; PylS_Cterm; 1.
DR Pfam; PF17759; tRNA_synthFbeta; 1.
DR SUPFAM; SSF55681; Class II aaRS and biotin synthetases; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:6EZD, ECO:0007829|PDB:6JP2};
KW Aminoacyl-tRNA synthetase {ECO:0000313|EMBL:AGI85861.1};
KW Ligase {ECO:0000313|EMBL:AGI85861.1};
KW Metal-binding {ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49};
KW Reference proteome {ECO:0000313|Proteomes:UP000012672}.
FT DOMAIN 64..166
FT /note="Aminoacyl-transfer RNA synthetases class-II family
FT profile"
FT /evidence="ECO:0000259|PROSITE:PS50862"
FT BINDING 69
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0007829|PDB:8C49"
FT BINDING 211
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49"
FT BINDING 218
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49"
FT BINDING 221
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49"
SQ SEQUENCE 275 AA; 30806 MW; 2DCE063D0388889B CRC64;
Query Match 100.0%; Score 1418; Length 275;
Best Local Similarity 100.0%;
Matches 275; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MTVKYTDAQIQRLREYGNGTYEQKVFEDLASRDAAFSKEMSVASTDNEKKIKGMIANPSR 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MTVKYTDAQIQRLREYGNGTYEQKVFEDLASRDAAFSKEMSVASTDNEKKIKGMIANPSR 60
Qy 61 HGLTQLMNDIADALVAEGFIEVRTPIFISKDALARMTITEDKPLFKQVFWIDEKRALRPM 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 HGLTQLMNDIADALVAEGFIEVRTPIFISKDALARMTITEDKPLFKQVFWIDEKRALRPM 120
Qy 121 LAPNLYSVMRDLRDHTDGPVKIFEMGSCFRKESHSGMHLEEFTMLNLVDMGPRGDATEVL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LAPNLYSVMRDLRDHTDGPVKIFEMGSCFRKESHSGMHLEEFTMLNLVDMGPRGDATEVL 180
Qy 181 KNYISVVMKAAGLPDYDLVQEESDVYKETIDVEINGQEVCSAAVGPHYLDAAHDVHEPWS 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 KNYISVVMKAAGLPDYDLVQEESDVYKETIDVEINGQEVCSAAVGPHYLDAAHDVHEPWS 240
Qy 241 GAGFGLERLLTIREKYSTVKKGGASISYLNGAKIN 275
|||||||||||||||||||||||||||||||||||
Db 241 GAGFGLERLLTIREKYSTVKKGGASISYLNGAKIN 275
Sequence alignment between the MaPylRS of SEQ ID NO:1 of the instant application (“Qy”) and the MaPylRS of SEQ ID NO:5 of Sakamoto (“Db”)
M9SC49_METAX
ID M9SC49_METAX Unreviewed; 275 AA.
AC M9SC49;
DT 26-JUN-2013, integrated into UniProtKB/TrEMBL.
DT 26-JUN-2013, sequence version 1.
DT 05-FEB-2025, entry version 50.
DE SubName: Full=Pyrrolysyl-tRNA synthetase {ECO:0000313|EMBL:AGI85861.1};
DE EC=6.1.1.26 {ECO:0000313|EMBL:AGI85861.1};
GN ORFNames=MMALV_11280 {ECO:0000313|EMBL:AGI85861.1};
OS Methanomethylophilus alvi (strain Mx1201).
OC Archaea; Methanobacteriati; Thermoplasmatota; Thermoplasmata;
OC Methanomassiliicoccales; Methanomethylophilaceae; Methanomethylophilus.
OX NCBI_TaxID=1236689 {ECO:0000313|EMBL:AGI85861.1, ECO:0000313|Proteomes:UP000012672};
RN [1] {ECO:0000313|EMBL:AGI85861.1, ECO:0000313|Proteomes:UP000012672}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Mx1201 {ECO:0000313|EMBL:AGI85861.1,
RC ECO:0000313|Proteomes:UP000012672};
RX PubMed=23209209; DOI=10.1128/JB.01867-12;
RA Borrel G., Harris H.M., Tottey W., Mihajlovski A., Parisot N.,
RA Peyretaillade E., Peyret P., Gribaldo S., O'Toole P.W., Brugere J.F.;
RT "Genome sequence of 'Candidatus Methanomethylophilus alvus' Mx1201, a
RT methanogenic archaeon from the human gut belonging to a seventh order of
RT methanogens.";
RL J. Bacteriol. 194:6944-6945(2012).
RN [2] {ECO:0007829|PDB:6EZD}
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS).
RA Fladischer P., Blamauer J., Pavkov-Keller T., Schweiger K., Darnhofer B.,
RA Birner-Gruenberger R., Gruber K., Wiltschi B.;
RT "A new archaeal pyrrolysyl-tRNA synthetase/amber suppressor tRNA pair for
RT orthogonal protein translation.";
RL Submitted (NOV-2017) to the PDB data bank.
RN [3] {ECO:0007829|PDB:6JP2}
RP X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS).
RX PubMed=32182048; DOI=10.1021/acssynbio.9b00288;
RA Seki E., Yanagisawa T., Kuratani M., Sakamoto K., Yokoyama S.;
RT "Fully Productive Cell-Free Genetic Code Expansion by Structure-Based
RT Engineering of <i>Methanomethylophilus alvus</i> Pyrrolysyl-tRNA
RT Synthetase.";
RL ACS Synth. Biol. 9:718-732(2020).
RN [4] {ECO:0007829|PDB:7U0R}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH MG(2+).
RX PubMed=37264106; DOI=10.1038/s41557-023-01224-y;
RA Fricke R., Swenson C.V., Roe L.T., Hamlish N.X., Shah B., Zhang Z.,
RA Ficaretta E., Ad O., Smaga S., Gee C.L., Chatterjee A., Schepartz A.;
RT "Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase
RT enzymes to include non-alpha-amino acids in vitro and in vivo.";
RL Nat. Chem. 15:960-971(2023).
RN [5] {ECO:0007829|PDB:8C49}
RP X-RAY CRYSTALLOGRAPHY (1.82 ANGSTROMS) IN COMPLEX WITH MG(2+).
RX PubMed=37051694; DOI=10.1002/pro.4640;
RA Taylor C.J., Hardy F.J., Burke A.J., Bednar R.M., Mehl R.A., Green A.P.,
RA Lovelock S.L.;
RT "Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of
RT functional histidine analogues.";
RL Protein Sci. 32:e4640-e4640(2023).
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; CP004049; AGI85861.1; -; Genomic_DNA.
DR RefSeq; WP_015505008.1; NC_020913.1.
DR PDB; 6EZD; X-ray; 2.40 A; A/B/C/D=1-275.
DR PDB; 6JP2; X-ray; 2.27 A; A/B/C/D=1-275.
DR PDB; 7U0R; X-ray; 1.80 A; A/B=1-275.
DR PDB; 8C49; X-ray; 1.82 A; A/B=1-275.
DR PDBsum; 6EZD; -.
DR PDBsum; 6JP2; -.
DR AlphaFoldDB; M9SC49; -.
DR SMR; M9SC49; -.
DR STRING; 1236689.MMALV_11280; -.
DR GeneID; 41321903; -.
DR KEGG; max:MMALV_11280; -.
DR eggNOG; arCOG00413; Archaea.
DR HOGENOM; CLU_1010485_0_0_2; -.
DR InParanoid; M9SC49; -.
DR OrthoDB; 52632at2157; -.
DR Proteomes; UP000012672; Chromosome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043767; F:pyrrolysyl-tRNA synthetase activity; IEA:UniProtKB-EC.
DR Gene3D; 3.30.930.10; Bira Bifunctional Protein, Domain 2; 1.
DR InterPro; IPR006195; aa-tRNA-synth_II.
DR InterPro; IPR045864; aa-tRNA-synth_II/BPL/LPL.
DR InterPro; IPR041616; PheRS_beta_core.
DR InterPro; IPR023877; Pyrrolysyl-tRNA_ligase_C.
DR NCBIfam; TIGR02367; PylS_Cterm; 1.
DR Pfam; PF17759; tRNA_synthFbeta; 1.
DR SUPFAM; SSF55681; Class II aaRS and biotin synthetases; 1.
DR PROSITE; PS50862; AA_TRNA_LIGASE_II; 1.
PE 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:6EZD, ECO:0007829|PDB:6JP2};
KW Aminoacyl-tRNA synthetase {ECO:0000313|EMBL:AGI85861.1};
KW Ligase {ECO:0000313|EMBL:AGI85861.1};
KW Metal-binding {ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49};
KW Reference proteome {ECO:0000313|Proteomes:UP000012672}.
FT DOMAIN 64..166
FT /note="Aminoacyl-transfer RNA synthetases class-II family
FT profile"
FT /evidence="ECO:0000259|PROSITE:PS50862"
FT BINDING 69
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0007829|PDB:8C49"
FT BINDING 211
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49"
FT BINDING 218
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49"
FT BINDING 221
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:7U0R, ECO:0007829|PDB:8C49"
SQ SEQUENCE 275 AA; 30806 MW; 2DCE063D0388889B CRC64;
Query Match 99.2%; Score 1410; Length 275;
Best Local Similarity 99.3%;
Matches 273; Conservative 1; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MTVKYTDAQIQRLREYGNGTYEQKVFEDLASRDAAFSKEMSVASTDNEKKIKGMIANPSR 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MTVKYTDAQIQRLREYGNGTYEQKVFEDLASRDAAFSKEMSVASTDNEKKIKGMIANPSR 60
Qy 61 HGLTQLMNDIADALVAEGFIEVRTPIFISKDALARMTITEDKPLFKQVFWIDEKRALRPM 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 HGLTQLMNDIADALVAEGFIEVRTPIFISKDALARMTITEDKPLFKQVFWIDEKRALRPM 120
Qy 121 LAPNLYSVLRDLRDHTDGPVKIFEMGSCFRKESHSGMHLEEFTMLNLCDMGPRGDATEVL 180
||||||||:|||||||||||||||||||||||||||||||||||||| ||||||||||||
Db 121 LAPNLYSVMRDLRDHTDGPVKIFEMGSCFRKESHSGMHLEEFTMLNLVDMGPRGDATEVL 180
Qy 181 KNYISVVMKAAGLPDYDLVQEESDVYKETIDVEINGQEVCSAAVGPHYLDAAHDVHEPWS 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 KNYISVVMKAAGLPDYDLVQEESDVYKETIDVEINGQEVCSAAVGPHYLDAAHDVHEPWS 240
Qy 241 GAGFGLERLLTIREKYSTVKKGGASISYLNGAKIN 275
|||||||||||||||||||||||||||||||||||
Db 241 GAGFGLERLLTIREKYSTVKKGGASISYLNGAKIN 275
Prosecution Insights