DETAILED ACTION
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 .
Election/Restriction
This application contains claims directed to the following patentably distinct species: SEQ ID NOs: 1, 7, 8, 9, 12, and 13. The species are independent or distinct because each of these amino acid sequences represents a unique structure. In addition, these species are not obvious variants of each other based on the current record.
Applicant is required under 35 U.S.C. 121 to elect a single disclosed species, or a single grouping of patentably indistinct species, for prosecution on the merits to which the claims shall be restricted if no generic claim is finally held to be allowable. Currently, no claim is generic.
There is a serious search and/or examination burden for the patentably distinct species as set forth above because at least the following reason(s) apply: each sequence will require its own separate sequence search. An amino acid sequence will return results from both protein and nucleic acid databases to identify amino acid sequences from the protein databases and from the nucleic acid databases to identify sequences that encode proteins with similar amino acid sequences. The protein search will query 8 separate databases and the nucleic acid search will also query 8 separate databases resulting in 16 sets of returns for the Examiner to analyze. Each hit from this search will require the Examiner to determine its earliest public availability and to acquire the reference or record associated with the sequence. These references/records will need to be analyzed for context and any information disclosed about the sequence, such as annotations, alternative designations, actual reduction to practice, etc. For any additional sequences, this process must be repeated, and this constitutes a serious search burden.
Applicant is advised that the reply to this requirement to be complete must include (i) an election of a species to be examined even though the requirement may be traversed (37 CFR 1.143) and (ii) identification of the claims encompassing the elected species or grouping of patentably indistinct species, including any claims subsequently added. An argument that a claim is allowable or that all claims are generic is considered nonresponsive unless accompanied by an election.
The election may be made with or without traverse. To preserve a right to petition, the election must be made with traverse. If the reply does not distinctly and specifically point out supposed errors in the election of species requirement, the election shall be treated as an election without traverse. Traversal must be presented at the time of election in order to be considered timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are added after the election, applicant must indicate which of these claims are readable on the elected species or grouping of patentably indistinct species.
Should applicant traverse on the ground that the species, or groupings of patentably indistinct species from which election is required, are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing them to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the species unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other species.
Upon the allowance of a generic claim, applicant will be entitled to consideration of claims to additional species which depend from or otherwise require all the limitations of an allowable generic claim as provided by 37 CFR 1.141.
Election by Phone
During a telephone conversation with Christopher Meyer on Feb. 23, 2026, a provisional election was made to prosecute the species of SEQ ID NO: 13, claims 1, 3, and 7-15 (see interview summary). Because SEQ ID NO: 1 is a fragment of SEQ ID NO: 13 with no mismatches, but merely lacking the first five amino acids, these two sequences will be examined together (claim 2 included in election). Affirmation of this election must be made by applicant in replying to this Office action. Claims and 4-6 are withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to non-elected species. The Examiner did not specifically ask if the election was made with or without traverse, and Applicant is invited to traverse in their response if they wish to.
Comment on Interview
In the interview, the Examiner had mentioned that it looked like all the sequences were from the same enzyme family, so they would make up a proper Markush grouping; however, after reviewing the sequence search results, this does not look like it is correct. The sequence search results show that SEQ ID NOs: 1, 3, and 4 belong with the elected sequence of SEQ ID NO: 13, however, the remaining sequences did not share enough homology to come up in the sequence search. It appears the remaining sequences are not structurally related to the elected sequence.
Claims
Claims 1-15 are pending, claims 4-6 are withdrawn, and claims 1-3 and 7-15 are examined in this Office Action.
Information Disclosure Statement
The listing of references in the specification on pages 21-26 is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The disclosure is objected to because it contains embedded hyperlinks and/or other forms of browser-executable code on page 15, ¶ 49 lines 5 and 8, and ¶ 51 line 6. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The title of the invention is not descriptive of the claimed invention. A new title is required that is clearly indicative of the invention to which the claims are directed.
The following title is suggested: - - COLLAGEN-PRODUCING GALACTOSYLHYDROXYLYSYL GLUCOSYLTRANSFERASE FROM MIMIVIRUS - - .
Claim Objections
Claim 15 is objected to because of the following informalities: in the first line there is a typographical error: “nuclei acid” should be - - nucleic acid - - . Appropriate correction is requested.
Claim Interpretation
Claims 1-3 and 7-9 are directed to “a system” for producing collagen, and this is interpreted to be a product or combination of products that contains at least one of the recited bacterial cells. Because claims 10-15 are directed to methods, the Examiner interprets a “system” to be different from a method.
Claim 1 requires expression of an enzyme with at least 85% identity to “an amino acid sequence as set forth in at least one of SEQ ID NOs: 1, 7, 8, 9, 12, or 13”, and this is interpreted to encompass expression of fragments of any one of the recited sequences. The use of the article “an” which is an indefinite article renders this phrase inclusive of fragments. If Applicant intends the claim to require an enzyme with at least 85% identity to the full length of any of the recited sequences, Applicant is advised to amend the claim to recite “an enzyme with at least 85% identity to the full length polypeptide of SEQ ID NO: 1, 7, 8, 9, 12, or 13”. This would exclude fragments.
Claims 2 and 3 require the bacterial cell to express SEQ ID NO: 1 and SEQ ID NO: 13, respectively. These claims are interpreted to require expression of the full length sequence of SEQ ID NO: 1 and SEQ ID NO: 13, respectively. Claim 12 is also interpreted to require the full length of SEQ ID NO: 13.
Improper Markush Grouping
Claims 1, 7-9, and 11 are rejected on the basis that claims 1 and 11 each contain an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). All dependent claims are included in these rejections unless they include a limitation that overcomes the deficiencies of the parent claim.
A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush groupings (claims 1 and 11) of SEQ ID NOs: 1, 7, 8, 9, 12, and 13 are improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: when the Examiner did the sequence search for SEQ ID NO: 13, the only sequences from the instant application that came up with good homology and alignment were SEQ ID NOs: 1, 3, and 4. Therefore, it appears that SEQ ID NOs: 7-9 and 12 do not share sufficient homology to belong in a proper Markush grouping with SEQ ID NOs: 1 and 13.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use. For example, providing an alignment that shows conserved domains that are involved in specific enzymatic activities or binding properties would be evidence of being members of a proper Markush group.
Claim Rejections – 35 USC § 112
Indefiniteness
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.
Claims 1-3, 7, 10, and 13-15 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. All dependent claims are included in these rejections unless they include a limitation that overcomes the deficiencies of the parent claim.
Claim 1 is directed to a system for “producing collagen”, however, there do not appear to be any components of the system that will actually produce collagen. This is confusing, because the preamble does not match the actual claim limitations. The claim currently reads like a system for producing an enzyme in a bacterial cell which is quite different from being a system for producing collagen.
Claim 10 requires a recombinant galactosylhydroxylysyl glucosyltransferase (GGT) “derived from” Acanthamoeba polyphaga mimivirus. When a product is “derived from” something, this converts it to a “product by process”. In the rejected claims, the claims are methods that require a product that is produced by a process of derivation from the recited mimivirus. It is unclear what structures are conferred by this derivation. Will the GGT retain the amino acid sequence of a wild-type native GGT from mimivirus? Will the GGT be truncated or mutated or engineered in any way? This indefiniteness renders the metes and bounds of these claims unclear.
Claims 13-15 each recite limitations regarding how the GGT utilized in the claimed method is produced. It is unclear if there is an active method step of “expressing the GGT recombinantly in a bacterial cell” that must be performed prior to the “contacting” with a collagen protein. Claim 10 reads as if the GGT does not need to be actively produced; for example, it could have been purchased from a catalog. For this reason, it is unclear if claims 13-15 are adding an additional active method step that precedes the method step recited in claim 10. If the intention is to encompass the additional method step, then Applicant is advised to amend claim 13 to recite - - wherein the method further comprises a step of recombinantly expressing the GGT in a bacterial cell prior to said contacting - - .
Failure to Further Limit
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection I, 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.
Claims 13-15 are 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. All dependent claims are included in these rejections unless they overcome the deficiencies of the parent claim. 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.
Claim 13 requires that “the GGT is recombinantly expressed in a bacterial cell”. As discussed, above, in the indefiniteness rejection, it is unclear if this means there is an additional active method step that is required for the claimed method, or if this is just further defining the properties of the GGT that is utilized in the claimed method. If there is an additional active method step, then the claim is, in fact, further limiting. However, if this is merely further defining the process by which the GGT was made, then it does not appear to add a limitation beyond those required by the parent claim. It is unclear how a GGT that is recombinantly expressed in a bacterial cell would have any different structures to distinguish it from any other recombinant GGT. Is there a particular post-translational modification that a GGT has that would be distinguishing? If so, please make that clear on the record.
Claim 14 has a similar issue, because it is unclear what structures would be different when comparing a GGT expressed in an Escherichia coli (E. coli) cell to a GGT expressed in a different bacterial cell.
Claim 15 recites “wherein the GGT is expressed from a nuclei[c] acid encoding the GGT within the bacterial cell”. The only way that the GGT can possibly be recombinantly expressed in a bacterial cell is if the bacterial cell has a nucleic acid encoding said GGT, therefore, this limitation is already inherently required by claim 13 from which claim 15 depends.
Lack of Scope of Enablement
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 1-3 and 7 are 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 a system for producing collagen comprising collagen precursor peptides and a bacterial cell expressing an enzyme with galactosylhydroxylysl glucosyltransferase (GGT) activity and having at least 85% identity to the full length polypeptide of SEQ ID NO: 1 or 13, does not reasonably provide enablement for a system for producing collagen that lacks collagen precursors or that expresses an enzyme with 85% identity to a small fragment of SEQ ID NO: 1 or 13. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Currently the system does not require the elements necessary for a system “for producing collagen. It is known in the art that an enzyme requires a substrate for its activity. The current claim language does not even require any particular enzyme activity. The only requirement currently is a bacterial cell expressing an enzyme.
Furthermore, the claimed enzyme is only required to have 85% identity to “an” amino acid sequence, and this renders it inclusive of small peptide fragments. In order for the “system” to be able to function for producing collagen, it would need the enzyme to have a particular collagen-producing activity, and the polypeptide would need to be large enough to comprise all the necessary domains to confer this activity.
For at least these two reasons, the claims are not enabled across the entire scope that is currently encompassed by the claims.
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.
Claim(s) 1, 7, 10 and 13-15 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Luther et al. ((2011) J. of Biological Chemistry; Vol. 286; pp. 43701-43709).
The claims are directed to a system comprising a bacterial cell expressing an enzyme with at least 85% identity to “an” amino acid sequence as set forth in SEQ ID NO: 1 or 13, and to a method comprising contacting a collagen protein with a recombinant galactosylhydroxylysl glucosyltransferase (GGT) derived from Acanthamoeba polyphaga mimivirus.
Luther teaches that Mimivirus L230 has both lysyl hydroxylase and glucosyltransferase activities, with a low level of galactosyltransferase activity (Luther 43705, Figure 3). Luther teaches expression of recombinant Mimivirus L230 in E. Coli using a pET16b-based expression vector comprising the L230 gene (Id. 43702). Luther teaches a method that involved contacting bovine collagen type I with the recombinant L230 (Id. 43704). This is a method of contacting a collagen protein with a recombinant Mimivirus-derived GGT produced in an E. coli cell wherein the E. coli cell comprises a nucleic acid encoding the GGT (the pET vector with the L230 gene). This anticipates claims 10 and 13-15.
The instant SEQ ID NO: 13 comprises a peptide with the amino acid sequence “GYYKRS” and this has 100% identity to the fragment of L230 from positions 245-250 (Id. 43704, Figure 1) aligned to amino acids at positions 279-384 of instant SEQ ID NO: 13. For this reason, Luther teaches a “system” that comprises an E. Coli bacterial cell expressing an enzyme with at least 85% identity to “an amino acid sequence” as set forth in SEQ ID NO: 13 or 1. This anticipates claims 1 and 7.
Claim Rejections - 35 USC § 103
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 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.
Claim(s) 2, 3, 9, 11, and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Luther et al. ((2011) J. of Biological Chemistry; Vol. 286; pp. 43701-43709) in view of Legendre et al (GenPept Accession AD018798.1 (2021) pp. 1-2).
The claims are directed to a system comprising a bacterial cell expressing SEQ ID NO: 1 or 13, and to a method comprising contacting a collagen protein with a recombinant galactosylhydroxylysl glucosyltransferase (GGT) derived from Acanthamoeba polyphaga mimivirus wherein the GGT comprises SEQ ID NO: 1 or 13.
Luther teaches that Mimivirus L230 has both lysyl hydroxylase and glucosyltransferase activities, with a low level of galactosyltransferase activity (Luther 43705, Figure 3). Luther teaches expression of recombinant Mimivirus L230 in E. Coli using a pET16b-based expression vector comprising the L230 gene (Id. 43702). Luther teaches a method that involved contacting bovine collagen type I with the recombinant L230 (Id. 43704). This is a method of contacting a collagen protein with a recombinant Mimivirus-derived GGT produced in an E. coli cell wherein the E. coli cell comprises a nucleic acid encoding the GGT (the pET vector with the L230 gene).
Luther does not teach a GGT comprising either SEQ ID NO: 1 or 13. Luther does not teach a system comprising human collagen.
The instant SEQ ID NO: 13 has 100% identity with the putative procollagen-lysine,2-oxogluterate dioxygenase taught by Legendre et al, alignment provided here:
Alignments with SEQ ID NO: 13
RESULT 1
A0A0G2YBU7_MIMIV
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
ID A0A0G2YBU7_MIMIV Unreviewed; 455 AA.
AC A0A0G2YBU7; E3VZT2;
DT 25-OCT-2017, integrated into UniProtKB/TrEMBL.
DT 25-OCT-2017, sequence version 1.
DT 08-OCT-2025, entry version 28.
DE SubName: Full=Putative procollagen-lysine,2-oxoglutarate dioxygenase {ECO:0000313|EMBL:ADO18798.1};
DE SubName: Full=Putative procollagen-lysine2-oxoglutarate dioxygenase {ECO:0000313|EMBL:AKI81377.1};
DE SubName: Full=Uncharacterized protein R699 {ECO:0000313|EMBL:AEJ34941.1};
GN Name=R699 {ECO:0000313|EMBL:ADO18798.1};
GN ORFNames=MIMI_R699 {ECO:0000313|EMBL:AEJ34941.1};
OS Acanthamoeba polyphaga mimivirus (APMV).
OC Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota; Megaviricetes;
OC Imitervirales; Mimiviridae; Megamimivirinae; Mimivirus;
OC Mimivirus bradfordmassiliense.
OX NCBI_TaxID=212035 {ECO:0000313|EMBL:ADO18798.1, ECO:0000313|Proteomes:UP000201519};
OH NCBI_TaxID=5757; Acanthamoeba polyphaga (Amoeba).
RN [1] {ECO:0000313|EMBL:AEJ34941.1, ECO:0000313|Proteomes:UP000240552}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=M4 {ECO:0000313|EMBL:AEJ34941.1};
RX PubMed=21646533; DOI=10.1073/pnas.1101118108;
RA Boyer M., Azza S., Barrassi L., Klose T., Campocasso A., Pagnier I.,
RA Fournous G., Borg A., Robert C., Zhang X., Desnues C., Henrissat B.,
RA Rossmann M.G., La Scola B., Raoult D.;
RT "Mimivirus shows dramatic genome reduction after intraamoebal culture.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:10296-10301(2011).
RN [2] {ECO:0000313|EMBL:ADO18798.1, ECO:0000313|Proteomes:UP000201519}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=21375749;
RA Legendre M., Santini S., Rico A., Abergel C., Claverie J.M.;
RT "Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and
RT transcriptome sequencing.";
RL Virol. J. 8:99-99(2011).
RN [3] {ECO:0000313|EMBL:AKI81377.1, ECO:0000313|Proteomes:UP000274448}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Amazonia {ECO:0000313|EMBL:AKI81377.1,
RC ECO:0000313|Proteomes:UP000274448};
RA Assis F.L., Abrahao J.S., Kroon E.G., Dornas F.P., Andrade K.R.,
RA Borato P.V.M., Pilotto M.R., Benamar S., LaScola B., Colson P.;
RT "Pan-genome analysis of Brazilian lineage A amoebal mimiviruses.";
RL Submitted (OCT-2014) to the EMBL/GenBank/DDBJ databases.
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; HQ336222; ADO18798.1; -; Genomic_DNA.
DR EMBL; JN036606; AEJ34941.1; -; Genomic_DNA.
DR EMBL; KM982403; AKI81377.1; -; Genomic_DNA.
DR RefSeq; YP_003987227.1; NC_014649.1.
DR GeneID; 9925352; -.
DR KEGG; vg:9925352; -.
DR OrthoDB; 7251at10239; -.
DR Proteomes; UP000201519; Genome.
DR Proteomes; UP000240552; Genome.
DR Proteomes; UP000274448; Genome.
DR GO; GO:0008475; F:procollagen-lysine 5-dioxygenase activity; IEA:TreeGrafter.
DR InterPro; IPR050757; Collagen_mod_GT25.
DR InterPro; IPR057589; GT_PLOD.
DR PANTHER; PTHR10730:SF45; PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE; 1.
DR PANTHER; PTHR10730; PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE/GLYCOSYLTRANSFERASE 25 FAMILY MEMBER; 1.
DR Pfam; PF25342; GT_PLOD; 1.
PE 4: Predicted;
KW Dioxygenase {ECO:0000313|EMBL:ADO18798.1};
KW Oxidoreductase {ECO:0000313|EMBL:ADO18798.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000201519}.
FT DOMAIN 8..233
FT /note="PLOD1-3-like GT"
FT /evidence="ECO:0000259|Pfam:PF25342"
SQ SEQUENCE 455 AA; 53086 MW; 823A18E6E63E47C1 CRC64;
Query Match 100.0%; Score 2437; Length 455;
Best Local Similarity 100.0%;
Matches 455; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MEQSNNDDNLLVLGIGISVHKTDGVLRFEKYCQAHNLQYMIVGEGKKWNGGNLESEAGGG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEQSNNDDNLLVLGIGISVHKTDGVLRFEKYCQAHNLQYMIVGEGKKWNGGNLESEAGGG 60
Qy 61 QKINELLIALESIKDNKLIVVCDTYDLIPLSGPEEILRKYRFLTPDNKVVFSSELYCWPD 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 QKINELLIALESIKDNKLIVVCDTYDLIPLSGPEEILRKYRFLTPDNKVVFSSELYCWPD 120
Qy 121 ASLVERYPKVDTKYKYLNSGAFMGYRDDIYEMIKNGVKDRDDDQLFFSIKFIETDKIVLD 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ASLVERYPKVDTKYKYLNSGAFMGYRDDIYEMIKNGVKDRDDDQLFFSIKFIETDKIVLD 180
Qy 181 YKCELFQAMYRCNSDLVVHKNRIFNGYTNSYPVFAHGNGPAKKLLNHMEGYFMTEPIDGS 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 YKCELFQAMYRCNSDLVVHKNRIFNGYTNSYPVFAHGNGPAKKLLNHMEGYFMTEPIDGS 240
Qy 241 SNTINTFKLDNEPKVFFALYVDSNDLSALKQFLGKVASIQYGNKVIYLYDRSDNEQNRKL 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 SNTINTFKLDNEPKVFFALYVDSNDLSALKQFLGKVASIQYGNKVIYLYDRSDNEQNRKL 300
Qy 301 IQISYPNYHTGVTKYVFDDFKKSDAQFYFLLEQNCIITKKDILHELIMQVKDNHRVISPM 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 IQISYPNYHTGVTKYVFDDFKKSDAQFYFLLEQNCIITKKDILHELIMQVKDNHRVISPM 360
Qy 361 IGYEQNSTRTNFWGDIEDGYYKRSENYLDLAKHKVRGLWNVPYVYGVILMHESVVRNWDL 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 IGYEQNSTRTNFWGDIEDGYYKRSENYLDLAKHKVRGLWNVPYVYGVILMHESVVRNWDL 420
Qy 421 SMVKYNDKDMDLCFSLRKHTIFMYMINNNNYGYMV 455
|||||||||||||||||||||||||||||||||||
Db 421 SMVKYNDKDMDLCFSLRKHTIFMYMINNNNYGYMV 455
When comparing SEQ ID NO: 1 to SEQ ID NO: 13, it has no mismatches but is missing the first five amino acids but otherwise is the same as SEQ ID NO: 13.
Legendre teaches that their protein is from Acanthamoeba polyphaga mimivirus (see “Source”). Legendre teaches this protein has the catalytic glycosyltransferase domain found in the lysyl hydroxylase family (see “Region”).
At the time the instant application was filed, it would have been obvious and within the scope of one of ordinary skill in the art to substitute the putative procollagen-lysine,2-oxogluterate dioxygenase taught by Legendre for the L230 protein taught by Luther. This is a substitution of a known equivalent, one procollagen lysylhydroxylase for another. One would have predicted the ability to transfer a galactose and/or glucose molecule onto a procollagen peptide. Given the success of Luther in expressing the L230 protein in bacteria and obtaining successful transferase activity, one would have had an expectation of success in getting a similar result using this equivalent protein from the same source organism.
It would have also been obvious to use a human collagen rather than a bovine collagen as a substrate for the recombinant enzyme. Luther mentions human collagen and the biological significance of the lysyl hydroxylase genes in their abstract and the first paragraph on page 43701. Substituting human collagen for bovine collagen would have been the substitution of a known equivalent and would have had a predictable result, that of providing human collagen as a substrate for the recombinant enzyme.
Summary
No claim is allowed.
Examiner’s Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHY KINGDON whose telephone number is (571)272-8784. The examiner can normally be reached M-F 9:00 - 5:30 EST.
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, Amjad A Abraham can be reached at (571) 270-7058. 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.
CATHY KINGDON
Primary Examiner
Art Unit 1663
/CATHY KINGDON/Primary Examiner, Art Unit 1663