DETAILED CORRESPONDENCE
Application Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Applicant’s amendment to the claims filed on 12/02/2025 in response to the Non-Final Rejection mailed on 09/22/2025 is acknowledged. This listing of claims replaces all prior listings of claims in the application.
3. Claims 1-14 are pending.
4. Claims 3-14 stand withdrawn pursuant to 37 CFR 1.142(b).
5. Applicant’s remarks filed on 12/02/2025 in response to the Non-Final Rejection mailed on 09/22/2025 have been fully considered and are deemed persuasive to overcome at least one of the rejections and/or objections as previously applied.
The text of those sections of Title 35 U.S. Code not included in the instant action can be found in the prior Office Action.
Information Disclosure Statement
6. The IDS filed on 09/24/2025 has been considered by the examiner and a copy of the Form PTO/SB/08 is attached to the office action.
Claim Rejections - 35 USC § 112(a)
7. The written description rejection of claims 1-2 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is withdrawn in view of applicants’ amendment to the claims to recite “ the amino acid sequence set forth in SEQ ID NO: 2”.
8. The scope of enablement rejection of claims 1-2 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is withdrawn in view of applicants’ amendment to the claims to recite “ the amino acid sequence set forth in SEQ ID NO: 2”.
Claim Rejections - 35 USC § 102
9. The rejection of claims 1-2 under 35 U.S.C. 102(a)(1) as being anticipated by Ikeda et al. (JP 2013081406A, 2013; cited on IDS filed on 12/19/2022 and machine translation cited on the PTO-892 mailed on 07/16/2025) is withdrawn in view of applicants’ amendment to the claims to remove the recitation of the amino acid “L-serine” in the claims.
Claim Rejections - 35 USC § 103
10. 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.
11. Claim(s) 1-2 is/are newly rejected under 35 U.S.C. 103 as being unpatentable over Ikeda et al. (JP 2013081406A, 2013; cited on IDS filed on 12/19/2022 and machine translation cited on the PTO-892 mailed on 07/16/2025) in view of Siloto et al. (Biocatalysis and Agricultural Biotechnology, 2012; examiner cited). This new grounds of rejection is necessitated by applicants’ amendment to the claims to remove the recitation of the amino acid “L-serine” in the claims.
12. With respect to claims 1-2, Ikeda et al. teach an L-amino acid alpha ligase having improved substrate specificity comprising an amino acid sequence that is 100% identical to the amino acid sequence of SEQ ID NO: 2 and having a mutation at position 107, (it is known that biological organisms predominantly produce L-amino acids) [see paragraphs 0002 and 0007; alignment attached as APPENDIX A].
However, Ikeda et al. does not teach the protein of claims 1 and 2, wherein for the amino acid residue at position 107, an amino acid residue selected from the group consisting of L-alanine, L-histidine, L-glutamine, L-aspartic acid, L-glutamic acid, glycine and L-methionine.
Siloto et al. teach that techniques such as alanine scanning mutagenesis and site saturation mutagenesis are used to study the function of a single amino acid in relation to the rest of the protein [see Abstract; p. 182, column 1]. Siloto et al. teach that in site saturation mutagenesis involves substitution of a single amino acid to any other 19 possible substituents which provides an advantage that all possible substitutions can be obtained, which allows for a more comprehensive analysis of the function of the original amino acid in the targeted position [see p. 182, column 1].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Ikeda et al. and Siloto et al. to use a site saturation mutagenesis strategy in the mutant proteins of Ikeda et al. such that all 20 amino acid residues could be represented at a single position for targeted mutagenesis because Ikeda et al. teach L-amino acid alpha ligase having improved substrate specificity. Siloto et al. teach that in site saturation mutagenesis involves substitution of a single amino acid to any other 19 possible substituents which provides an advantage that all possible substitutions can be obtained, which allows for a more comprehensive analysis of the function of the original amino acid in the targeted position. One of ordinary skill in the art desiring to substitute the positions of Ikeda et al. with the amino acid residue to improved substrate specificity and would have a reasonable expectation of success, a reasonable level of predictability, and would be motivated to combine the teachings of Ikeda et al. and Siloto et al. because Siloto et al. acknowledges that site saturation mutagenesis provides an advantage that all possible substitutions can be obtained, which allows for a more comprehensive analysis of the function of the original amino acid in the targeted position. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Response to Remarks Regarding Prior Art Rejections
13. Applicants’ remarks filed on 12/02/2025 have been fully considered by the examiner; however, they are rendered moot in view of the new rejection set forth above, which is necessitated by applicants’ amendment to the claims.
Conclusion
14. Status of the claims:
Claims 1-14 are pending.
Claims 3-14 stand withdrawn pursuant to 37 CFR 1.142(b).
Claims 1-2 are rejected.
No claims are in condition for an allowance.
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 PAUL J HOLLAND whose telephone number is (571)270-3537. The examiner can normally be reached Monday to Friday from 8AM to 5PM.
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, Manjunath Rao can be reached at 571-272-0939. 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.
/PAUL J HOLLAND/Primary Examiner, Art Unit 1656
APPENDIX A
Ikeda et al. with SEQ ID NO: 2
Query Match 100.0%; Score 2433; Length 472;
Best Local Similarity 100.0%;
Matches 472; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MERKTVLVIADLGGCPPHMFYKSAAEKYNLVSFIPRPFAITASHAALIEKYSVAVIKDKD 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MERKTVLVIADLGGCPPHMFYKSAAEKYNLVSFIPRPFAITASHAALIEKYSVAVIKDKD 60
Qy 61 YFKSLADFEHPDSIYWAHEDHNKPEEEVVEQIVKVAEMFGADAITTNNELFIAPMAKACE 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 YFKSLADFEHPDSIYWAHEDHNKPEEEVVEQIVKVAEMFGADAITTNNELFIAPMAKACE 120
Qy 121 RLGLRGAGVQAAENARDKNKMRDAFNKAGVKSIKNKRVTTLEDFRAALEEIGTPLILKPT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 RLGLRGAGVQAAENARDKNKMRDAFNKAGVKSIKNKRVTTLEDFRAALEEIGTPLILKPT 180
Qy 181 YLASSIGVTLITDTETAEDEFNRVNDYLKSINVPKAVTFEAPFIAEEFLQGEYGDWYQTE 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 YLASSIGVTLITDTETAEDEFNRVNDYLKSINVPKAVTFEAPFIAEEFLQGEYGDWYQTE 240
Qy 241 GYSDYISIEGIMADGEYFPIAIHDKTPQIGFTETSHITPSILDEEAKKKIVEAAKKANEG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GYSDYISIEGIMADGEYFPIAIHDKTPQIGFTETSHITPSILDEEAKKKIVEAAKKANEG 300
Qy 301 LGLQNCATHTEIKLMKNREPGLIESAARFAGWNMIPNIKKVFGLDMAQLLLDVLCFGKDA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 LGLQNCATHTEIKLMKNREPGLIESAARFAGWNMIPNIKKVFGLDMAQLLLDVLCFGKDA 360
Qy 361 DLPDGLLDQEPYYVADCHLYPQHFKQNGQIPETAEDLVIEAIDIPDGLLKGDTEIVSFSA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 DLPDGLLDQEPYYVADCHLYPQHFKQNGQIPETAEDLVIEAIDIPDGLLKGDTEIVSFSA 420
Qy 421 AAPGTSVDLTLFEAFNSIAAFELKGSNSQDVAESIRQIQQHAKLTAKYVLPV 472
||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 AAPGTSVDLTLFEAFNSIAAFELKGSNSQDVAESIRQIQQHAKLTAKYVLPV 472