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/JP2021/032083.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on June 10, 2026 has been entered.
Election/Restrictions
Applicant elected without traverse of Group I with a species election of (A1) positions 34-928 of SEQ ID NO:2 as the parent polypeptide, (A2) D241M/Q311L as the amino acid modifications made in the parent polypeptide or the polypeptide having the amino acid sequence of SEQ ID NO:7, (B) improvement in the transglycosylation rate as the property of the amino acid modifications, and the N-linked sugar [N3-PEG(3)]-MSG1-)Asn-PEG(3)-N3 as the sugar donor in in the reply filed on July 11, 2025 is acknowledged.
Claims 12-15 and 17-44 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species and invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on July 22, 2025.
Status of Claims
Claims 1, 5-7, 9-15, and 17-45 are pending.
Claims 12-15 and 17-44 are withdrawn.
Claims 1, 5-7, 9-11, and 45 are under examination.
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.
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.
Claim(s) 1, 5-7, 9-11, and 45 is/are rejected under 35 U.S.C. 103 as being unpatentable over A0A3L8GF62_STRIN (UniProtKB/TrEMBL Database. April 10, 2019 – cited previously on form PTO-892) and Kawaguchi (US 2018/0208915– form PTO-1449).
Regarding claims 1 and 5, A0A3L8GF62_STRIN discloses a Streptococcus endo-beta-N-acetylglucosaminidase having 100% sequence identity to the endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of the instant application (page 1 and see the sequence alignment below). The endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN has sugar chain hydrolysis activity.
A0A3L8GF62_STRIN does not disclose endo-beta-N-acetylglucosaminidase variants having the amino acid sequence of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), or SEQ ID NO:5 (D241Q/E360Q) of the instant application. SEQ ID NO:3-5 are endo-beta-N-acetylglucosaminidase variants of Streptococcus endo-beta-N-acetylglucosaminidase, wherein the variant consists of a D241Q, D241Q/Q311L, or D241Q/E360Q amino acid substitutions, respectively.
Regarding claim 1 and 5, Kawaguchi discloses endo-beta-N-acetylglucosaminidase mutants having the amino acid sequence of SEQ ID NO:1, 4, and 7, which are “EndoS D233Q”, “EndoS D233Q /Q303L”, and “EndoS D233Q/E350Q”, respectively, in Figure 4 (abstract, Figure 4, and [0111]). The amino acid position D233, Q303, and E350 of Kawaguchi corresponds to D241, Q311, and E360 of the endo-beta-N-acetylglucosaminidase of SEQ ID NO:3, 4, or 5 of the instant application (see the sequence alignments below).
Regarding claims 6 and 45 the endo-beta-N-acetylglucosaminidase mutants have hydrolysis activity and improved transglycosylation activity on a fucosylate core GlcNAc of an IgG Fc region ([0028]-[0030], [0081]-[0084], [0093]-[0095], [0111], and [0123]-[0127]).
Regarding claims 7 and 45, the fucosylated core GlcNAc is in an N-linked sugar chain ([0081]-[0084], [0093]-[0095], [0111], and [0123]-[0127]).
Regarding claims 9 and 45, the N-linked sugar chain is N297-linked sugar chain linked to an Asn at position 297 of the IgG Fc region ([0081]-[0084], [0093]-[0095], [0111], and [0123]-[0127]).
Regarding claims 10 and 45, the N297-linked sugar chain is a complex-type sugar chain having a non-reducing end ([0081]-[0084], [0093]-[0095], [0111], and [0123]-[0127]).
Regarding claims 11 and 45, the N-297 linked sugar chain is a fucosylated core GlcNAc ([0081]-[0084], [0093]-[0095], [0111], and [0123]-[0127]).
Regarding the properties recited in claims 6-7, 9-11, and 45, transglycosylation activity and/or hydrolysis activity compared to wildtype Endo-S is an inherent property of the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN, wherein the variants consist of D241Q, D241Q/Q311L or D241Q/E360Q amino acid substitution(s), because said variants have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), and SEQ ID NO:5 (D241Q/E360Q), respectively, of the instant application. MPEP 2112.01 states that “Products of identical chemical composition can not have mutually exclusive properties.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable.” Since the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3, 4, or 5 of the instant application, the recited property “significantly improved transglycosylation activity compared to wildtype Endo-S” is necessarily present. MPEP 2112 II states that “There is no requirement that a person of ordinary skill in the art would have recognized the inherent disclosure at the relevant time, but only that the subject matter is in fact inherent in the prior art reference.”
Therefore, in combining the teachings of A0A3L8GF62_STRIN and Kawaguchi, it would have been obvious to one having ordinary skill in the art before the claimed invention was effectively filed to enhance the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN by introducing D241Q, D241Q/Q311L, or D241Q/E360Q amino acid substitution as taught by Kawaguchi to arrive at the endo-beta-N-acetylglucosaminidase variants having the amino acid sequence of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), and SEQ ID NO:5 (D241Q/E360Q). One having ordinary skill in the art would have been motivated to do in order to impart transglycosylation activity to the endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN. One having ordinary skill in the art would have had a reasonable expectation of success since A0A3L8GF62_STRIN teaches endo-beta-N-acetylglucosaminidase having 100% sequence identity to the unmodified endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of the instant application and Kawaguchi teaches amino acid substitutions of an endo-beta-N-acetylglucosaminidase that improve transglysylation activity. Using the known technique of introducing amino acid substitutions (D241Q, D241Q/Q311L, or D241Q/E360Q) in the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN for improving transglycosylation would have been obvious to one of ordinary skill. The rationale supporting that the claims would have been obvious is that a method of enhancing a particular class of devices (Streptococcus endo-beta-N-acetylglucosaminidase having improved transglycosylation due to D241Q, D241Q/Q311L, or D241Q/E360Q amino acid substitutions) has been made part of the ordinary capabilities of one skilled in the art based upon the teaching of such improvement in other situations. One of ordinary skill in the art would have been capable of applying this known method of enhancement to a “base” device (Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN) in the prior art and the results would have been predictable to one of ordinary skill in the art.
Therefore, the above references render claims 1, 5-7, 9-11, and 45 prima facie obvious.
Applicant's arguments filed June 10, 2026 have been fully considered but they are not persuasive.
Applicant argues that in the response filed on April 9, 2026, Applicant provided a declaration under 37 CFR 1.132 by Dr. Mitsuhiro Iwamoto (hereafter referred to as "132 Declaration") that provided testimony from an actual person of skill in the art attesting that the Examiner's assumptions about "corresponding amino acids" across different enzyme types were factually incorrect and not how a person of ordinary skill would view the art. This alone should have been sufficient to rebut the rejection because the Examiner is not person of ordinary skill in the art, and the Examiner's unsupported assumptions about the art cannot trump declaratory testimony of a verifiable expert.
This not found persuasive.
Applicant and the 132 Declaration specified that the enzymes of Examples 1 and 2 of the 132 Declaration are variants of hypothetical proteins. Applicant states at page 10 of the Remarks filed on June 10, 2026 that the term "hypothetical proteins" is a term of art and it refers to proteins whose sequences were predicted based on genomic study rather than sequenced. Since the two proteins of Examples 1 and 2 are not endo-beta-N-acetylglucosaminidase but are hypothetical proteins with unknown function, a person of ordinary skill would not assume that mutations in the “corresponding” amino acids of the hypothetic proteins would result in the hypothetical proteins having transglycosylation and/or hydrolysis activity. Therefore, the 132 Declaration is insufficient to demonstrate Applicant’s assertion: that the recited amino acid substitutions do not confer transglycosylation and/or hydrolysis activity of Endo-beta-N-acetylglucosaminidases.
Applicant argues that in addition to proffering an opinion from the perspective of a person skilled in the art, Dr. Iwamoto's declaration also provided data relating to Enzymes 1 and 2 each of which have are also classified as members of the GH18 family-empirically showing that the Examiner's assumptions were incorrect. The amino acid positions of Kawaguchi or Yu that the Examiner alleges "correspond to" distinct positions in the claimed sequences are not common across enzymes of the GH18 family, as the declaration shows. Thus, the Examiner's reliance on the endo-beta-N-acetylglucosaminidase enzymes of Kawaguchi and Yu to show allegedly "corresponding" amino acids across GH18 family enzymes can be nothing other than hindsight.
This is not found persuasive.
Since the two hypothetical proteins of Examples 1 and 2 are predicted to be classified as members of GH18 family, the two hypothetical proteins may or may not be a member of the GH18 family or the two hypothetical proteins may be chitinases, which have different function compared to an endo-beta-N-acetylglucosaminidase (according to the regions of Enzyme 1 and Enzymes 2 at page 11 of the Remarks filed on June 10, 2026). Further, in response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). In the instant case, A0A3L8GF62_STRIN, Kawaguchi, and Yu all relate to endo-beta-N-acetylglucosaminidases. 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, one of ordinary skill in the art would have had a reasonable expectation of success since A0A3L8GF62_STRIN discloses an endo-beta-N-acetylglucosaminidase and Kawaguchi and Yu disclose amino acid substitutions resulting in transglycosylation activity and/or hydrolysis activity of endo-beta-N-acetylglucosaminidases. Further, having transglycosylation activity and/or hydrolysis activity compared to wildtype Endo-S is an inherent property of the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN, wherein the variants consist of D241Q, D241Q/Q311L, D241Q/E360Q or D241M amino acid substitution(s), because said variants have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), SEQ ID NO:5 (D241Q/E360Q), and SEQ ID NO:6 (D241M), respectively, of the instant application. MPEP 2112.01 states that “Products of identical chemical composition can not have mutually exclusive properties.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable.” Since the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3, 4, 5, or 6 of the instant application, the recited property “transglycosylation activity compared to wildtype Endo-S” is necessarily present. MPEP 2112 II states that “There is no requirement that a person of ordinary skill in the art would have recognized the inherent disclosure at the relevant time, but only that the subject matter is in fact inherent in the prior art reference.”
Applicant argues that the Advisory Action focuses on the fact that Enzymes 1 and 2 of the declaration are "hypothetical proteins." The term "hypothetical proteins" seems to have been interpreted as meaning that the Examples in the declaration, as a whole, were hypothetical and that no empirical experimentation was performed (i.e., the data is theoretical). This is an incorrect interpretation. The term "hypothetical proteins" is a term of art, and it refers to proteins whose sequences were predicted based on genomic study rather than sequenced. In other words, the experiments in the examples were indeed performed and Enzymes 1 and 2 are real, physical examples of GH18 family enzymes from Helcococcus ovis (GenBank accession number: TFF64741.1) and Fastidiosipila sanguinis (GenBank accession number: AVM42050). See 132 Declaration at para. 8. Notably, the AOA3L8GF62_STRIN enzyme was also listed as a "hypothetical protein" in the sequence database prior to the filing date, and is similar to the enzymes mentioned in the Declaration. Even though these are described as "hypothetical proteins," the three enzymes mentioned above all (i) are classified as glycosyl hydrolase, family 18, and (ii) are enzymes that cleave the GlcNAc-GlcNAc bond. Since they share these characteristics, they are unquestionably similar enzymes that exhibit the same activity; therefore, a person skilled in the art would infer that enzymes with mutations in certain amino acid residues of these enzymes would also exhibit similar activity behavior. In other words, in contrast to the Examiner's allegation, Enzymes 1 and 2 are clearly germane to the enzyme of the main prior art. Contrary to expectations and unlike the results of Enzymes 1 and 2, which exhibited only low transglycosylation rates, the claimed enzymes exhibited remarkably high transglycosylation rates.
This is not found persuasive.
Contrary to Applicant’s arguments, A0A3L8GF62_STRIN (UniProtKB/TrEMBL Database. April 10, 2019 – cited previously on form PTO-892) clearly discloses that the polypeptide is an Endo-beta-N-acetylglucosaminidase (line “DE”). Further, since the two hypothetical proteins of Examples 1 and 2 are predicted to be classified as members of GH18 family, the two hypothetical proteins may or may not be a member of the GH18 family or the two hypothetical proteins may be chitinases (according to the regions of Enzyme 1 and Enzymes 2 at page 11 of the Remarks filed on June 10, 2026). Also, the Advisory did not indicate that that no empirical experimentation was performed (i.e., the data is theoretical). Applicant and the 132 Declaration specified that the enzymes of Examples 1 and 2 of the 132 Declaration are variants of hypothetical proteins. Applicant states that the term "hypothetical proteins" is a term of art, and it refers to proteins whose sequences were predicted based on genomic study rather than sequenced. Since the two proteins of Examples 1 and 2 are not endo-beta-N-acetylglucosaminidase but are hypothetical proteins with unknown function, a person of ordinary skill would not assume that mutations in the “corresponding” amino acids of the hypothetic proteins would result in the hypothetical proteins having transglycosylation and/or hydrolysis activity. Therefore, the 132 Declaration is insufficient to demonstrate Applicant’s assertion: that the recited amino acid substitutions do not confer transglycosylation and/or hydrolysis activity of Endo-beta-N-acetylglucosaminidases.
Applicant argues that the data of the 132 Declaration shows that the position that corresponds with D233 in Endo-S enzymes does not confer a corresponding improved function on all GH18 family enzymes. The effect of mutating GH18 family enzymes is not predictable, nor would a person of ordinary skill assume that "corresponding" amino acids have the same function in different enzymes, and a person of ordinary skill reading Kawaguchi or Yu would not expect that mutating a "corresponding" residue in AOA3L8GF62_STRIN or SEQ ID NO: 2 of the present application would also result in an enzyme with improved transglycosylation activity. See 132 Declaration at para. 10. It would not have been obvious to make the claimed substitutions, nor would the resulting transglycosylation activity have been predictable. While the Examiner alleges that "absolute predictability" is not required, the declaration establishes that the there is not even reasonable predictability, which is required. Even if Kawaguchi and Yu showed two examples of GH18 enzymes with "corresponding" amino acids (and Applicant does not concede that is the case), Dr. Iwamoto's declaration shows two more than do not. At best, the evidence of record shows a coin flip; not reasonable predictability.
This is not found persuasive.
The 132 Declaration is insufficient to demonstrate Applicant’s assertion, that the recited amino acid substitutions do not confer transglycosylation and/or hydrolysis activity of Endo-beta-N-acetylglucosaminidases, see above. 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, one of ordinary skill in the art would have had a reasonable expectation of success since A0A3L8GF62_STRIN discloses an endo-beta-N-acetylglucosaminidase that is identical to the unmodified endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of the instant application and Kawaguchi and Yu disclose amino acid substitutions that improved transglycosylation activity of endo-beta-N-acetylglucosaminidases. Further, improved transglycosylation activity compared to wildtype Endo-S is an inherent property of the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN, wherein the variants consist of D241Q, D241Q/Q311L or D241Q/E360Q amino acid substitution(s), because said variants have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), and SEQ ID NO:5 (D241Q/E360Q), respectively, of the instant application. MPEP 2112.01 states that “Products of identical chemical composition can not have mutually exclusive properties.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable.” Since the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3, 4, or 5 of the instant application, the recited property “significantly improved transglycosylation activity compared to wildtype Endo-S” is necessarily present. MPEP 2112 II states that “There is no requirement that a person of ordinary skill in the art would have recognized the inherent disclosure at the relevant time, but only that the subject matter is in fact inherent in the prior art reference.”
Applicant argues that the Examiner has not established prima facie obviousness because AOA3L8GF62_STRIN does not explicitly state that the enzyme described therein possesses trans-glycosylation activity, so a person of ordinary skill in the art would not focus on it as a starting point in the first place. The cited website merely describes the function of the AOA3L8GF62_STRIN enzyme (hereinafter, referred to as "the AOA3L8GF62_STRIN enzyme") as the hydrolysis of oligosaccharides. It does not state at all that the enzyme possesses transglycosylation activity.
This is not found persuasive.
Improved transglycosylation activity compared to wildtype Endo-S is an inherent property of the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN, wherein the variants consist of D241Q, D241Q/Q311L or D241Q/E360Q amino acid substitution(s), because said variants have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), and SEQ ID NO:5 (D241Q/E360Q), respectively, of the instant application. MPEP 2112.01 states that “Products of identical chemical composition can not have mutually exclusive properties.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable.” Since the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3, 4, or 5 of the instant application, the recited property “significantly improved transglycosylation activity compared to wildtype Endo-S” is necessarily present. MPEP 2112 II states that “There is no requirement that a person of ordinary skill in the art would have recognized the inherent disclosure at the relevant time, but only that the subject matter is in fact inherent in the prior art reference.”
Applicant argues that as described in Kawaguchi and in the specification of the present application, there are few cases where endo-beta-N-acetylglucosaminidases also possess trans-glycosylation activity in addition to hydrolysis activity. A person skilled in the art who referred to the "Function" of the AOA3L8GF62_STRIN enzyme would have no reason to believe that this enzyme is an exception to this general principle. In fact, Endo-Si WT (SEQ ID NO: 2) described in the present specification, which has the same sequence as the enzyme of the main prior art, does not exhibit trans-glycosylation activity (see Table 6 of Example 2). Therefore, a person skilled in the art who aimed at obtaining new enzymes with trans-glycosylation activity would not focus on and thus use the AOA3L8GF62_STRIN enzyme as a starting point in the first place.
This is not found persuasive.
Improved transglycosylation activity compared to wildtype Endo-S is an inherent property of the variants of the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN, wherein the variants consist of D241Q, D241Q/Q311L or D241Q/E360Q amino acid substitution(s), because said variants have identical chemical structure as the endo-beta-N-acetylglucosaminidase variants of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), and SEQ ID NO:5 (D241Q/E360Q), respectively, of the instant application. Further, the endo-beta-N-acetylglucosaminidase variants having the amino acid sequence of SEQ ID NO:3-6 of the instant application are variants of SEQ ID NO:2 of the instant application, wherein the variant consists of D241Q (SEQ ID NO:3), D241Q/Q311L (SEQ ID NO:4), D241Q/E360Q (SEQ ID NO:5), and D241M (SEQ ID NO:6) of the instant application. A0A3L8GF62_STRIN discloses a Streptococcus endo-beta-N-acetylglucosamines having 100% sequence identity to the endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of the instant application. Kawaguchi and Yu discloses endo-beta-N-acetylglucosaminidase mutants having D223Q, D233Q /Q303L, D233Q/E350Q, or D234M amino acid substitution(s). The amino acid position D233, Q303, and E350 of Kawaguchi corresponds to D241, Q311, and E360 of the endo-beta-N-acetylglucosaminidase of SEQ ID NO:2, 3, 4, or 5 of the instant application. The amino acid position D234 of Yu corresponds to D241 of the endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 or 6 of the instant application. Therefore, in combining the teachings of A0A3L8GF62_STRIN and Kawaguchi or Yu, it would have been obvious to one having ordinary skill in the art before the claimed invention was effectively filed to enhance the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN by introducing D241Q, D241Q/Q311L, or D241Q/E360Q amino acid substitution as taught by Kawaguchi to arrive at the endo-beta-N-acetylglucosaminidase variants having the amino acid sequence of SEQ ID NO:3 (D241Q), SEQ ID NO:4 (D241Q/Q311L), SEQ ID NO:5 (D241Q/E360Q), and SEQ ID NO:6 (D241M) of the instant application. One having ordinary skill in the art would have been motivated to do in order to impart transglycosylation activity to the endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN. The rationale supporting that the claims would have been obvious is that a method of enhancing a particular class of devices (Streptococcus endo-beta-N-acetylglucosaminidase having improved transglycosylation due to D241Q, D241Q/Q311L, D241Q/E360Q , or D241M amino acid substitutions) has been made part of the ordinary capabilities of one skilled in the art based upon the teaching of such improvement in other situations. One of ordinary skill in the art would have been capable of applying this known method of enhancement to a “base” device (Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN) in the prior art and the results would have been predictable to one of ordinary skill in the art.
Hence the rejection has been maintained.
Claim(s) 1, 5-7, 9-11, and 45 is/are rejected under 35 U.S.C. 103 as being unpatentable over A0A3L8GF62_STRIN (UniProtKB/TrEMBL Database. April 10, 2019 – cited previously on form PTO-892) and Yu (US 2020/0062861– cited previously on form PTO-892 or US 11,203,645 – cited previously on form PTO-892. US 2020/0062861 is used for specific passages of Yu).
Regarding claims 1 and 5, A0A3L8GF62_STRIN discloses a Streptococcus endo-beta-N-acetylglucosaminidase having 100% sequence identity to the endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of the instant application (page 1 and see the sequence alignment below). The endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN has sugar chain hydrolysis activity.
A0A3L8GF62_STRIN does not disclose endo-beta-N-acetylglucosaminidase variants having the amino acid sequence of SEQ ID NO:6 (D241M). SEQ ID NO:6 is endo-beta-N-acetylglucosaminidase variant of Streptococcus endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of the instant application, wherein the variant consists of a D241M amino acid substitution.
Regarding claims 1 and 5, Yu discloses an “EndoSn-D234M” variant, which is an endo-beta-N-acetylglucosaminidase mutant having the amino acid sequence of SEQ ID NO:2 (abstract, Figure 4, page 3). The amino acid position D234 of Yu corresponds to D241 of the endo-beta-N-acetylglucosaminidase of SEQ ID NO:6 (see the sequence alignments below). The EndoSn-D234M mutant has hydrolysis activity and improved transglycosylation activity ([0027]-[0029]).
Regarding claims 6 and 45, the EndoSn-D234M mutant has hydrolysis activity and improved transglycosylation activity on a fucosylated core GlcNAc of an IgG Fc region ([0027]-[0029]).
Regarding claims 7 and 45, the fucosylated core GlcNAc is an N-linked sugar chain ([0027]-[0029]).
Regarding claims 9 and 45, the N-linked sugar chain is an N297-linked sugar chain linked to an Asn at position 297 of the IgG Fc region ([0027]-[0029]).
Regarding claims 10 and 45, the N297-linked sugar chain is a complex-type sugar chain having a non-reducing end ([0027]-[0029] and [0061]-[0062]).
Regarding claims 11 and 45, the N-297 linked sugar chain is a fucosylated core GlcNAc ([0027]-[0029]).
Therefore, in combining the teachings of A0A3L8GF62_STRIN and Yu, it would have been obvious to one having ordinary skill in the art before the claimed invention was effectively filed to enhance the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN by introducing D241M amino acid substitution as taught by Yu to arrive at the endo-beta-N-acetylglucosaminidase variant having the amino acid sequence of SEQ ID NO:6 (D241M) of the instant application. One having ordinary skill in the art would have been motivated to do in order to impart transglycosylation activity to the endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN. One having ordinary skill in the art would have had a reasonable expectation of success since A0A3L8GF62_STRIN teaches an endo-beta-N-acetylglucosaminidase having 100% sequence identity to the unmodified endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of the instant application and Yu teaches an amino acid substitution of an endo-beta-N-acetylglucosaminidase that improves transglysylation activity. Using the known technique of introducing amino acid substitutions (D241M) in the Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN for improving transglycosylation of the would have been obvious to one of ordinary skill. The rationale supporting that the claims would have been obvious is that a method of enhancing a particular class of devices (Streptococcus endo-beta-N-acetylglucosaminidase having improved transglycosylation due to D241M amino acid substitution) has been made part of the ordinary capabilities of one skilled in the art based upon the teaching of such improvement in other situations. One of ordinary skill in the art would have been capable of applying this known method of enhancement to a “base” device (Streptococcus endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN) in the prior art and the results would have been predictable to one of ordinary skill in the art.
Therefore, the above references render claims 1, 5-7, 9-11, and 45 prima facie obvious.
Applicant has submitted arguments to both rejections. See the rebuttal above.
Hence the rejection has been maintained.
Duplicate Claims, Warning
Applicant is advised that should claim 5 be found allowable, claim 45 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. 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). Claims 5 and 45 are both directed to identical polypeptides and the properties recited in claim 45 are inherent to polypeptides recited in claims 5 and 45. MPEP 2112.01 states that “Products of identical chemical composition can not have mutually exclusive properties.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable.”
Conclusion
Claims 1, 5-7, 9-15, and 17-45 are pending.
Claims 12-15 and 17-44 are withdrawn.
Claims 1, 5-7, 9-11, and 45 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YONG D PAK whose telephone number is (571)272-0935. The examiner can normally be reached M-Th: 5:30 am - 3:30 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert Mondesi can be reached on 408-918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YONG D PAK/Primary Examiner, Art Unit 1652
Sequence alignment between the polypeptide of SEQ ID NO:2 of the instant application (“Qy”) and the endo-beta-N-acetylglucosaminidase of A0A3L8GF62_STRIN (“Db”)
A0A3L8GF62_STRIN
ID A0A3L8GF62_STRIN Unreviewed; 928 AA.
AC A0A3L8GF62;
DT 10-APR-2019, integrated into UniProtKB/TrEMBL.
DT 10-APR-2019, sequence version 1.
DT 18-JUN-2025, entry version 27.
DE RecName: Full=mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase {ECO:0000256|ARBA:ARBA00012566};
DE EC=3.2.1.96 {ECO:0000256|ARBA:ARBA00012566};
GN ORFNames=DIY07_08980 {ECO:0000313|EMBL:RLU55257.1};
OS Streptococcus iniae (Streptococcus shiloi).
OC Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=1346 {ECO:0000313|EMBL:RLU55257.1, ECO:0000313|Proteomes:UP000269148};
RN [1] {ECO:0000313|EMBL:RLU55257.1, ECO:0000313|Proteomes:UP000269148}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=QMA0445 {ECO:0000313|EMBL:RLU55257.1,
RC ECO:0000313|Proteomes:UP000269148};
RA Barnes A.C., Silayeva O.;
RT "Mutators as drivers of adaptation in pathogenic bacteria and a risk factor
RT for host jumps and vaccine escape.";
RL Submitted (JUN-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=an N(4)-(oligosaccharide-(1->3)-[oligosaccharide-(1->6)]-beta-
CC D-Man-(1->4)-beta-D-GlcNAc-(1->4)-alpha-D-GlcNAc)-L-asparaginyl-
CC [protein] + H2O = an oligosaccharide-(1->3)-[oligosaccharide-(1->6)]-
CC beta-D-Man-(1->4)-D-GlcNAc + N(4)-(N-acetyl-beta-D-glucosaminyl)-L-
CC asparaginyl-[protein]; Xref=Rhea:RHEA:73067, Rhea:RHEA-COMP:12603,
CC Rhea:RHEA-COMP:18176, ChEBI:CHEBI:15377, ChEBI:CHEBI:132248,
CC ChEBI:CHEBI:192714, ChEBI:CHEBI:192715; EC=3.2.1.96;
CC Evidence={ECO:0000256|ARBA:ARBA00034414};
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 18 family.
CC {ECO:0000256|ARBA:ARBA00009336}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:RLU55257.1}.
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DR EMBL; QLQD01000076; RLU55257.1; -; Genomic_DNA.
DR RefSeq; WP_003102174.1; NZ_QLSP01000075.1.
DR AlphaFoldDB; A0A3L8GF62; -.
DR SMR; A0A3L8GF62; -.
DR STRING; 1346.BMF34_08885; -.
DR KEGG; sio:DW64_08875; -.
DR KEGG; siq:DQ08_08895; -.
DR KEGG; siz:SI82_08880; -.
DR OrthoDB; 7183084at2; -.
DR Proteomes; UP000269148; Unassembled WGS sequence.
DR GO; GO:0004553; F:hydrolase activity, hydrolyzing O-glycosyl compounds; IEA:InterPro.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:InterPro.
DR CDD; cd06542; GH18_EndoS-like; 1.
DR Gene3D; 3.20.20.80; Glycosidases; 1.
DR Gene3D; 3.80.10.10; Ribonuclease Inhibitor; 1.
DR InterPro; IPR049410; EndoS-like_Ig-like.
DR InterPro; IPR057016; EndoS_F2-like_TIM-barrel.
DR InterPro; IPR001579; Glyco_hydro_18_chit_AS.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR InterPro; IPR032675; LRR_dom_sf.
DR Pfam; PF20746; EndoS_Ig-like; 1.
DR Pfam; PF23952; LRR_EndoS; 1.
DR Pfam; PF23916; TIM-barrel_EndoS; 1.
DR SUPFAM; SSF51445; (Trans)glycosidases; 1.
DR PROSITE; PS01095; GH18_1; 1.
PE 3: Inferred from homology;
KW Glycosidase {ECO:0000256|ARBA:ARBA00023295};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Signal {ECO:0000256|ARBA:ARBA00022729}.
FT DOMAIN 124..408
FT /note="Endo-beta-N-acetylglucosaminidase EndoS/F2-like TIM-
FT barrel"
FT /evidence="ECO:0000259|Pfam:PF23916"
FT DOMAIN 638..760
FT /note="Endo-beta-N-acetylglucosaminidase EndoS-like Ig-
FT like"
FT /evidence="ECO:0000259|Pfam:PF20746"
FT REGION 905..928
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 928 AA; 104646 MW; 0EE526322AEA087B CRC64;
Query Match 100.0%; Score 4809; Length 928;
Best Local Similarity 100.0%;
Matches 928; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MNKRLLVKRTFGCVCAAAILGVAPLSHPTIVEAREELKMPNGLEQSIADVEAKIDALTYL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MNKRLLVKRTFGCVCAAAILGVAPLSHPTIVEAREELKMPNGLEQSIADVEAKIDALTYL 60
Qy 61 SKNSKDEFKHSMYEIPSNREHKPVSPKQALQNAKKADAQAERLAKMTIPKKEELKALEGP 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 SKNSKDEFKHSMYEIPSNREHKPVSPKQALQNAKKADAQAERLAKMTIPKKEELKALEGP 120
Qy 121 LYGGYFRTWQDKTSDPTETNKVNSFGELPKEVDLAFVFHDYTKDYSLFWEELATKQVPKL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LYGGYFRTWQDKTSDPTETNKVNSFGELPKEVDLAFVFHDYTKDYSLFWEELATKQVPKL 180
Qy 181 NKQGTRVIRTIPWRFLSGADHSDISADKEKFPNTEAGNKALAKAIVDEYVYKYNLDGLDI 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 NKQGTRVIRTIPWRFLSGADHSDISADKEKFPNTEAGNKALAKAIVDEYVYKYNLDGLDI 240
Qy 241 DIERDSVPKVNDKEDPEALARTVEVFKEIGKLIGANGADKSRLLIMDTTYTAEENPLIKE 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 DIERDSVPKVNDKEDPEALARTVEVFKEIGKLIGANGADKSRLLIMDTTYTAEENPLIKE 300
Qy 301 TAQYLNLLLVQVYGFSGENGNYLHHKNILDETSSMEGRWQGYSKYIRPEQYMVGFSFYEE 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 TAQYLNLLLVQVYGFSGENGNYLHHKNILDETSSMEGRWQGYSKYIRPEQYMVGFSFYEE 360
Qy 361 KDFNNRWKDINEEDPSDPHIGEKIQGTRAERYAKWQPKTGGLKGGLFSYAIDRDGVAQPK 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 KDFNNRWKDINEEDPSDPHIGEKIQGTRAERYAKWQPKTGGLKGGLFSYAIDRDGVAQPK 420
Qy 421 QKTEHPELDKIVKSEYKVSKALKKLMMTDDQYQPIDQSDFPDKALRESIIKQVGTRRGDL 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 QKTEHPELDKIVKSEYKVSKALKKLMMTDDQYQPIDQSDFPDKALRESIIKQVGTRRGDL 480
Qy 481 ERFKGTLRLDNPEIKDLTGLNKLKRVAKLELINLPKITKIDKDDLPQNLKPLTDNQKSNL 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 ERFKGTLRLDNPEIKDLTGLNKLKRVAKLELINLPKITKIDKDDLPQNLKPLTDNQKSNL 540
Qy 541 EIKGTYDDSKLYKDIPAFDLVISGLSGLESLDISGHQRDTLSGIDASTLPSLKAINISDN 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 EIKGTYDDSKLYKDIPAFDLVISGLSGLESLDISGHQRDTLSGIDASTLPSLKAINISDN 600
Qy 601 HFDLAQGTENRHILDTILATLAKNGASTASFDKQKPKGLYPESYSTAPLHLQVGQGKINV 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 HFDLAQGTENRHILDTILATLAKNGASTASFDKQKPKGLYPESYSTAPLHLQVGQGKINV 660
Qy 661 IDDLIFGTRTNQNTLINTENDFEAYKEQTIQGKPFIAPDYLYDNFKVSYKEYSASIVDST 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 IDDLIFGTRTNQNTLINTENDFEAYKEQTIQGKPFIAPDYLYDNFKVSYKEYSASIVDST 720
Qy 721 LAETTDKTIDTAKAETYQVTVSNKDGKTVHSVKVIVGDEKPMMVNLAQDAKIIGTDNMTQ 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 LAETTDKTIDTAKAETYQVTVSNKDGKTVHSVKVIVGDEKPMMVNLAQDAKIIGTDNMTQ 780
Qy 781 SAKVFDGQKDQFLLSWNKDSSVIFELKTPGTAKHWRFFDDGKNDSVTLSVFKGDASNFET 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 SAKVFDGQKDQFLLSWNKDSSVIFELKTPGTAKHWRFFDDGKNDSVTLSVFKGDASNFET 840
Qy 841 EKDKAENWVEITKDSRKNDDKVFSSPLEVDNAKYLKVTIKKEAKYIYFNELQILGYPGVV 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 EKDKAENWVEITKDSRKNDDKVFSSPLEVDNAKYLKVTIKKEAKYIYFNELQILGYPGVV 900
Qy 901 AKKTADDLRPTEADKSDDKSDKNDTEAK 928
||||||||||||||||||||||||||||
Db 901 AKKTADDLRPTEADKSDDKSDKNDTEAK 928
Sequence alignment between the polypeptide of SEQ ID NO:2 of the instant application (“Qy”) and the endoglycosidase “EndoSn-D234M” of SEQ ID NO:2 of Yu (“Db”)
US-16-454-750-2
Sequence 2, US/16454750
Publication No. US20200062861A1
GENERAL INFORMATION
APPLICANT: OBI PHARMA, INC.
TITLE OF INVENTION: GLYCOSYNTHASE VARIANTS FOR GLYCOPROTEIN ENGINEERING AND METHODS
TITLE OF INVENTION: OF USE
FILE REFERENCE: G3004-01101
CURRENT APPLICATION NUMBER: US/16/454,750
CURRENT FILING DATE: 2019-06-27
PRIOR APPLICATION NUMBER: 62/690,669
PRIOR FILING DATE: 2018-06-27
NUMBER OF SEQ ID NOS: 8
SEQ ID NO 2
LENGTH: 998
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Description of Artificial Sequence: Synthetic
polypeptide
Query Match 50.9%; Score 2448; Length 998;
Best Local Similarity 55.4%;
Matches 500; Conservative 134; Mismatches 230; Indels 38; Gaps 15;
Qy 19 ILGVAPLSHPTIVEAREELKMPNGLEQSIADVEAKIDALTYLSKNSKDEFKHSMYEIPSN 78
:: : | ::: : | | | |: | | |||| |||:||| ||| : ::
Db 1 MVAILAAQHDSLIRVKAEDK----LVQTSPSVSA-IDALHYLSENSKKEFKEELSKV--- 52
Qy 79 REHKPVSPKQALQNAKKADAQAERLAKMTIPKKEELKALEGPLYGGYFRTWQDKTSDPTE 138
: :| |: : |::|| ||: ||:| :|:| :| |:||||||||||| |||||| |
Db 53 EKAQPEKLKEIVSKAQQADKQAKTLAEMKVPEKIPMKPLKGPLYGGYFRTWHDKTSDPAE 112
Qy 139 TNKVNSFGELPKEVDLAFVFHDYTKDYSLFWEELATKQVPKLNKQGTRVIRTIPWRFLSG 198
:|||| |||||||||||||||:||||||||:||||| || |||||||||||||||||:|
Db 113 KDKVNSMGELPKEVDLAFVFHDWTKDYSLFWQELATKHVPTLNKQGTRVIRTIPWRFLAG 172
Qy 199 ADHSDISADKEKFPNTEAGNKALAKAIVDEYVYKYNLDGLDIDIERDSVPKVNDKEDPEA 258
||| |: | :|:||| |||||||||||||||||||||||: |||||:|||| :| |
Db 173 GDHSGIAEDAQKYPNTPEGNKALAKAIVDEYVYKYNLDGLDVMIERDSIPKVNKEESKEG 232
Qy 259 LARTVEVFKEIGKLIGANGADKSRLLIMDTTYTAEENPLIKETAQYLNLLLVQVYGFSGE 318
: |:::||:||||||| ||||||| |||:|| |::||||: | |::|||||||| ||
Db 233 IERSIQVFEEIGKLIGPKGADKSRLFIMDSTYMADKNPLIERGAPYIDLLLVQVYGTQGE 292
Qy 319 NGNY--LHHKNILDETSSMEGRWQGYSKYIRPEQYMVGFSFYEEK-DFNNRWKDINEEDP 375
| : :|| : :|| ||: |||||||||||||||||||| : | | |:| ||
Db 293 KGGFDNANHKAV----DTMEERWESYSKYIRPEQYMVGFSFYEEKANSGNLWYDVNVEDD 348
Qy 376 SDPHIGEKIQGTRAERYAKWQPKTGGLKGGLFSYAIDRDGVAQPKQK-TEHPELDKIVKS 434
::|:|| :|:||||||||||||||||:|||:||| ||||||| ||: : |:|||||||
Db 349 TNPNIGSEIKGTRAERYAKWQPKTGGVKGGIFSYGIDRDGVAHPKKNGPKTPDLDKIVKS 408
Qy 435 EYKVSKALKKLMMTDDQYQPIDQSDFPDKALRESIIKQVGTRRGDLERFKGTLRLDNPEI 494
:|||||||||:| | |: ||| |||||||||::| |||:|||:|||| ||||||||:|
Db 409 DYKVSKALKKVMENDKSYELIDQKDFPDKALREAVIAQVGSRRGNLERFNGTLRLDNPDI 468
Qy 495 KDLTGLNKLKRVAKLELINLPKITKIDKDDLPQNLKPLTDNQKSNLEIKGTYDDSKLYKD 554
| | ||||||::|||||| | :|||:| ||:|:|| | | || | : |
Db 469 KSLEGLNKLKKLAKLELIGLSQITKLDSSVLPENIKPTKDTLVSVLETYKNDDRKEEAKA 528
Qy 555 IPAFDLVISGLSGLESLDISGHQRDTLSGIDASTLPSLKAINISDNHFDLAQGTENRHIL 614
|| | ||||:||: |:::| ||:|:||||::| ||: :::| | ||| ||||| ||
Db 529 IPQVALTISGLTGLKELNLAGFDRDSLAGIDAASLTSLEKVDLSSNKLDLAAGTENRQIL 588
Qy 615 DTILATLAKNGA---STASFDKQKPKGLYPESYSTAPLHLQVGQGKINVIDDLIFGTRTN 671
||:|||: |:| | || ||| ||||::| | | | | |:: |:||| ||
Db 589 DTMLATVTKHGGVSEKTFVFDHQKPTGLYPDTYGTKSLQLPVANDTIDLQAKLLFGTVTN 648
Qy 672 QNTLINTENDFEAYKEQTIQGKPFIAPDYLYDNFKVSYKEYSASIVDSTLAETTDKTIDT 731
| ||||:| |::||:|| | | |: | | | |:||:| : |||| | | : |
Db 649 QGTLINSEADYKAYQEQEIAGHRFVDSSYDYKAFAVTYKDYKIKVTDSTLGVTDHKDLST 708
Qy 732 AKAETYQVTVSN--KDGKTVHSVKVIVGDEKPMMVNLAQDAKIIGTD-NMTQSAKVFDG- 787
:| |||:| : | || |::||:|| ||||||: | ||| | : | : |||||
Db 709 SKEETYKVEFFSPINSTKPVHEAKIVVGEEKTMMVNLAEGATIIGGDADPTNAKKVFDGL 768
Qy 788 -QKDQFLLSWNKDSSVIFELKTPGTAKHWRFFDDGKND------SVTLSVFKG---DASN 837
| || : :|:||||| || ||||||:| | | | | |:|
Db 769 LNNDTTTLSTSNKASIIFELKEPGLVKHWRFFNDSKISKADYIKEAKLEAFVGHLEDSSK 828
Qy 838 FETEKDKAENWVEITKDSRKNDDKVFSSPLEVDNAKYLKVTI---KKEAKYIYFNELQIL 894
: :|: || :: | : : || || ||| ::|| | : |: ||||:
Db 829 VKDSLEKSTEWVTVSDYS--GEAQEFSQPLNNIGAKYWRITIDNKKSQYGYVSLPELQII 886
Qy 895 GY 896
|:
Db 887 GH 888
Sequence alignment between the polypeptide of SEQ ID NO:2 of the instant application (“Qy”) and the endo-beta-N-acetylglucosaminidase of SEQ ID NO:5 of Kawaguchi (“Db”)
US-15-745-357A-5
Sequence 5, US/15745357A
Patent No. 11001819
GENERAL INFORMATION
APPLICANT: Daiichi Sankyo Company, Limited
TITLE OF INVENTION: NOVEL ENDOS MUTANT ENZYME
FILE REFERENCE: DAISAN-1-65131
CURRENT APPLICATION NUMBER: US/15/745,357A
CURRENT FILING DATE: 2018-01-16
PRIOR APPLICATION NUMBER: JP2015-141901
PRIOR FILING DATE: 2015-07-16
PRIOR APPLICATION NUMBER: PCT/JP2016/070921
PRIOR FILING DATE: 2016-07-15
NUMBER OF SEQ ID NOS: 9
SEQ ID NO 5
LENGTH: 995
TYPE: PRT
ORGANISM: Artificial sequence
FEATURE:
OTHER INFORMATION: Synthetic
FEATURE:
NAME/KEY: MISC_FEATURE
LOCATION: (1)..(995)
OTHER INFORMATION: D233Q mutant of Endo-S
Query Match 49.5%; Score 2381; Length 995;
Best Local Similarity 52.1%;
Matches 509; Conservative 136; Mismatches 262; Indels 70; Gaps 24;
Qy 1 MNKRLLVKRTFGCVCAAAILGVAPLSH----PTIVEAREELKMPNGLEQSIADVEAKIDA 56
|:| |||||| |||||| ::| | :| |: : ::: || ||:
Db 1 MDKHLLVKRTLGCVCAATLMGAALATHHDSLNTVKAEEKTVQVQKGL--------PSIDS 52
Qy 57 LTYLSKNSKDEFKHSMYEIPSNREHKPVSPKQALQNAKKADAQAERLAKMTIPKKEELKA 116
| |||:||| ||| : : : :| : | |: | |::|| ||: |||| ||:| :|
Db 53 LHYLSENSKKEFKEELSK--AGQESQKV--KEILAKAQQADKQAQELAKMKIPEKIPMKP 108
Qy 117 LEGPLYGGYFRTWQDKTSDPTETNKVNSFGELPKEVDLAFVFHDYTKDYSLFWEELATKQ 176
| ||||||||||| |||||||| :|||| |||||||||||:|||:||||||||:|||||
Db 109 LHGPLYGGYFRTWHDKTSDPTEKDKVNSMGELPKEVDLAFIFHDWTKDYSLFWKELATKH 168
Qy 177 VPKLNKQGTRVIRTIPWRFLSGADHSDISADKEKFPNTEAGNKALAKAIVDEYVYKYNLD 236
||||||||||||||||||||:| |:| |: | |:||| ||||||||||||||||||||
Db 169 VPKLNKQGTRVIRTIPWRFLAGGDNSGIAEDTSKYPNTPEGNKALAKAIVDEYVYKYNLD 228
Qy 237 GLDIDIERDSVPKVNDKEDPEALARTVEVFKEIGKLIGANGADKSRLLIMDTTYTAEENP 296
|||: :| ||:|||: ||| : |:::||:||||||| | ||||| |||:|| |::||
Db 229 GLDVQVEHDSIPKVDKKEDTAGVERSIQVFEEIGKLIGPKGVDKSRLFIMDSTYMADKNP 288
Qy 297 LIKETAQYLNLLLVQVYGFSGENGNYLHHKNILDETSSMEGRWQGYSKYIRPEQYMVGFS 356
||: | |:||||| ||| || | : | ::| || |||||||||||||||:|||
Db 289 LIERGAPYINLLLVLVYGSQGEKGGWEPVSNRPEKT--MEERWQGYSKYIRPEQYMIGFS 346
Qy 357 FYEEK-DFNNRWKDINEEDPSDP--HIGEKIQGTRAERYAKWQPKTGGLKGGLFSYAIDR 413
|||: | | ||| | | | ||||||||:|||||||:|||:|||||||
Db 347 FYEQNAQEGNLWYDINSRKDEDKANGINTDITGTRAERYARWQPKTGGVKGGIFSYAIDR 406
Qy 414 DGVA-QPKQKTEHPEL----DKIVKSEYKVSKALKKLMMTDDQYQPIDQSDFPDKALRES 468
|||| |||: : | | | |:| |||||| :|: | | ||: |||||||||:
Db 407 DGVAHQPKKYAKQKEFKDATDNIFHSDYSVSKALKTVMLKDKSYDLIDEKDFPDKALREA 466
Qy 469 IIKQVGTRRGDLERFKGTLRLDNPEIKDLTGLNKLKRVAKLELINLPKITKIDKDDLPQN 528
:: |||||:|||||| |||||||| |: | |||| |::|:|:|| | :|||:|: || |
Db 467 VMAQVGTRKGDLERFNGTLRLDNPAIQSLEGLNKFKKLAQLDLIGLSRITKLDRSVLPAN 526
Qy 529 LKPLTDNQKSNLEIKGTY--DDSKLYKDIPAFDLVISGLSGLESLDISGHQRDTLSGIDA 586
:|| | :: || || |: : || | :|||:||: ||:|| |:||:|:||
Db 527 MKPGKDTLETVLE---TYKKDNKEEPATIPPVSLKVSGLTGLKELDLSGFDRETLAGLDA 583
Qy 587 STLPSLKAINISDNHFDLAQGTENRHILDTILATLAKNGAS---TASFDKQKPKGLYPES 643
:|| ||: ::|| | ||| ||||| | ||:|:|:: : | | |||||| | ||::
Db 584 ATLTSLEKVDISGNKLDLAPGTENRQIFDTMLSTISNHVGSNEQTVKFDKQKPTGHYPDT 643
Qy 644 YSTAPLHLQVGQGKINVIDDLIFGTRTNQNTLINTENDFEAYKEQTIQGKPFIAPDYLYD 703
| | | | |::: |:||| ||| ||||:| |::||: | |: |: :| |:
Db 644 YGKTSLRLPVANEKVDLQSQLLFGTVTNQGTLINSEADYKAYQNHKIAGRSFVDSNYHYN 703
Qy 704 NFKVSYKEYSASIVDSTLAETTDKTIDTAKAETYQVTVSNKDGKT--VHSVKVIVGDEKP 761
||||||: |: : |||| |||||: | | |||:| : || ||: ||||||||
Db 704 NFKVSYENYTVKVTDSTLGTTTDKTLATDKEETYKVDFFSPADKTKAVHTAKVIVGDEKT 763
Qy 762 MMVNLAQDAKII-GTDNMTQSAKVFDGQ----KDQFLLSWNKDSSVIFELKTPGTAKHWR 816
||||||: | :| |: : : |||||| | | |: |:||:|| | ||||
Db 764 MMVNLAEGATVIGGSADPVNARKVFDGQLGSETDNISLGWDSKQSIIFKLKEDGLIKHWR 823
Qy 817 FFDD-GKNDSVT--------LSVFKGDASNFE------TEKDKAENWVEI-TKDSRKNDD 860
||:| :| | | :| | : : | : |: : | ::
Db 824 FFNDSARNPETTNKPIQEASLQIFNIKDYNLDNLLENPNKFDDEKYWITVDTYSAQGERA 883
Qy 861 KVFSSPLEVDNAKYLKVTI-KKEAKYI--YFNELQILGYPGVVAKKTADDLRPT-----E 912
||: | :|| :| | :| |||||||| || : | |
Db 884 TAFSNTLNNITSKYWRVVFDTKGDRYSSPVVPELQILGYP----LPNADTIMKTVTTAKE 939
Qy 913 ADKSDDK-SDKNDTEAK 928
: || | | | |
Db 940 LSQQKDKFSQKMLDELK 956
Sequence alignment between the polypeptide of SEQ ID NO:2 of the instant application (“Qy”) and the endo-beta-N-acetylglucosaminidase of SEQ ID NO:2 of Kawaguchi (“Db”)
Title: US-18-024-258A-2
Perfect score: 4809
Sequence: 1 MNKRLLVKRTFGCVCAAAIL..........RPTEADKSDDKSDKNDTEAK 928
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 995 residues
Total number of hits satisfying chosen parameters: 1
Minimum DB seq length: 0
Maximum DB seq length: inf
Post-processing: Minimum Match 0%
Maximum Match 100%
Listing first 1 summaries
Database : AASEQ2_08262025_111711.pep:*
SUMMARIES
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 2313 48.1 995 1 AASEQ2_08262025_111711
ALIGNMENTS
RESULT 1
AASEQ2_08262025_111711
Query Match 48.1%; Score 2313; DB 1; Length 995;
Best Local Similarity 51.2%;
Matches 500; Conservative 135; Mismatches 272; Indels 70; Gaps 24;
Qy 1 MNKRLLVKRTFGCVCAAAILGVAPLSH----PTIVEAREELKMPNGLEQSIADVEAKIDA 56
|:| |||||| |||||| ::| | :| |: : ::: || ||:
Db 1 MDKHLLVKRTLGCVCAATLMGAALATHHDSLNTVKAEEKTVQVQKGL--------PSIDS 52
Qy 57 LTYLSKNSKDEFKHSMYEIPSNREHKPVSPKQALQNAKKADAQAERLAKMTIPKKEELKA 116
| |||:||| ||| : : : :| : | |: | |::|| ||: |||| ||:| :|
Db 53 LHYLSENSKKEFKEELSK--AGQESQKV--KEILAKAQQADKQAQELAKMKIPEKIPMKP 108
Qy 117 LEGPLYGGYFRTWQDKTSDPTETNKVNSFGELPKEVDLAFVFHDYTKDYSLFWEELATKQ 176
| ||||||||||| |||||||| :|||| |||||||||||:|||:||||||||:|||||
Db 109 LHGPLYGGYFRTWXDKTSDPTEKDKVNSMGELPKEVDLAFIFHDWTKDYSLFWKELATKH 168
Qy 177 VPKLNKQGTRVIRTIPWRFLSGADHSDISADKEKFPNTEAGNKALAKAIVDEYVYKYNLD 236
||||||||||||||| || |:| |:| |: | |:||| ||||||||||||||||||||
Db 169 VPKLNKQGTRVIRTIXWRXLAGGDNSGIAEDTSKYPNTPEGNKALAKAIVDEYVYKYNLD 228
Qy 237 GLDIDIERDSVPKVNDKEDPEALARTVEVFKEIGKLIGANGADKSRLLIMDTTYTAEENP 296
|||: :| ||:|||: ||| : |:::||:||||||| | ||||| || : |::||
Db 229 GLDVQVEHDSIPKVDKKEDTAGVERSIQVFEEIGKLIGPKGVDKSRLFIMXSXXMADKNP 288
Qy 297 LIKETAQYLNLLLVQVYGFSGENGNYLHHKNILDETSSMEGRWQGYSKYIRPEQYMVGFS 356
||: | |:||||| ||| || | : | ::| || |||||||||||||||:|||
Db 289 LIERGAPYINLLLVXVYGSQGEKGGWEPVSNRPEKT--MEERWQGYSKYIRPEQYMIGFS 346
Qy 357 FYE-EKDFNNRWKDINEEDPSDP--HIGEKIQGTRAERYAKWQPKTGGLKGGLFSYAIDR 413
| | | | ||| | | | ||||||||:|||||||:|||:|| ||
Db 347 FXEXNAQEGNLWYDINSRKDEDKANGINTDITGTRAERYARWQPKTGGVKGGIFSXAIXX 406
Qy 414 DGVA-QPKQKTEHPEL----DKIVKSEYKVSKALKKLMMTDDQYQPIDQSDFPDKALRES 468
|||| |||: : | | | |:| |||||| :|: | | ||: |||||||||:
Db 407 DGVAHQPKKYAKQKEFKDATDNIFHSDYSVSKALKTVMLKDKSYDLIDEKDFPDKALREA 466
Qy 469 IIKQVGTRRGDLERFKGTLRLDNPEIKDLTGLNKLKRVAKLELINLPKITKIDKDDLPQN 528
:: |||||:|||||| |||||||| |: | |||| |::|:|:|| | :|||:|: || |
Db 467 VMAQVGTRKGDLERFNGTLRLDNPAIQSLEGLNKFKKLAQLDLIGLSRITKLDRSVLPAN 526
Qy 529 LKPLTDNQKSNLEIKGTY--DDSKLYKDIPAFDLVISGLSGLESLDISGHQRDTLSGIDA 586
:|| | :: || || |: : || | :|||:||: ||:|| |:||:|:||
Db 527 MKPGKDTLETVLE---TYKKDNKEEPATIPPVSLKVSGLTGLKELDLSGFDRETLAGLDA 583
Qy 587 STLPSLKAINISDNHFDLAQGTENRHILDTILATLAKNGAS---TASFDKQKPKGLYPES 643
:|| ||: ::|| | ||| ||||| | ||:|:|:: : | | |||||| | ||::
Db 584 ATLTSLEKVDISGNKLDLAPGTENRQIFDTMLSTISNHVGSNEQTVKFDKQKPTGHYPDT 643
Qy 644 YSTAPLHLQVGQGKINVIDDLIFGTRTNQNTLINTENDFEAYKEQTIQGKPFIAPDYLYD 703
| | | | |::: |:||| ||| ||||:| |::||: | |: |: :| |:
Db 644 YGKTSLRLPVANEKVDLQSQLLFGTVTNQGTLINSEADYKAYQNHKIAGRSFVDSNYHYN 703
Qy 704 NFKVSYKEYSASIVDSTLAETTDKTIDTAKAETYQVTVSNKDGKT--VHSVKVIVGDEKP 761
||||||: |: : |||| |||||: | | |||:| : || ||: ||||||||
Db 704 NFKVSYENYTVKVTDSTLGTTTDKTLATDKEETYKVDFFSPADKTKAVHTAKVIVGDEKT 763
Qy 762 MMVNLAQDAKII-GTDNMTQSAKVFDGQ----KDQFLLSWNKDSSVIFELKTPGTAKHWR 816
||||||: | :| |: : : |||||| | | |: |:||:|| | ||||
Db 764 MMVNLAEGATVIGGSADPVNARKVFDGQLGSETDNISLGWDSKQSIIFKLKEDGLIKHWR 823
Qy 817 FFDD-GKNDSVT--------LSVFKGDASNFE------TEKDKAENWVEI-TKDSRKNDD 860
||:| :| | | :| | : : | : |: : | ::
Db 824 FFNDSARNPETTNKPIQEASLQIFNIKDYNLDNLLENPNKFDDEKYWITVDTYSAQGERA 883
Qy 861 KVFSSPLEVDNAKYLKVTI-KKEAKYI--YFNELQILGYPGVVAKKTADDLRPT-----E 912
||: | :|| :| | :| |||||||| || : | |
Db 884 TAFSNTLNNITSKYWRVVFDTKGDRYSSPVVPELQILGYP----LPNADTIMKTVTTAKE 939
Qy 913 ADKSDDK-SDKNDTEAK 928
: || | | | |
Db 940 LSQQKDKFSQKMLDELK 956
Prosecution Insights