Engineered sucrose phosphorylase variant enzymes

Patent metadata

Field	Value
Publication number	US-12480104-B2
Application number	US-202017617533-A
Country	US
Kind code	B2
Filing date	Jun 30, 2020
Priority date	Jul 2, 2019
Publication date	Nov 25, 2025
Grant date	Nov 25, 2025

Abstract

The present invention provides engineered sucrose phosphorylase (SP) enzymes, polypeptides having SP activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing SP enzymes are also provided. The present invention further provides compositions comprising the SP enzymes and methods of using the engineered SP enzymes. The present invention finds particular use in the production of pharmaceutical compounds.

First claim

We claim:

1 . An engineered sucrose phosphorylase comprising a polypeptide sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity to SEQ ID NO: 2, wherein the polypeptide sequence of said engineered sucrose phosphorylase comprises at least one substitution at position 397 and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 2, and wherein the engineered sucrose phosphorylase exhibits improved activity on a substrate selected from the group consisting of sucrose, sucrose-related disaccharides and/or inorganic phosphate as compared to wild-type Alloscardovia omnicolens sucrose phosphorylase set forth in SEQ ID NO: 2.

2 . The engineered sucrose phosphorylase of claim 1 , wherein said polypeptide sequence has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity to SEQ ID NO: 2, and wherein the polypeptide sequence of said engineered sucrose phosphorylase further comprises at least one substitution or substitution set at one or more positions in said polypeptide sequence selected from 7, 10, 48, 136, 158, 205, 207, 211, 215, 301, 333, 378, and 400, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 2.

3 . The engineered sucrose phosphorylase of claim 1 , wherein said polypeptide sequence of said engineered sucrose phosphorylase has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more sequence identity to SEQ ID NO: 4, and wherein said polypeptide sequence of said engineered sucrose phosphorylase further comprises at least one substitution or substitution set at one or more positions selected from 10/215/400, 158, 158/207/215, 158/207/215/301/400, 158/207/215/400, 158/207/400, 158/211/400, 158/215/301/400, 158/215/400, 158/301/400, 158/400, 205, 207, 207/215, 207/215/400, 207/400, 215/301, 215/400, 242/400, 301, 301/400, and 400, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

4 . The engineered sucrose phosphorylase of claim 1 , wherein said engineered sucrose phosphorylase comprises a variant engineered sucrose phosphorylase set forth in SEQ ID NO: 4.

5 . The engineered sucrose phosphorylase of claim 1 , wherein said engineered sucrose phosphorylase comprises a polypeptide sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the sequence of at least one engineered sucrose phosphorylase variant set forth in the even numbered sequences of SEQ ID NOS: 4, 24, 26, and 42-84.

6 . The engineered sucrose phosphorylase of claim 1 , wherein said engineered sucrose phosphorylase comprises a polypeptide sequence set forth in at least one of the even numbered sequences of SEQ ID NOS: 4, 24, 26, and 42-84.

7 . The engineered sucrose phosphorylase of claim 1 , wherein engineered sucrose phosphorylase further exhibits improved production of

8 . The engineered sucrose phosphorylase of claim 1 , wherein said engineered sucrose phosphorylase is purified.

9 . The engineered sucrose phosphorylase of claim 1 , wherein said engineered sucrose phosphorylase is part of a multi-enzyme system for producing a nucleoside analogue.

10 . A composition comprising at least one engineered sucrose phosphorylase of claim 1 .

11 . A polynucleotide sequence encoding at least one engineered sucrose phosphorylase of claim 1 .

12 . A polynucleotide sequence encoding at least one engineered sucrose phosphorylase of claim 1 .

13 . The polynucleotide sequence of claim 11 , wherein said polynucleotide sequence is operably linked to a control sequence.

14 . The polynucleotide sequence of claim 11 , wherein said polynucleotide sequence is codon optimized.

15 . The polynucleotide sequence of claim 11 , wherein said polynucleotide sequence comprises a polynucleotide sequence set forth in the odd numbered sequences of SEQ ID NOS: 3, 23, 25 and 41-83.

16 . An expression vector comprising at least one polynucleotide sequence of claim 11 .

17 . A host cell comprising at least one expression vector of claim 16 .

18 . A host cell comprising at least one polynucleotide sequence of claim 11 .

19 . A method of producing an engineered sucrose phosphorylase in a host cell, comprising culturing the host cell of claim 17 , under suitable conditions, such that at least one engineered sucrose phosphorylase is produced.

20 . The method of claim 19 , further comprising recovering at least one engineered sucrose phosphorylase from the culture and/or host cell.

21 . The method of claim 19 , further comprising the step of purifying said at least one engineered sucrose phosphorylase.

Assignees

• Codexis Inc

Inventors

• Vroom Jonathan
• Sivaramakrishnan Santhosh
• Subramanian Nandhitha

Classifications

• C12Y204/01007

  Sucrose phosphorylase (2.4.1.7) · CPC title

• C12N2800/101

  for bacteria · CPC title

• C12N15/72

  Expression systems using regulatory sequences derived from the lac-operon · CPC title

• C12N1/20

  Bacteria; Culture media therefor · CPC title

• A61K38/45

  Transferases (2) · CPC title