Engineered adenylate kinase variant enzymes

Inventors: Da Duan (Foster City, CA); Auric Anthony Sowell-Kantz (Mill Valley, CA); Aksiniya Lyubenova Petkova (Sunnyvale, CA); Oscar Alvizo (Fremont, CA)

Assignee: Codexis, Inc.

C12N9/1229 C12Y207/04003

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Quick Facts

Patent No.: US 11,913,037
App. No.: 17/711,382
Granted: Feb 27, 2024
Kind: B2

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Abstract

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

Claims (17)

1. An engineered adenylate kinase comprising a polypeptide sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 4, wherein the polypeptide sequence of said engineered adenylate kinase comprises a substitution at position 42 and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

2. The engineered adenylate kinase of claim 1 , wherein said polypeptide sequence has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 4, and wherein the polypeptide sequence of said engineered adenylate kinase comprises at least one substitution or substitution set at one or more positions in said polypeptide sequence selected from 34/35/51, 34/35/51/53/138, 34/35/51/53/172, 34/35/51/76, 34/35/51/76/172/202, 34/35/51/119, 34/35/51/119/172, 34/35/51/172, 34/35/52/53/119/172, 34/35/52/76/119, 34/35/53/76, 34/35/53/202, 34/35/76, 34/35/76/119/172, 34/35/119, 34/35/138, 34/35/138/172, 34/51, 34/51/52/53/76, 34/51/53/76/172, 34/51/53/138, 34/51/53/172, 34/51/76, 34/51/119/138/172, 34/51/131, 34/51/202, 34/76/138/172, 34/119, 34/119/172, 34/138/172, 35/51, 35/51/52/53, 35/51/52/53/76/119/172/202, 35/51/52/53/119, 35/51/53/138/172, 35/51/53/172, 35/51/53/202, 35/51/76,35/51/76/131, 35/51/76/138, 35/51/76/172, 35/51/119, 35/51/119/138, 35/51/119/138/172, 35/51/119/172, 35/51/172, 35/51/172/202, 35/51/202, 35/52/53/119, 35/52/53/119/138, 35/53/119/131/202, 35/53/119/138, 35/76, 35/76/119, 35/76/119/138, 35/76/119/138/172, 35/76/172, 35/119, 35/119/138, 35/119/172, 35/138/172, 35/172, 35/172/186, 35/172/202, 51, 51/52/53/172/202, 51/53, 51/53/119, 51/53/172, 51/76/119, 51/76/119/172, 51/119/138, 51/119/172/202, 51/138, 51/172, 52/53/76/172/202, 52/76/172, 52/138/172, 53/76/202, 53/172, 76, 76/119, 76/119/172, 76/172/202, 119/138/172, 119/172, 138/202, 172/202, and 202, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

3. The engineered adenylate kinase of claim 1 , wherein said polypeptide sequence of said engineered adenylate kinase has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 4, and wherein said polypeptide sequence of said engineered adenylate kinase comprises at least one substitution or substitution set at one or more positions selected from 1/2/104, 16, 29, 41, 46, 49, 50, 51, 61, 65, 72, 74, 76, 77, 79, 81, 108, 110, 127, 152, 191, 214, 218, and 222, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

4. The engineered adenylate kinase of claim 1 , wherein the polypeptide sequence of said engineered adenylate kinase further comprises at least one substitution or substitution set at one or more positions selected from 16, 16/29/49/104/108/191/218, 16/29/49/104/108/210, 16/29/49/104/191, 16/29/49/104/191/218, 16/29/49/108, 16/29/49/108/191, 16/29/49/108/210, 16/29/49/191, 16/29/49/191/210, 16/29/76/210, 16/29/104/108/191/218, 16/29/104/210, 16/29/108/191, 16/49, 16/49/76/104/191, 16/49/104/108, 16/49/104/108/191, 16/49/104/108/210, 16/49/104/191, 16/49/104/210, 16/49/108/210, 16/49/108/218, 16/49/191, 16/49/191/210, 16/81/104, 16/104/191/210, 16/108, 16/108/191/210, 16/108/218, 16/191/210, 29, 29/49/77/81/108, 29/76/77/104/191/210, 29/76/104/108, 29/104/108/191/210, 29/104/108/191/218, 29/108, 29/108/191, 29/108/191/210, 29/108/210, 29/49/76/77/81/191/210, 29/49/77/81/104/108/191, 29/49/81/108, 29/49/104/108, 29/49/104/108/191, 29/49/104/108/191/210, 29/49/104/108/191/210/218, 29/49/104/108/210, 29/49/104/191, 29/49/104/191/210, 29/49/108/191, 29/49/108/191/210, 29/49/108/191/210/218, 29/49/108/191/218, 29/49/108/210, 29/49/191, 29/49/191/210, 29/49/191/210/218, 29/49/210/215, 29/76/191/210, 29/104, 29/104/108, 29/104/108/191/210, 29/104/108/210, 29/104/191, 29/104/191/210, 29/104/191/210/218, 29/104/210, 29/108, 29/108/191, 29/108/191/210, 29/108/191/210/218, 29/108/191/218, 29/108/210, 29/191/210, 49/76/81/108/210, 49/108/191/210/218, 77/108/191, 108/191/210, 49, 49/76/77/81/104/191/210, 49/76/81/104/108, 49/76/108/191, 49/76/108/191/210, 49/81/104/108, 49/81/108, 49/104/108, 49/104/108/180/191, 49/104/108/191, 49/104/108/191/210, 49/104/108/210, 49/104/191, 49/104/191/210, 49/104/218, 49/108, 49/108/191, 49/108/191/210, 49/108/191/210/218, 49/108/210, 49/191, 49/191/210, 49/210, 76/77/81/108/191, 76/77/81/108/191/210, 76/77/81/210/218, 76/81/108, 76/81/108/191/218, 77/81/108/191, 104/108/191, 104/108/191/210, 104/108/191/210/218, 104/108/210, 104/108/218, 104/191, 104/191/210, 108/191, 108/191/210, 108/191/218, and 108/210, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

5. The engineered adenylate kinase of claim 1 , wherein the polypeptide sequence of said engineered adenylate kinase further comprises at least one substitution or substitution set at one or more positions selected from 16, 16/29, 16/29/51/110/191, 16/29/51/191, 16/29/51/214, 16/29/119/191, 16/29/119/191/214, 16/29/191, 16/51/107, 16/51/107/110/214, 16/51/110/202/214, 16/51/191/202, 16/51/191/202/214, 16/51/214, 16/107/110/119, 16/107/110/119/191/202/214, 16/107/110/191, 16/107/191/214, 16/110/119, 16/110/191, 16/191, 16/191/202, 16/214, 29, 29/46/79/107/110/202/214, 29/46/110/202/214, 29/46/110/214, 29/46/191, 29/51/107/110/191, 29/51/107/110/191/214, 29/51/107/110/202/214, 29/51/107/119/191, 29/51/110/191/202, 29/51/119/191/214, 29/51/191, 29/51/191/202, 29/51/191/214, 29/74/79/107/214, 29/74/107/191, 29/74/191, 29/107/119/191, 29/110/119/191, 29/119, 29/191/214, 51, 51/107/110, 51/107/110/119, 51/107/110/191, 51/107/110/191/214/218, 51/107/119/191/214, 51/107/214, 51/110/191, 51/110/214, 51/191, 51/191/202/214, 51/191/214, 51/202, 51/214, 74/79/107/110/191/202, 107/110/119/191, 107/110/119/207/214, 107/110/123/191/202, 110/191/202/214, 119, 119/191, 191/202, and 191/214, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

6. The engineered adenylate kinase of claim 1 , wherein said engineered adenylate kinase comprises the amino acid sequence of SEQ ID NO: 230.

7. The engineered adenylate kinase of claim 1 , wherein said engineered adenylate kinase comprises a polypeptide sequence set forth in at least one of the sequences of SEQ ID NOs: 358, 360, 362, 364, 366, 368, 370, 372, 374, 376, 378, 380, 382, 384, 386, 388, 390, 392, 394, 396, 398, 400, 402, 404, 406, 408, 410, 412, 414, 416, 418, 420, 422, 424, 426, 428, 430, 432, 434, 436, 438, 440, 442, 444, 446, 448, 450, 452, 454, 456, 458, 460, 462, 464, 466, 468, 470, 472, 474, 476, 478, 480, 482, 484, 486, 488, 490, 492, 494, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 522, 524, 526, 528, 530, 532, 534, 536, 538, 540, 542, 544, 546, 548, 550, 552, 554, 556, 558, 560, 562, 564, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 592, 594, 596, 598, 600, 602, 604, 606, 608, 610, 612, 614, 616, 618, 620, 622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 644, 646, 648, 650, 652, 654, 656, 658, 660, 662, 664, 666, 668, 670, 672, 674, 676, 678, 680, 682, 684, 686, 688, 690, 692, 694, 696, 698, 700, 702, 704, 706, 708, 710, 712, 714, 716, 718, 720, 722, 724, 726, 728, 730, 732, 734, 736, 738, 740, 742, 744, 746, 748, 750, 752, 754, 756, 758, 760, 762, 764, 766, 768, 770, 772, 774, 776, 778, 780, 782, 784, 786, 788, 790, 792, 794, 796, 798, 800, 802, 804, 806, 808, 810, 812, 814, 816, 818, 820, 822, 824, 826, 828, 830, 832, 834, 836, 838, 840, 842, 844, 846, and 848.

8. The engineered adenylate kinase of claim 1 , wherein said engineered adenylate kinase comprises improved activity on 2′F-ara-adenosine-5′-(1-thio)-monophosphate (F-thioAMP) and/or Sp-2′F-ara-adenosine-5′-(1-thio)-triphosphate (F-thioATP) as compared to the engineered adenylate kinase of SEQ ID NO: 4.

9. The engineered adenylate kinase of claim 1 , wherein said engineered adenylate kinase is purified.

10. A composition comprising at least one engineered adenylate kinase of claim 1 .

11. A polynucleotide sequence encoding at least one engineered adenylate kinase of claim 1 .

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

13. A host cell comprising at least one expression vector of claim 12 .

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

15. A method of producing an engineered adenylate kinase in a host cell, comprising culturing the host cell of claim 13 in a culture medium under suitable conditions such that at least one engineered adenylate kinase is produced.

16. The method of claim 15 , further comprising recovering the engineered adenylate kinase from the culture and/or the host cell.

17. The method of claim 15 , further comprising purifying said engineered adenylate kinase.

Assignments (2)

SECURITY INTEREST Recorded Feb 15, 2024

From: CODEXIS, INC.

To: INNOVATUS LIFE SCIENCES LENDING FUND I, LP, AS COLLATERAL AGENT

Reel/Frame 066600/0650 →

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded May 25, 2022

From: DUAN, DA; SOWELL-KANTZ, AURIC ANTHONY; PETKOVA, AKSINIYA LYUBENOVA; ALVIZO, OSCAR

To: CODEXIS, INC.

Reel/Frame 060019/0499 →

Continuity (2)

Provisional Application 63170000 · Apr 2, 2021

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