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Shen Lab Research: Project 2

(ii)   Discovery and elucidation of novel enzymes, biochemistry, and mechanism of catalysis

1. Discovery and biochemical characterization of BlmI as the first type II peptidyl carrier protein (PCP) (Chem. Biol. 1999, 6, 507-517)

Diagram of NRPS, type I and II

2. Proposal of the bleomycin biosynthetic gene cluster as a model hybrid peptide synthetase (NRPS)-polyketide synthase (PKS) for hybrid peptide-polyketide biosynthesis (Chem. Biol. 2000, 7, 623-642; Met. Engineer. 2001, 3, 78-95; Curr. Opin. Drug Disco. Decelop. 2001, 4, 215-228; J. Ind. Microbiol. Biotechnol. 2001, 27, 378-385; J. Nat. Prod. 2002, 65, 422-531)

Diagram of BLM aglycon

3. Discovery of an oxidation (Ox) domain of NRPS for thiazole biosynthesis (FEMS Microbiol. Lett. 2000, 189, 171-175; Biochemistry 2003, 42, 9722-9730)

Diagram of Thiazoline, Thiazole, and Thiazolidine

4. Characterization of triple hydroxylation by TcmG or ElmG (J. Biol. Chem. 1994, 48, 30726-30733; Org. Lett. 2000, 2, 3225-3227; J. Nat. Prod. 2001, 64, 444-449)

Diagram of Tetracenomycin

5. Discovery of a pair of enantio-complementary pathways for macrotetrolide biosynthesis (Antimicrob. Agents Chemther. 2000, 44, 1943-1953; J. Am. Chem. Soc. 2001, 123, 3385-3386)

Diagram of Nonactin

6. Discovery of the Svp phosphopantetheinyl transferase with broad substrate specificity for both ACP and PCP to activate hybrid NRPS-PKS (Chem. Biol. 2001, 8, 725-738)

Diagram of Svp phosphopantetheinyl transferase

7. Discovery of an iterative PKS for enediyne biosynthesis (Science 2002, 297, 1170-1173; Nat. Biotechnol. 2003, 21, 187-190)

Diagram of  iterative PKS for enediyne biosynthesis

8. Discovery of a type II PKS for C-O bond formation (Science 2002, 297, 1327-1330; Chem. Rec. 2002, 2, 389-396)

Diagram of  type II PKS for C-O bond formation

9. Development of a PCR method for NRPS domains (Cy and Ox domains) to clone thiazole-containing natural product biosynthetic pathways (J. Bacteriol. 2002, 184, 7013-7024)

Diagram of Leinamycin

10. Discovery of NRPS domain “skipping” (A and Ox domains) in nonribosomal peptide biosynthesis (Biochemistry 2003, 42, 9722-9730; Biochemistry 2003, 42, 9731-9740)

Diagram of NRPS domain

11. Discovery of an AT-less PKS (Proc. Natl. Acad. Sci. USA 2003, 100, 3149-3154; Chem. Biol. 2004, 11, 33-45)

Diagram of AT-less PKS

12. Discovery of a 4-methylideneimidazole-5-one (MIO)-containing tyrosine aminomutase (J. Am. Chem. Soc. 2003, 125, 6062-6063; Biochemistry 2003, 42, 12708-12718; J. Am. Chem. Soc. 2007, 129, 15744-15745; Bioorg. Med. Chem. Lett. 2008, 18, 3099-3102)

Diagram of 4-methylideneimidazole-5-one (MIO)-containing tyrosine aminomutase

13. Determination of the structure of the SgcC4 4-methylideneimidazole-5-one (MIO)-containing tyrosine aminomutase (Biochemistry 2007, 46, 7205-7214)

Diagram of the  structure of the SgcC4 4-methylideneimidazole-5-one (MIO)-containing tyrosine aminomutase

14. Development of a PCR method for enediyne PKS to clone enediyne biosynthetic pathways (Proc. Natl. Acad. Soc. USA  2003, 100, 11959-11963)

Diagram of PCR method for enediyne PKS to clone enediyne biosynthetic pathways

15. Characterization of SgcA1 as a a-D-glucopyranosyl-1-phosphate thymidylytransferase for biosynthesis of the C-1027 enediyne antitumor antibiotic (J. Nat. Prod. 2004, 67, 206-213)

Diagram of SgcA1 as a a-D-glucopyranosyl-1-phosphate thymidylytransferase for biosynthesis of the C-1027 enediyne antitumor antibiotic

16. Discovery of migrastatin and dorrigocins as shunt metabolites of iso-migrastatin (J. Am. Chem. Soc. 2005, 127, 1622-1623)

Diagram of migrastatin and dorrigocins as shunt metabolites of iso-migrastatin

17. Discovery of an adenylation enzyme (A) of NRPS that activate b-tyrosine (J. Am. Chem. Soc. 2005, 127, 11594-11595; J. Biol. Chem. 2006, 281, 29633-29640)

Diagram of an adenylation enzyme (A) of NRPS that activate b-tyrosine

18. Discovery of PKS domain “skipping” (ACP domain) in polyketide biosynthesis by type I PKS (J. Nat. Prod. 2006, 69, 387-393)

Diagram of PKS domain “skipping” (ACP domain) in polyketide biosynthesis by type I PKS

19. Development of a PCR method for cloning methoxymalonate-incorporating polyketide biosynthetic pathways (J. Bacteriol. 2006, 198, 4148-4152; J. Bacteriol. 2006, 198, 4141-4147)

Diagram of a PCR method for cloning methoxymalonate-incorporating polyketide biosynthetic pathways

20. Discovery of the first holo-ACP synthase-type phosphopantetheinyl transferase for a type II PKS (J. Am. Chem. Soc. 2005, 127, 16442-16452; J. Biol. Chem. 2006, 281, 29660-29668)

Diagram of the first holo-ACP synthase-type phosphopantetheinyl transferase for a type II PKS

21. Identification of 1,3-bisphosphoglycerate as the direct precursor for methoxymalonyl-ACP biosynthesis (J. Am. Chem. Soc. 2006, 128, 10386-10387)

Diagram of 1,3-bisphosphoglycerate as the direct precursor for methoxymalonyl-ACP biosynthesis

22. Discovery of a [3,3]-sigmtropic rearrangement for iso-migratsatin to migratsatin (Org. Lett. 2006, 8, 5865-5868)

Diagram of a [3,3]-sigmtropic rearrangement for iso-migratsatin to migratsatin

23. Characterization of NcsB2 as a promiscuous naphthoic acid-coenzyme A ligase for the biosynthesis of the neocarzinostatin enediyne antitumor antibiotic (J. Am. Chem. Soc. 2007, 129, 7728-7729)

Diagram of NcsB2 as a promiscuous naphthoic acid-coenzyme A ligase for the biosynthesis of the neocarzinostatin enediyne antitumor antibiotic

24. Discovery of an unprecedented NRPS initiation module that is consisted of a discrete D-alanine-specific adenylation enzyme (LnmQ) and a discrete PCP (LnmP) (J. Biol. Chem. 2007, 282, 20273-20282)

Diagram of D-alanine-specific adenylation enzyme

25. Characterization of SgcC3 as an FAD-dependent halogenase that acts on a carrier protein-tethered substrate for the biosynthesis of the C-1027 enediyne antitumor antibiotic (J. Am. Chem. Soc. 2007, 129, 12432-12438)

Diagram of SgcC3 as an FAD-dependent halogenase

26. Discovery of a new branch point in chorismate metabolism from the biosynthesis of the C-1027 enediyne antitumor antibiotic (Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 494-499)

Diagram of biosynthesis of the C-1027

27. Discovery of the enediyne polyketide synthases as a new class of phosphopantetheinylating iterative polyketide synthases from the biosynthesis of the C-1027, neocarzinostatin, and maduropeptin enediyne antitumor antibiotics (Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1460-1465)

Diagram of phosphopantetheinylating iterative polyketide synthases

28. Characterization of SgcC as a FAD-dependent monooxygenase that acts on a carrier protein-tethered substrate for the biosynthesis of the C-1027 enediyne antitumor antibiotic (J. Am. Chem. Soc. 2008, 130, 6616-6623)

Diagram of SgcC

29. Characterization of NcsB1 as a promiscuous O-methyltransferase for the biosynthesis of the neocarzinostatin enediyne antitumor antibiotic (J. Biol. Chem. 2008, 283, 14694-14702)

Diagram of NcsB1

30. Determination of the structure of the NcsB1 O-methyltransferase for the biosynthesis of the neocarzinostatin enediyne antitumor antibiotic (J. Biol. Chem. 2008, 283, 14694-14702)

Diagram of NcsB1 O-methyltransferase

31. Discovery of the role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis (J. Am. Chem. Soc. 2008, 130, 6336-6337)

Diagram of tandem acyl

32. Discovery of a free-standing condensation enzyme that can catalyze both C-O ester and C-N amide bond formation for the biosynthesis of the C-1027 enediyne antitumor antibiotic (Prod. natl. Acad. Sci. 2009, 106, 4183-4188)

Diagram of a free-standing condensation enzyme

33. Characterization of TlmK as a glycosyltransferase for tallysomycin biosynthesis (J. Biol. Chem. 2009, 284, 8256-8264)

Diagram of TlmK as a glycosyltransferase for tallysomycin biosynthesis

34. Characterization of TtmM as a a-ketoglutarate-dependent hydroxylase for tautomycin biosynthesis (Org. Lett. 2009, 11, 1639-1642)

Diagram of TtmM as a a-ketoglutarate-dependent hydroxylase for tautomycin biosynthesis

35. Discovery of LnmK, a bifunctional acyltransferase/decarboxylase, as the missing link for b-alkylation in polyketide biosynthesis (J. Am.  Chem. Soc. 2009, 132, 6900-6901)

Diagram of LnmK, a bifunctional acyltransferase/decarboxylase

36. Discovery of FdmM and FdmM1 as cofactor-independent novel oxygenases for fredericamycin biosynthesis (J. Biol. Chem. 2009, 284, 24735-24743)

Diagram of fredericamycin biosynthesis

37. Characterization of SgcE6 as a FAD reductase component for the FAD-dependent halogenations and hydroxylation steps in the biosynthesis of the C-1027 enediyne antitumor antibiotic (FEMS Microbiol. Lett. 2009, 300, 237-241)

Diagram of C-1027 enediyne antitumor antibiotic

38. Characterization of SgcF as an epoxide hydrolase to yield an (R)-vicinal diol providing direct evidence for its intermediacy in enediyne core biosynthesis (J. Am. Chem. Soc. 2009, 131, 16410-16417)

Diagram of SgcF

39. Characterization of TlmH as a a-ketoglutarate-dependent hydroxylase for tallysomycin biosynthesis (Mol. BioSyst. 2010, 6, 349-256)

Diagram of TlmH

40. Characterization of TtnDF as putative decarboxylase and dehydratase for tautomycetin biosynthesis (J. Am. Chem. Soc. 2010, 132, 6663-6671)

Diagram of TtnDF

41. Establishment of the common PKSE chemistry for the biosynthesis of both 9- and 10-membered enediyne cores with the PKSE accessory enzymes directing enediyne core pathway divergence (Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 11331-11335)

Diagram of both 9- and 10-membered enediyne cores

42. Discovery of the MdpB1 C-methyltransferase that acts on a CoA-tethered aromatic substrate for biosynthesis of the maduropeptin enediyne antitumor antibiotic (J. Am. Chem. Soc. 2010, 132, 12534-12536)

Diagram of MdpB1 C-methyltransferase

43. Discovery of NcsF2 and SgcF as a pair of complementary epoxide hydrolases and demonstration of their utilities in preparation of an optically pure diol from a racemic epoxide substrate (Org. Lett. 2010, 12, 3816-3819)

Diagram of NcsF2 and SgcF

44. Characterization of FdmV as an amide synthase for fredericamycin biosynthesis (J. Biol. Chem. 2010, 285, 38853-38860)

Diagram of fredericamycin biosynthesis

45. Discovery of LnmKLM to install the b-branch for leinamycin biosynthesis (Org. Lett. 2011, 13, 498-501)

Diagram of leinamycin biosynthesis