Structural and functional analysis of A-type ketoreductases from the amphotericin modular polyketide synthase

Structure

Volumn 18, Issue 8, 2010, Pages 913-922

  Zheng, Jianting ^a   Taylor, Clint A ^a   Piasecki, Shawn K ^a   Keatinge Clay, Adrian T ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Proteins

Indexed keywords

POLYKETIDE SYNTHASE;

ARTICLE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; STEREOCHEMISTRY;

ALCOHOL OXIDOREDUCTASES; AMINO ACID SEQUENCE; CATALYTIC DOMAIN; CHROMATOGRAPHY, GEL; CRYSTALLIZATION; DIMERIZATION; MALATES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; POLYKETIDE SYNTHASES; PROTEIN CONFORMATION; STEREOISOMERISM;

EID: 77955477986     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2010.04.015     Document Type: Article

References (36)

1. Alekseyev V.Y., Liu C.W., Cane D.E., Puglisi J.D., Khosla C. Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Protein Sci. 2007, 16:2093-2107.
2. Andrusier N., Nussinov R., Wolfson H.J. FireDock: fast interaction refinement in molecular docking. Proteins 2007, 69:139-159.
3. Baerga-Ortiz A., Popovic B., Siskos A.P., O'Hare H.M., Spiteller D., Williams M.G., Campillo N., Spencer J.B., Leadlay P.F. Directed mutagenesis alters the stereochemistry of catalysis by isolated ketoreductase domains from the erythromycin polyketide synthase. Chem. Biol. 2006, 13:277-285.
4. Caffrey P. Conserved amino acid residues correlating with ketoreductase stereospecificity in modular polyketide synthases. ChemBioChem 2003, 4:654-657.
5. Caffrey P., Lynch S., Flood E., Finnan S., Oliynyk M. Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes. Chem. Biol. 2001, 8:713-723.
6. Castonguay R., He W., Chen A.Y., Khosla C., Cane D.E. Stereospecificity of ketoreductase domains of the 6-deoxyerythronolide B synthase. J. Am. Chem. Soc. 2007, 129:13758-13769.
7. Castonguay R., Valenzano C.R., Chen A.Y., Keatinge-Clay A., Khosla C., Cane D.E. Stereospecificity of ketoreductase domains 1 and 2 of the tylactone modular polyketide synthase. J. Am. Chem. Soc. 2008, 130:11598-11599.
8. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 1994, 50:760-763. CCP4 (Collaborative Computational Project, Number 4).
9. DeLano W.L. The PyMOL Molecular Graphics System User's Manual 2002, DeLano Scientific, San Carlos, CA.
10. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:2126-2132.
11. Holzbaur I.E., Harris R.C., Bycroft M., Cortes J., Bisang C., Staunton J., Rudd B.A., Leadlay P.F. Molecular basis of Celmer's rules: the role of two ketoreductase domains in the control of chirality by the erythromycin modular polyketide synthase. Chem. Biol. 1999, 6:189-195.
12. Keatinge-Clay A.T. A tylosin ketoreductase reveals how chirality is determined in polyketides. Chem. Biol. 2007, 14:898-908.
13. Keatinge-Clay A.T., Stroud R.M. The structure of a ketoreductase determines the organization of the beta-carbon processing enzymes of modular polyketide synthases. Structure 2006, 14:737-748.
14. Kellenberger L., Galloway I.S., Sauter G., Bohm G., Hanefeld U., Cortes J., Staunton J., Leadlay P.F. A polylinker approach to reductive loop swaps in modular polyketide synthases. ChemBioChem 2008, 9:2740-2749.
15. Khosla C., Tang Y., Chen A.Y., Schnarr N.A., Cane D.E. Structure and mechanism of the 6-deoxyerythronolide B synthase. Annu. Rev. Biochem. 2007, 76:195-221.
16. Khosla C., Kapur S., Cane D.E. Revisiting the modularity of modular polyketide synthases. Curr. Opin. Chem. Biol. 2009, 13:135-143.
17. Koshland D.E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 1958, 44:98-104.
18. Maier T., Jenni S., Ban N. Architecture of mammalian fatty acid synthase at 4.5 A resolution. Science 2006, 311:1258-1262.
19. Maier T., Leibundgut M., Ban N. The crystal structure of a mammalian fatty acid synthase. Science 2008, 321:1315-1322.
20. Mashiach E., Schneidman-Duhovny D., Andrusier N., Nussinov R., Wolfson H.J. FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res. 2008, 36:W229-W232.
21. McCarthy A.A., Baker H.M., Shewry S.C., Patchett M.L., Baker E.N. Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold. Structure 2001, 9:637-646.
22. McPherson M., Khosla C., Cane D.E. Erythromycin biosynthesis: the b-ketoreductase domains catalyze the stereospecific transfer of the 4-pro-S hydride of NADPH. J. Am. Chem. Soc. 1998, 120:3267-3268.
23. Meier J.L., Burkart M.D. The chemical biology of modular biosynthetic enzymes. Chem. Soc. Rev. 2009, 38:2012-2045.
24. O'Hare H.M., Baerga-Ortiz A., Popovic B., Spencer J.B., Leadlay P.F. High-throughput mutagenesis to evaluate models of stereochemical control in ketoreductase domains from the erythromycin polyketide synthase. Chem. Biol. 2006, 13:287-296.
25. Oppermann U., Filling C., Hult M., Shafqat N., Wu X., Lindh M., Shafqat J., Nordling E., Kallberg Y., Persson B., Jornvall H. Short-chain dehydrogenases/reductases (SDR): the 2002 update. Chem. Biol. Interact. 2003, 143-144:247-253.
26. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology, Volume 276: Macromolecular Crystallography, Part A 1997, 307-326. Academic Press, New York. C.W. Carter, R.M. Sweet (Eds.).
27. Reid R., Piagentini M., Rodriguez E., Ashley G., Viswanathan N., Carney J., Santi D.V., Hutchinson C.R., McDaniel R. A model of structure and catalysis for ketoreductase domains in modular polyketide synthases. Biochemistry 2003, 42:72-79.
28. Roujeinikova A., Simon W.J., Gilroy J., Rice D.W., Rafferty J.B., Slabas A.R. Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates. J. Mol. Biol. 2007, 365:135-145.
29. Schneidman-Duhovny D., Inbar Y., Nussinov R., Wolfson H.J. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 2005, 33:W363-W367.
30. Siskos A.P., Baerga-Ortiz A., Bali S., Stein V., Mamdani H., Spiteller D., Popovic B., Spencer J.B., Staunton J., Weissman K.J., Leadlay P.F. Molecular basis of Celmer's rules: stereochemistry of catalysis by isolated ketoreductase domains from modular polyketide synthases. Chem. Biol. 2005, 12:1145-1153.
31. Valenzano C.R., Lawson R.J., Chen A.Y., Khosla C., Cane D.E. The biochemical basis for stereochemical control in polyketide biosynthesis. J. Am. Chem. Soc. 2009, 131:18501-18511.
32. Wallace A.C., Laskowski R.A., Thornton J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995, 8:127-134.
33. Weissman K.J., Timoney M., Bycroft M., Grice P., Hanefeld U., Staunton J., Leadlay P.F. The molecular basis of Celmer's rules: the stereochemistry of the condensation step in chain extension on the erythromycin polyketide synthase. Biochemistry 1997, 36:13849-13855.
34. Wong F.T., Chen A.Y., Cane D.E., Khosla C. Protein-protein recognition between acyltransferases and acyl carrier proteins in multimodular polyketide synthases. Biochemistry 2010, 49:95-102.
35. Yin Y., Gokhale R., Khosla C., Cane D.E. Erythromycin biosynthesis. The 4-pro-S hydride of NADPH is utilized for ketoreduction by both module 5 and module 6 of the 6-deoxyerythronolide B synthase. Bioorg. Med. Chem. Lett. 2001, 11:1477-1479.
36. Zhang Y.M., Rao M.S., Heath R.J., Price A.C., Olson A.J., Rock C.O., White S.W. Identification and analysis of the acyl carrier protein (ACP) docking site on beta-ketoacyl-ACP synthase III. J. Biol. Chem. 2001, 276:8231-8238.