Structural classification and properties of ketoacyl synthases

Protein Science

Volumn 20, Issue 10, 2011, Pages 1659-1667

  Chen, Yingfei ^a   Kelly, Erin E ^a   Masluk, Ryan P ^a   Nelson, Charles L ^a   Cantu, David C ^a   Reilly, Peter J ^a  

^a Iowa State University   (United States)

Author keywords

Chalcone synthase; Fatty acid elongase; Ketoacyl synthase; Oxoacyl synthase; Phylogeny; Primary structure; Stilbene synthase; Tertiary structure; ThYme

Indexed keywords

3 OXOACYL ACYL CARRIER PROTEIN SYNTHASE; ACETYL COENZYME A ACYLTRANSFERASE; ACYL COENZYME A; BACTERIAL ENZYME; CHALCONE; FATTY ACID; KETOACYL SYNTHASE; MALONYL COENZYME A; NARINGENIN; POLYKETIDE SYNTHASE; STILBENE; SYNTHETASE; UNCLASSIFIED DRUG;

CATALYSIS; CHEMICAL REACTION; ENZYME STRUCTURE; ENZYME SYNTHESIS; EUKARYOTE; NONHUMAN; PRIORITY JOURNAL; REVIEW;

3-OXOACYL-(ACYL-CARRIER-PROTEIN) SYNTHASE; ACETYLTRANSFERASES; ACYLTRANSFERASES; ANIMALS; BACTERIA; BACTERIAL PROTEINS; HUMANS; MODELS, MOLECULAR; PHYLOGENY; PLANT PROTEINS; PLANTS; PROTEIN CONFORMATION;

ANIMALIA; BACTERIA (MICROORGANISMS); EUKARYOTA; THYMUS VULGARIS;

EID: 80053136100     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.712     Document Type: Review

References (34)

1. Smith S, Tsai S (2007) The type I fatty acid and polyketide synthases: a tale of two megasynthases. Nat Prod Rep 24:1041-1072. (Pubitemid 47493392)
2. Cantu DC, Chen Y, Reilly PJ (2010) Thioesterases: a new perspective based on their primary and tertiary structures. Protein Sci 19:1281-1295.
3. Cantu DC, Chen Y, Lemons ML, Reilly PJ (2011) ThYme: a database for thioester-active enzymes. Nucleic Acids Res 39:D342-D346.
4. Moche M, Dehesh K, Edwards P, Lindqvist Y (2001) The crystal structure of b-ketoacyl-acyl carrier protein synthase II from Synechocystis sp. at 1.54 Å resolution and its relationship to other condensing enzymes. J Mol Biol 305:491-503. (Pubitemid 33032856)
5. Blacklock BJ, Jaworski JG (2006) Substrate specificity of Arabidopsis 3-ketoacyl-CoA synthases. Biochem Biophys Res Commun 346:583-590. (Pubitemid 43902723)
6. González-Mellado D, Wettstein-Knowles P, Garcés R, Martínez-Force E (2010) The role of b-ketoacyl-acyl carrier protein synthase III in the condensation steps of fatty acid biosynthesis in sunflower. Planta 231: 1277-1289.
7. Leonard AE, Pereira SL, Sprecher H, Huang Y-S (2004) Elongation of long-chain fatty acids. Prog Lipid Res 43:36-54. (Pubitemid 37433866)
8. Fritzler JM, Millership JJ, Zhu G (2007) Cryptosporidium parvum fatty acid elongase. Eukaryot Cell 6: 2018-2028. (Pubitemid 350221270)
9. Lee SH, Stephens JL, Englund PT (2007) A fatty-acid synthesis mechanism specialized for parasitism. Nat Rev Microbiol 5:287-297. (Pubitemid 46443605)
10. Iskandarov U, Khozin-Goldberg I, Ofir R, Cohen Z (2009) Cloning and characterization of the Δ6 polyunsaturated fatty acid elongase from the green microalga Parietochloris incisa. Lipids 44:545-554.
11. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman, DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-2402.
12. UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res 36:D190-D195.
13. Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) (1992) Enzyme nomenclature. San Diego, CA: Academic Press.
14. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunesekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211-D222.
15. Durbin R, Eddy S, Krogh A, Mitchison G (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University Press.
16. National Center for Biotechnology Information (NCBI) (2011) RefSeq. Available at: http://www.ncbi.nlm.nih.gov/RefSeq/.
17. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
18. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. (Pubitemid 350162903)
19. Rose, PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlić A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res 39: D392-D401.
20. Shatsky M, Nussinov R, Wolfson HJ (2004) A method for simultaneous alignment of multiple protein structures. Proteins 56:143-156. (Pubitemid 38720846)
21. The MathWorks, Inc. (2011) Available at: http://www.mathworks.com/ matlabcentral/.
22. Schrödinger, LLC (2011) The PyMOL molecular graphics system, version 1.3. Available at: http://www.pymol.org/.
23. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599. (Pubitemid 47236692)
24. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. New York: Oxford University Press.
25. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282.
26. Mertz B, Kuczenski RS, Larsen RT, Hill AD, Reilly PJ (2005) Phylogenetic analysis of family 6 glycoside hydrolases. Biopolymers 79:197-206. (Pubitemid 43078447)
27. Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490.
28. Jakobsson A, Westerberg R, Jacobsson A (2006) Fatty acid elongases in mammals: their regulation and roles in metabolism. Prog Lipid Res 45:237-249.
29. Huang W, Jia J, Edward P, Dehesh K, Schneider G, Lindqvist Y (1998) Crystal structure of β-ketoacyl-acyl carrier protein synthase II from E. coli reveals the molecular architecture of condensing enzymes. EMBO J 17:1183-1191. (Pubitemid 28105497)
30. Plowman KM (1972) Enzyme kinetics. New York: McGraw-Hill, pp 41-42.
31. Qiu X, Janson CA, Konstantinidis AK, Nwagwu S, Silverman C, Smith WW, Khandekar S, Lonsdale J, Abdel-Meguid SS (1999) Crystal structure of β-ketoacyl-acyl carrier protein synthase. III. A key condensing enzyme in bacterial fatty acid biosynthesis. J Biol Chem 274:36465-36471.
32. Ghanevati M, Jaworski JG (2002) Engineering and mechanistic studies of the Arabidopsis FAE1 β-ketoacyl-CoA synthase, FAE1 KCS. Eur J Biochem 269:3531-3539. (Pubitemid 34988997)
33. Zhang Y, Hulbert J, White SW, Rock CO (2006) Roles of the active site water, histidine 303, and phenylalanine 396 in the catalytic mechanism of the elongation condensing enzyme of Streptococcus pneumoniae. J Biol Chem 281:17390-17399.
34. Austin MB, Noel JP (2003) The chalcone synthase superfamily of type III polyketide synthases. Nat Prod Rep 20:79-110. (Pubitemid 36219433)