Structural Snapshots for the Conformation-dependent Catalysis by Human Medium-chain Acyl-coenzyme A Synthetase ACSM2A

Journal of Molecular Biology

Volumn 388, Issue 5, 2009, Pages 997-1008

  Kochan, Grazyna ^a   Pilka, Ewa S ^a   von Delft, Frank ^a   Oppermann, Udo ^a,b   Yue, Wyatt W ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b NIHR OXFORD BIOMEDICAL RESEARCH CENTRE   (United Kingdom)

Author keywords

adenylation; coenzyme A; fatty acid; synthetase; thioesterification

Indexed keywords

ACSM2A ENZYME; ADENYLATE CYCLASE; FATTY ACID; MAGNESIUM ION; MEDIUM CHAIN ACYL COENZYME A DEHYDROGENASE; UNCLASSIFIED DRUG;

ADENYLATION; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; ESTERIFICATION; GENE EXPRESSION; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN PURIFICATION;

EID: 67349140643     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.03.064     Document Type: Article

References (46)

1. Watkins P.A. Fatty acid activation. Prog. Lipid Res. 36 (1997) 55-83
2. Schomburg D., and Schomburg I. In: Schomburg D., and Schomburg I. (Eds). Springer Handbook of Enzymes. 2nd edit. vol. 2 (2001), Springer-Verlag, Berlin 186-218
3. Schomburg I., Chang A., Ebeling C., Gremse M., Heldt C., Huhn G., and Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res. 32 (2004) D431-D433
4. Kleinkauf H., and Von Dohren H. A nonribosomal system of peptide biosynthesis. Eur. J. Biochem. 236 (1996) 335-351
5. White H.E., Miano J.D., and Umbreit M. Letter: on the mechanism of firefly luciferin luminescence. J. Am. Chem. Soc. 97 (1975) 198-200
6. Bar-Tana J., Rose G., and Shapiro B. The purification and properties of microsomal palmitoyl-coenzyme A synthetase. Biochem. J. 122 (1971) 353-362
7. Marahiel M.A., Stachelhaus T., and Mootz H.D. Modular peptide synthetases involved in nonribosomal peptide synthesis. Chem. Rev. 97 (1997) 2651-2674
8. Reger A.S., Carney J.M., and Gulick A.M. Biochemical and crystallographic analysis of substrate binding and conformational changes in acetyl-CoA synthetase. Biochemistry 46 (2007) 6536-6546
9. Gulick A.M., Starai V.J., Horswill A.R., Homick K.M., and Escalante-Semerena J.C. The 1.75 Å crystal structure of acetyl-CoA synthetase bound to adenosine-5'-propylphosphate and coenzyme A. Biochemistry 42 (2003) 2866-2873
10. Jogl G., and Tong L. Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP. Biochemistry 43 (2004) 1425
11. Hisanaga Y., Ago H., Nakagawa N., Hamada K., Ida K., et al. Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. J. Biol. Chem. 279 (2004) 31717-31726
12. Conti E., Franks N.P., and Brick P. Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure 4 (1996) 287-298
13. Nakatsu T., Ichiyama S., Hiratake J., Saldanha A., Kobashi N., Sakata K., and Kato H. Structural basis for the spectral difference in luciferase bioluminescence. Nature 440 (2006) 372-376
14. Conti E., Stachelhaus T., Marahiel M.A., and Brick P. Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J. 16 (1997) 4174-4183
15. Drake E.J., Nicolai D.A., and Gulick A.M. Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain. Chem. Biol. 13 (2006) 409-419
16. Gulick A.M., Lu X., and Dunaway-Mariano D. Crystal structure of 4-chlorobenzoate:CoA ligase/synthetase in the unliganded and aryl substrate-bound states. Biochemistry 43 (2004) 8670-8679
17. Reger A.S., Wu R., Dunaway-Mariano D., and Gulick A.M. Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry 47 (2008) 8016-8025
18. Du L., He Y., and Luo Y. Crystal structure and enantiomer selection by D-alanyl carrier protein ligase DltA from Bacillus cereus. Biochemistry 47 (2008) 11473-11480
19. Yonus H., Neumann P., Zimmermann S., May J.J., Marahiel M.A., and Stubbs M.T. Crystal structure of DltA. Implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains. J. Biol. Chem. 283 (2008) 32484-32491
20. Fujino T., Takei Y.A., Sone H., Ioka R.X., Kamataki A., Magoori K., et al. Molecular identification and characterization of two medium-chain acyl-CoA synthetases, MACS1 and the Sa gene product. J. Biol. Chem. 276 (2001) 35961-35966
21. Kasuya F., Igarashi K., and Fukui M. Inhibition of a medium chain acyl-CoA synthetase involved in glycine conjugation by carboxylic acids. Biochem. Pharmacol. 52 (1996) 1643-1646
22. Vessey D.A., Hu J., and Kelley M. Interaction of salicylate and ibuprofen with the carboxylic acid: CoA ligases from bovine liver mitochondria. J. Biochem. Toxicol. 11 (1996) 73-78
23. Iwai N., Mannami T., Tomoike H., Ono K., and Iwanaga Y. An acyl-CoA synthetase gene family in chromosome 16p12 may contribute to multiple risk factors. Hypertension 41 (2003) 1041-1046
24. Lindner I., Rubin D., Helwig U., Nitz I., Hampe J., and Schreiber S. The L513S polymorphism in medium-chain acyl-CoA synthetase 2 (MACS2) is associated with risk factors of the metabolic syndrome in a Caucasian study population. Mol. Nutr. Food Res. 50 (2006) 270-274
25. Bar-Tana J., and Rose G. Studies on medium-chain fatty acyl-coenzyme a synthetase. Enzyme fraction II: mechanism of reaction and specific properties. Biochem. J. 109 (1968) 283-292
26. Bar-Tana J., Rose G., and Shapiro B. Studies on medium-chain fatty acyl-coenzyme a synthetase. Purification and properties. Biochem. J. 109 (1968) 269-274
27. Bar-Tana J., and Rose G. Studies on medium-chain fatty acyl-coenzyme a synthetase. Enzyme fraction I: mechanism of reaction and allosteric properties. Biochem. J. 109 (1968) 275-282
28. Hallows W.C., Lee S., and Denu J.M. Sirtuins deacetylate and activate mammalian acetyl-CoA synthetases. Proc. Natl Acad. Sci. USA 103 (2006) 10230-10235
29. Scheffzek K., Klebe C., Fritz-Wolf K., Kabsch W., and Wittinghofer A. Crystal structure of the nuclear Ras-related protein Ran in its GDP-bound form. Nature 374 (1995) 378-381
30. Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A., et al. The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J. 13 (1994) 327-337
31. Wu R., Cao J., Lu X., Reger A.S., Gulick A.M., and Dunaway-Mariano D. Mechanism of 4-chlorobenzoate:coenzyme a ligase catalysis. Biochemistry 47 (2008) 8026-8039
32. Horswill A.R., and Escalante-Semerena J.C. Characterization of the propionyl-CoA synthetase (PrpE) enzyme of Salmonella enterica: residue Lys592 is required for propionyl-AMP synthesis. Biochemistry 41 (2002) 2379-2387
33. Chang K.H., Xiang H., and Dunaway-Mariano D. Acyl-adenylate motif of the acyl-adenylate/thioester-forming enzyme superfamily: a site-directed mutagenesis study with the Pseudomonas sp. strain CBS3 4-chlorobenzoate:coenzyme A ligase. Biochemistry 36 (1997) 15650-15659
34. Stuible H., Buttner D., Ehlting J., Hahlbrock K., and Kombrink E. Mutational analysis of 4-coumarate:CoA ligase identifies functionally important amino acids and verifies its close relationship to other adenylate-forming enzymes. FEBS Lett. 467 (2000) 117-122
35. Branchini B.R., Murtiashaw M.H., Magyar R.A., and Anderson S.M. The role of lysine 529, a conserved residue of the acyl-adenylate-forming enzyme superfamily, in firefly luciferase. Biochemistry 39 (2000) 5433-5440
36. May J.J., Kessler N., Marahiel M.A., and Stubbs M.T. Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases. Proc. Natl Acad. Sci. USA 99 (2002) 12120-12125
37. Ingram-Smith C., Woods B.I., and Smith K.S. Characterization of the acyl substrate binding pocket of acetyl-CoA synthetase. Biochemistry 45 (2006) 11482-11490
38. Leslie A.G. The integration of macromolecular diffraction data. Acta Crystallogr. D 62 (2006) 48-57
39. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26 (1993) 795-800
40. Collaborative Computing Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50 (1994) 760-763
41. McCoy A.J., Grosse-Kunstleve R.W., Storoni L.C., and Read R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D 61 (2005) 458-464
42. Schwarzenbacher R., Godzik A., Grzechnik S.K., and Jaroszewski L. The importance of alignment accuracy for molecular replacement. Acta Crystallogr. D 60 (2004) 1229-1236
43. Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6 (1999) 458-463
44. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53 (1997) 240-255
45. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60 (2004) 2126-2132
46. Hayward S., and Lee R.A. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J. Mol. Graph. Model. 21 (2002) 181-183