Crystal structure of enoyl-coenzyme A (CoA) hydratase at 2.5 Å resolution: A spiral fold defines the CoA-binding pocket

EMBO Journal

Volumn 15, Issue 19, 1996, Pages 5135-5145

  Engel, Christian K ^a   Mathieu, Magali ^a   Zeelen, Johan Ph ^a   Hiltunen, J Kalervo ^b   Wierenga, Rik K ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITY OF OULU   (Finland)

Author keywords

CoA; Hydratase; Isomerase; Multifunctional enzymes; oxidation

Indexed keywords

ENOYL COENZYME A HYDRATASE; GLUTAMIC ACID; WATER;

ALPHA HELIX; ANIMAL TISSUE; ARTICLE; BETA CHAIN; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME INHIBITOR COMPLEX; LIGAND BINDING; LIVER MITOCHONDRION; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; RAT; STEREOCHEMISTRY;

ANIMALIA;

EID: 0029791410     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1002/j.1460-2075.1996.tb00897.x     Document Type: Article

References (42)

1. Allen, F.M. and Kennard, O. (1993) 3D search and research using the Cambridge Structural Database. Chem. Design Automation News, 8, 31-37.
2. Babbitt, P.C., Kenyon, G.L., Martin, B.M., Charest, H. and Slyvestre, M. (1992) Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases. Biochemistry, 31, 5594-5604.
3. Bahnson, B.J. and Anderson, V.E. (1991) Crotonase-catalyzed β-elimination is concerted: a double isotope effect study. Biochemistry, 30, 5894-5906.
4. Brünger, A.T. (1992) X-PLOR: Version 3.1, A System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
5. Collaborative Computing Project. Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr., D50, 760-763.
6. Creighton, D.J. and Murthy, N.S.R.K. (1990) Stereochemistry of enzyme catalyzed reactions at carbons. In Sigman, D.S. and Boyer, P.D. (eds), The Enzymes. Academic Press, San Diego, CA, pp. 324-421.
7. D'Ordine, R.L., Bahnson, B.J., Tonge, P.J. and Anderson, V.E. (1994a) Enoyl-coenzyme A hydratase-catalyzed exchange of the α-protons of coenzyme A thiol esters: a model for an enolized intermediate in the enzyme-catalyzed elimination? Biochemistry, 33, 14733-14742.
8. D'Ordine, R.L., Tonge, P.J., Carey, P.R. and Anderson, V.E. (1994b) Electronic rearrangement induced by substrate analog binding to the enoyl-CoA hydrase active site: evidence for substrate activation. Biochemistry, 33, 12635-12643.
9. Engel, C., Wierenga, R. and Tucker, P.A. (1996) A removable arc for mounting and recovering flash-cooled crystals. J. Appl. Crystallogr., 29, 208-210.
10. 2-enoyl-CoA isomerase acting on 3-cis-enoyl-CoA and 3-trans-enoyl-CoA. Eur. J. Biochem., 196, 699-705.
11. Euler-Bertram, S. and Stoffel, W. (1990) Purification and characterization of bovine liver 3-cis-2-(tans-enoyl-CoA isomerase. Biol. Chem. Hoppe-Seyler, 371, 603-610.
12. Fersht, A. (1985) Enzyme Structure and Mechanism W.H. Freeman & Co., New York.
13. Gerlt, J.A. and Gassman, P.G. (1992) Understanding enzyme-calalyzed proton abstraction from carbon acids: details of stepwise mechanisms for β-elimination reactions. J. Am. Chem. Soc., 114, 5928-5934.
14. Gerlt, J.A. and Gassman, P.G. (1993) An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: importance of late trasition states in concerted mechanisms. J. Am. Chem. Soc., 115, 11552-11568.
15. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
16. Jones, T.A., Zou, J.-Y. and Cowan, S.W. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., A47, 110-119.
17. Jurnak, F., Yoder, M.D., Pickersgill, R. and Jenkins, J. (1994) Parallel β-domains: a new fold in protein structures. Curr. Opin. Struct. Biol., 4, 802-806.
18. Kabsch, W. (1988) Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. Acta Crystallogr., A21, 916-924.
19. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
20. Kleywegt, G.J. and Jones, T.A. (1996) Efficient rebuilding of protein structures. Acta Crystallogr., D52, 829-832.
21. Kobe, B. and Deisenhofer, J. (1993) Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. Nature, 366, 751-756.
22. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
23. Mancia, F., Keep, N.H., Nakagawa, A., Leadlay, P.F., McSweeney, S., Rasmussen, B., Boesecke, P., Diat, O. and Evans, P.R. (1996) How coenzyme B12 radicals are generated: the crystal structure of methylmalonyl-coenzyme A mutase at 2Â resolution. Structure. 4, 339-350.
24. Minami-Ishii, N., Taketani, S., Osumi, T. and Hashimoto, T. (1989) Molecular cloning and sequence analysis of the cDNA for rat mitochondrial enoyl-CoA hydratase. Structural and evolutionary relationships linked to the bifunctional enzyme of the peroxisomal β-oxidation system. Eur. J. Biochem., 185, 73-78.
25. Mohrig, J.R., Moerke, K.A., Cloutier, D.L., Lane, B.D., Person, E.C. and Onasch, T.B. (1995) Importance of historical contingency in the stereochemistry of hydratase-dehydratase enzymes. Science, 269, 527-529.
26. Müller-Newen, G., Janssen, U. and Stoffel, W. (1995) Enoyl-CoA hydratase and isomerase form a superfamily with a common active-site glutamate residue. Eur. J. Biochem., 2218, 68-73.
27. Noble, M.E.M., Zeelen, J.P. and Wierenga, R.K. (1993) Structure of triosephosphate isomerase from Escherichia coli determined at 2.6 Å resolution. Acta Crystallogr., D49, 403-417.
28. Otwinowski, Z. (1991) Maximum likelihood refinement of heavy atom parameters. In Wolf, W., Evans, P.R. and Leslie, A.G.W. (eds), Proceedings of the CCP4 Study Weekend. SERC, Daresbury, UK, pp. 80-85.
29. Otwinowski, Z. (1993) Oscillation data reduction program. In Sawyer, L., Isaacs, N. and Bailey, S. (eds), Proceedings of the CCP4 Study Weekend SERC, Daresbury, UK, pp. 56-62.
30. 2-Enoyl-CoA isomerases. Characterization of the mitochondrial isoenzyme in the rat. J. Biol. Chem., 265, 3347-3353.
31. 2-enoyl-CoA isomerase, 2-enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase enzyme in rat liver. The proposed occurrence of isomerization and hydration in the same catalytic domain of the multifunctional enzyme. J. Biol. Chem., 266, 10750-10753.
32. Rao, S.T. and Rossmann, M.G. (1973) Comparison of super-secondary structures in proteins. J. Mol. Biol. 76, 241-256.
33. 2) biosynthesis: nucleotide sequence and expression of the menB gene from Escherichia coli. J. Bacteriol., 174, 5057-5062.
34. Thunnissen, A.M.W.H., Dijkstra, A.J., Kalk, K.H., Rozeboom, H.J., Engel, H., Keck, W. and Dijkstra, B.W. (1994) Doughnut-shaped structure of a bacterial muramidase revealed by X-ray crystallography. Nature, 367, 750-753.
35. Tong, L. and Rossmann, M.G. (1990) The locked rotation function. Acta Crystallogr., A46, 783-792.
36. Vellieux, F.M.D.A.P., Hunt, J.F., Roy, S. and Read, R.J. (1995) Computer Programs DEMON/ANGEL: a suite of programs to carry out density modification. J. Appl. Crystallogr., 28, 347-351.
37. Vriend, G. (1990) WHAT IF: a molecular modeling and drug design program. J. Mol. Graphics, 8, 52-56.
38. Waterson, R.M. and Hill, R.L. (1972) Enoyl coenzyme A hydratase (crotonase). Catalytic properties of crotonase and its possible regulatory role in fatty acid oxidation. J. Biol. Chem., 247, 5258-5265.
39. Willadsen, P. and Eggerer, H. (1975) Substrate stereochemistry of the enoyl-CoA hydratase reaction. Eur. J. Biochem., 54, 247-252.
40. Wolodko, W.T., Fraser, M.E., James, M.N.G. and Bridgers, W.A. (1994) The crystal structure of succinyl-CoA synthetase from Escherichia coli at 2.5Å resolution. J. Biol. Chem., 269, 10883-10890.
41. 2-enoyl-coenzyme A catalyzed by the multienzyme complex of fatty acid oxidation from Escherichia coli. Biochemistry, 34, 6441-6447.
42. Zeelen, J.P. Hiltunen, J.K., Ceska, T.A. and Wierenga, R.K. (1994) Crystallization experiments with 2-enoyl-CoA hydratase, using an automated 'fast-screening' crystallization protocol. Acta Crystallogr., D50, 443-447.