Crystal Structure of Yeast Peroxisomal Multifunctional Enzyme: Structural Basis for Substrate Specificity of (3R)-hydroxyacyl-CoA Dehydrogenase Units

Journal of Molecular Biology

Volumn 358, Issue 5, 2006, Pages 1286-1295

  Ylianttila, Mari S ^a   Pursiainen, Niko V ^a   Haapalainen, Antti M ^a   Juffer, André H ^a   Poirier, Yves ^b   Kalervo Hiltunen, J ^a   Glumoff, Tuomo ^a  

^a UNIVERSITY OF OULU   (Finland)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

(3R) hydroxyacyl CoA dehydrogenase; multifunctional enzyme type 2; peroxisome; SDR; oxidation

Indexed keywords

ACYL COENZYME A DEHYDROGENASE; BUTYRYL COENZYME A DEHYDROGENASE; ENOYL COENZYME A HYDRATASE; ENZYME; HETERODIMER; HYDROXYACYL COENZYME A DEHYDROGENASE; LEUCINE; MEDIUM CHAIN ACYL COENZYME A DEHYDROGENASE; MULTIFUNCTIONAL ENZYME 2; NICOTINAMIDE ADENINE DINUCLEOTIDE; OXIDOREDUCTASE; POLYPEPTIDE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CANDIDA TROPICALIS; CATALYSIS; CRYSTAL STRUCTURE; ENZYME ANALYSIS; ENZYME BINDING; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBUNIT; HYDROPHOBICITY; NONHUMAN; PEROXISOME; PRIORITY JOURNAL; YEAST;

CANDIDA TROPICALIS; MAMMALIA;

EID: 33646480064     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.03.001     Document Type: Article

References (36)

1. Hiltunen J.K., and Qin Y.M. β-Oxidation-strategies for the metabolism of a wide variety of acyl-CoA esters. Biochim. Biophys. Acta 1484 (2000) 117-128
2. Hiltunen J.K., Mursula A.M., Rottensteiner H., Wierenga R.K., Kastaniotis A.J., and Gurvitz A. The biochemistry of peroxisomal β-oxidation in the yeast Saccharomyces cerevisiae. FEMS Microbiol. Rev. 27 (2003) 35-64
3. Russell D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137-174
4. Verhoeven N.M., and Jakobs C. Human metabolism of phytanic acid and pristanic acid. Prog. Lipid Res. 40 (2001) 453-466
5. Bartlett K., and Eaton S. Mitochondrial β-oxidation. Eur. J. Biochem. 271 (2004) 462-469
6. Bhaumik P., Koski M.K., Glumoff T., Hiltunen J.K., and Wierenga R.K. Structural biology of the thioester-dependent degradation and synthesis of fatty acids. Curr. Opin. Struct. Biol. 15 (2005) 621-628
7. Hiltunen J.K., Wenzel B., Beyer A., Erdmann R., Fosså A., and Kunau W.H. Peroxisomal multifunctional β-oxidation protein of Saccharomyces cerevisiae. Molecular analysis of the fox2 gene and gene product. J. Biol. Chem. 267 (1992) 6646-6653
8. Qin Y.M., Marttila M.S., Haapalainen A.M., Siivari K.M., Glumoff T., and Hiltunen J.K. Yeast peroxisomal multifunctional enzyme: (3R)-hydroxyacyl-CoA dehydrogenase domains A and B are required for optimal growth on oleic acid. J. Biol. Chem. 274 (1999) 28619-28625
9. Marchesini S., Erard N., Glumoff T., Hiltunen J.K., and Poirier Y. Modification of the monomer composition of polyhydroxyalkanoate synthesized in Saccharomyces cerevisiae expressing variants of the β-oxidation-associated multifunctional enzyme. Appl. Environ. Microbiol. 69 (2003) 6495-6499
10. Ylianttila M.S., Qin Y.M., Hiltunen J.K., and Glumoff T. Site-directed mutagenesis to enable and improve crystallizability of Candida tropicalis (3R)-hydroxyacyl-CoA dehydrogenase. Biochem. Biophys. Res. Commun. 324 (2004) 25-30
11. Haapalainen A.M., Koski M.K., Qin Y.M., Hiltunen J.K., and Glumoff T. Binary structure of the two-domain (3R)-hydroxyacyl-CoA dehydrogenase from rat peroxisomal multifunctional enzyme type 2 at 2.38 Å resolution. Structure (Camb) 11 (2003) 87-97
12. Tanaka N., Nonaka T., Tanabe T., Yoshimoto T., Tsuru D., and Mitsui Y. Crystal structures of the binary and ternary complexes of 7 α-hydroxysteroid dehydrogenase from Escherichia coli. Biochemistry 35 (1996) 7715-7730
13. Grimm C., Maser E., Mobus E., Klebe G., Reuter K., and Ficner R. The crystal structure of 3 α-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short-chain dehydrogenase/reductase family. J. Biol. Chem. 275 (2000) 41333-41339
14. Chapman A.D., Cortés A., Dafforn T.R., Clarke A.R., and Brady R.L. Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, α-ketomalonate and tetrahydoNAD. J. Mol. Biol. 285 (1999) 703-712
15. Alphey M.S., Yu W., Byres E., Li D., and Hunter W.N. Structure and reactivity of human mitochondrial 2,4-dienoyl-CoA reductase: enzyme-ligand interactions in a distinctive short-chain reductase active site. J. Biol. Chem. 280 (2005) 3068-3077
16. Barycki J.J., O'Brien L.K., Strauss A.W., and Banaszak L.J. Sequestration of the active site by interdomain shifting. Crystallographic and spectroscopic evidence for distinct conformations of L-3-hydroxyacyl-CoA dehydrogenase. J. Biol. Chem. 275 (2000) 27186-27196
17. 2+-dependent dimerization mode. Structure (Camb) 10 (2002) 773-786
18. Jiang L.L., Kobayashi A., Matsuura H., Fukushima H., and Hashimoto T. Purification and properties of human D-3-hydroxyacyl-CoA dehydratase: medium-chain enoyl-CoA hydratase is D-3-hydroxyacyl-CoA dehydratase. J. Biochem. (Tokyo) 120 (1996) 624-632
19. Koski K.M., Haapalainen A.M., Hiltunen J.K., and Glumoff T. Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2. J. Mol. Biol. 345 (2005) 1157-1169
20. Koski M.K., Haapalainen A.M., Hiltunen J.K., and Glumoff T. A two-domain structure of one subunit explains unique features of eukaryotic hydratase 2. J. Biol. Chem. 279 (2004) 24666-24672
21. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallog. 26 (1993) 795-800
22. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A 50 (1994) 157-163
23. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
24. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
25. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
26. Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6 (1999) 458-463
27. Wriend G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8 (1990) 52-56
28. Laskowski R.A., McArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
29. Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723
30. Peitsch M.C. Protein modeling by E-mail. Bio/Technology 13 (1995) 658-660
31. Peitsch M.C. ProMod and Swiss-Model: internet-based tools for automated comparative protein modelling. Biochem. Soc. Trans. 24 (1996) 274-279
32. Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 1 (2001) 306-317
33. Abagyan R.A., and Totrov M.M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235 (1994) 983-1002
34. Abagyan R.A., Totrov M.M., and Kuznetsov D.N. ICM-a new method for protein modeling and design. Applications to docking and structure prediction from the distorted native conformation. J. Comp. Chem. 15 (1994) 488-506
35. Fernández-Recio J., Totrov M., and Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci. 11 (2002) 280-291
36. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res 25 (1997) 4876-4882