1afw Citations

The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism.

Abstract

The dimeric, peroxisomal 3-ketoacyl-CoA thiolase catalyses the conversion of 3-ketoacyl-CoA into acyl-CoA, which is shorter by two carbon atoms. This reaction is the last step of the beta-oxidation pathway. The crystal structure of unliganded peroxisomal thiolase of the yeast Saccharomyces cerevisiae has been refined at 1.8 A resolution. An unusual feature of this structure is the presence of two helices, completely buried in the dimer and sandwiched between two beta-sheets. The analysis of the structure shows that the sequences of these helices are not hydrophobic, but generate two amphipathic helices. The helix in the N-terminal domain exposes the polar side-chains to a cavity at the dimer interface, filled with structured water molecules. The central helix in the C-terminal domain exposes its polar residues to an interior polar pocket. The refined structure has also been used to predict the mode of binding of the substrate molecule acetoacetyl-CoA, as well as the reaction mechanism. From previous studies it is known that Cys125, His375 and Cys403 are important catalytic residues. In the proposed model the acetoacetyl group fits near the two catalytic cysteine residues, such that the oxygen atoms point towards the protein interior. The distance between SG(Cys125) and C3(acetoacetyl-CoA) is 3.7 A. The O2 atom of the docked acetoacetyl group makes a hydrogen bond to N(Gly405), which would favour the formation of the covalent bond between SG(Cys125) and C3(acetoacetyl-CoA) of the intermediate complex of the two-step reaction. The CoA moiety is proposed to bind in a groove on the surface of the protein molecule. Most of the interactions of the CoA molecule are with atoms of the loop domain. The three phosphate groups of the CoA moiety are predicted to interact with side-chains of lysine and arginine residues, which are conserved in the dimeric thiolases.

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  1. The biochemistry of peroxisomal beta-oxidation in the yeast Saccharomyces cerevisiae. Hiltunen JK, Mursula AM, Rottensteiner H, Wierenga RK, Kastaniotis AJ, Gurvitz A. FEMS Microbiol. Rev. 27 35-64 (2003)
  2. Forty years of bacterial fatty acid synthesis. Rock CO, Jackowski S. Biochem. Biophys. Res. Commun. 292 1155-1166 (2002)
  3. The thiolase superfamily: condensing enzymes with diverse reaction specificities. Haapalainen AM, Meriläinen G, Wierenga RK. Trends Biochem. Sci. 31 64-71 (2006)
  4. The structures and physicochemical properties of organic cofactors in biocatalysis. Fischer JD, Holliday GL, Rahman SA, Thornton JM. J. Mol. Biol. 403 803-824 (2010)
  5. Two crystal structures of N-acetyltransferases reveal a new fold for CoA-dependent enzymes. Modis Y, Wierenga R. Structure 6 1345-1350 (1998)
  6. The structures and physicochemical properties of organic cofactors in biocatalysis. Fischer JD, Holliday GL, Rahman SA, Thornton JM. J. Mol. Biol. 403 803-824 (2010)
  7. The thiolase superfamily: condensing enzymes with diverse reaction specificities. Haapalainen AM, Meriläinen G, Wierenga RK. Trends Biochem. Sci. 31 64-71 (2006)
  8. The biochemistry of peroxisomal beta-oxidation in the yeast Saccharomyces cerevisiae. Hiltunen JK, Mursula AM, Rottensteiner H, Wierenga RK, Kastaniotis AJ, Gurvitz A. FEMS Microbiol. Rev. 27 35-64 (2003)
  9. Forty years of bacterial fatty acid synthesis. Rock CO, Jackowski S. Biochem. Biophys. Res. Commun. 292 1155-1166 (2002)
  10. Two crystal structures of N-acetyltransferases reveal a new fold for CoA-dependent enzymes. Modis Y, Wierenga R. Structure 6 1345-1350 (1998)

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  1. Multi-resolution contour-based fitting of macromolecular structures. Chacón P, Wriggers W. J. Mol. Biol. 317 375-384 (2002)
  2. Polygenic control of Caenorhabditis elegans fat storage. Mak HY, Nelson LS, Basson M, Johnson CD, Ruvkun G. Nat. Genet. 38 363-368 (2006)
  3. Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes. Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y. EMBO J. 17 1183-1191 (1998)
  4. Association of a lysine-232/alanine polymorphism in a bovine gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content. Winter A, Krämer W, Werner FA, Kollers S, Kata S, Durstewitz G, Buitkamp J, Womack JE, Thaller G, Fries R. Proc. Natl. Acad. Sci. U.S.A. 99 9300-9305 (2002)
  5. The 1.8 A crystal structure and active-site architecture of beta-ketoacyl-acyl carrier protein synthase III (FabH) from escherichia coli. Davies C, Heath RJ, White SW, Rock CO. Structure 8 185-195 (2000)
  6. The X-ray crystal structure of beta-ketoacyl [acyl carrier protein] synthase I. Olsen JG, Kadziola A, von Wettstein-Knowles P, Siggaard-Andersen M, Lindquist Y, Larsen S. FEBS Lett. 460 46-52 (1999)
  7. Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus. Hamelryck TW, Loris R, Bouckaert J, Dao-Thi MH, Strecker G, Imberty A, Fernandez E, Wyns L, Etzler ME. J. Mol. Biol. 286 1161-1177 (1999)
  8. Structures of beta-ketoacyl-acyl carrier protein synthase I complexed with fatty acids elucidate its catalytic machinery. Olsen JG, Kadziola A, von Wettstein-Knowles P, Siggaard-Andersen M, Larsen S. Structure 9 233-243 (2001)
  9. Crystallographic analysis of the reaction pathway of Zoogloea ramigera biosynthetic thiolase. Modis Y, Wierenga RK. J. Mol. Biol. 297 1171-1182 (2000)
  10. Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex. Ishikawa M, Tsuchiya D, Oyama T, Tsunaka Y, Morikawa K. EMBO J. 23 2745-2754 (2004)
  11. Molecular and phenotypic heterogeneity in mitochondrial trifunctional protein deficiency due to beta-subunit mutations. Spiekerkoetter U, Sun B, Khuchua Z, Bennett MJ, Strauss AW. Hum. Mutat. 21 598-607 (2003)
  12. Structures of type 2 peroxisomal targeting signals in two trypanosomatid aldolases. Chudzik DM, Michels PA, de Walque S, Hol WG. J. Mol. Biol. 300 697-707 (2000)
  13. The crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Synechocystis sp. at 1.54 A resolution and its relationship to other condensing enzymes. Moche M, Dehesh K, Edwards P, Lindqvist Y. J. Mol. Biol. 305 491-503 (2001)
  14. Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway. Pan H, Tsai Sc, Meadows ES, Miercke LJ, Keatinge-Clay AT, O'Connell J, Khosla C, Stroud RM. Structure 10 1559-1568 (2002)
  15. A biosynthetic thiolase in complex with a reaction intermediate: the crystal structure provides new insights into the catalytic mechanism. Modis Y, Wierenga RK. Structure 7 1279-1290 (1999)
  16. The 1.3-Angstrom-resolution crystal structure of beta-ketoacyl-acyl carrier protein synthase II from Streptococcus pneumoniae. Price AC, Rock CO, White SW. J. Bacteriol. 185 4136-4143 (2003)
  17. 2,4,6-trinitrotoluene reduction by an Fe-only hydrogenase in Clostridium acetobutylicum. Watrous MM, Clark S, Kutty R, Huang S, Rudolph FB, Hughes JB, Bennett GN. Appl. Environ. Microbiol. 69 1542-1547 (2003)
  18. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. Almonacid DE, Yera ER, Mitchell JB, Babbitt PC. PLoS Comput. Biol. 6 e1000700 (2010)
  19. Using reaction mechanism to measure enzyme similarity. O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. J. Mol. Biol. 368 1484-1499 (2007)
  20. Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate. Bera AK, Atanasova V, Robinson H, Eisenstein E, Coleman JP, Pesci EC, Parsons JF. Biochemistry 48 8644-8655 (2009)
  21. Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model. Kawabata T. Biophys. J. 95 4643-4658 (2008)
  22. High resolution crystal structures of human cytosolic thiolase (CT): a comparison of the active sites of human CT, bacterial thiolase, and bacterial KAS I. Kursula P, Sikkilä H, Fukao T, Kondo N, Wierenga RK. J. Mol. Biol. 347 189-201 (2005)
  23. Multi-resolution anchor-point registration of biomolecular assemblies and their components. Birmanns S, Wriggers W. J. Struct. Biol. 157 271-280 (2007)
  24. Descriptor-based protein remote homology identification. Zhang Z, Kochhar S, Grigorov MG. Protein Sci. 14 431-444 (2005)
  25. Evidence for catalytic cysteine-histidine dyad in chalcone synthase. Suh DY, Kagami J, Fukuma K, Sankawa U. Biochem. Biophys. Res. Commun. 275 725-730 (2000)
  26. Identification, purification and characterization of an acetoacetyl-CoA thiolase from rat liver peroxisomes. Antonenkov VD, Croes K, Waelkens E, Van Veldhoven PP, Mannaerts GP. Eur. J. Biochem. 267 2981-2990 (2000)
  27. Studies into factors contributing to substrate specificity of membrane-bound 3-ketoacyl-CoA synthases. Blacklock BJ, Jaworski JG. Eur. J. Biochem. 269 4789-4798 (2002)
  28. Targeted disruption of the peroxisomal thiolase B gene in mouse: a new model to study disorders related to peroxisomal lipid metabolism. Chevillard G, Clémencet MC, Latruffe N, Nicolas-Francès V. Biochimie 86 849-856 (2004)
  29. Characterisation of the gene family encoding acetoacetyl-CoA thiolase in Arabidopsis Ahumada Iván, Cairó Albert, Hemmerlin Andréa, González Víctor, Pateraki Irene, Bach ThomasJ, Rodríguez-Concepción Manuel, Campos Narciso, Boronat Albert. Funct. Plant Biol. 35 1100-1111 (2008)
  30. Peroxisomal plant 3-ketoacyl-CoA thiolase structure and activity are regulated by a sensitive redox switch. Pye VE, Christensen CE, Dyer JH, Arent S, Henriksen A. J. Biol. Chem. 285 24078-24088 (2010)
  31. The crystal structure of a plant 3-ketoacyl-CoA thiolase reveals the potential for redox control of peroxisomal fatty acid beta-oxidation. Sundaramoorthy R, Micossi E, Alphey MS, Germain V, Bryce JH, Smith SM, Leonard GA, Hunter WN. J. Mol. Biol. 359 347-357 (2006)
  32. Expression and purification of His-tagged rat mitochondrial 3-ketoacyl-CoA thiolase wild-type and His352 mutant proteins. Zeng J, Li D. Protein Expr. Purif. 35 320-326 (2004)
  33. The Saccharomyces cerevisiae RAD9, RAD17 and RAD24 genes are required for suppression of mutagenic post-replicative repair during chronic DNA damage. Murakami-Sekimata A, Huang D, Piening BD, Bangur C, Paulovich AG. DNA Repair (Amst.) 9 824-834 (2010)
  34. A template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes. Dawe JH, Porter CT, Thornton JM, Tabor AB. Proteins 52 427-435 (2003)
  35. A thermostable beta-ketothiolase of polyhydroxyalkanoates (PHAs) in Thermus thermophilus: purification and biochemical properties. Pantazaki AA, Ioannou AK, Kyriakidis DA. Mol. Cell. Biochem. 269 27-36 (2005)
  36. Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum. Kim S, Jang YS, Ha SC, Ahn JW, Kim EJ, Lim JH, Cho C, Ryu YS, Lee SK, Lee SY, Kim KJ. Nat Commun 6 8410 (2015)
  37. FadA5 a thiolase from Mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis. Schaefer CM, Lu R, Nesbitt NM, Schiebel J, Sampson NS, Kisker C. Structure 23 21-33 (2015)
  38. Crystal structures of SCP2-thiolases of Trypanosomatidae, human pathogens causing widespread tropical diseases: the importance for catalysis of the cysteine of the unique HDCF loop. Harijan RK, Kiema TR, Karjalainen MP, Janardan N, Murthy MR, Weiss MS, Michels PA, Wierenga RK. Biochem. J. 455 119-130 (2013)
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  40. Comprehensive transcription analysis of human pathogenic fungus Penicillium marneffei in mycelial and yeast cells. Lin X, Ran Y, Gou L, He F, Zhang R, Wang P, Dai Y. Med. Mycol. 50 835-842 (2012)
  41. Protein-protein interactions in the β-oxidation part of the phenylacetate utilization pathway: crystal structure of the PaaF-PaaG hydratase-isomerase complex. Grishin AM, Ajamian E, Zhang L, Rouiller I, Bostina M, Cygler M. J. Biol. Chem. 287 37986-37996 (2012)
  42. Cloning, expression, and purification of glyoxysomal 3-oxoacyl-CoA thiolase from sunflower cotyledons. Schiedel AC, Oeljeklaus S, Minihan P, Dyer JH. Protein Expr. Purif. 33 25-33 (2004)
  43. The native molecular size of alkyl-dihydroxyacetonephosphate synthase and dihydroxyacetonephosphate acyltransferase. Biermann J, Schoonderwoerd K, Hom ML, Luthjens LH, Van den Bosch H. Biochim. Biophys. Acta 1393 137-142 (1998)
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  50. The SCP2-thiolase-like protein (SLP) of Trypanosoma brucei is an enzyme involved in lipid metabolism. Harijan RK, Mazet M, Kiema TR, Bouyssou G, Alexson SE, Bergmann U, Moreau P, Michels PA, Bringaud F, Wierenga RK. Proteins 84 1075-1096 (2016)