Structural biology of the thioester-dependent degradation and synthesis of fatty acids

Current Opinion in Structural Biology

Volumn 15, Issue 6, 2005, Pages 621-628

  Bhaumik, Prasenjit ^a   Koski, M Kristian ^a   Glumoff, Tuomo ^a   Hiltunen, J Kalervo ^a   Wierenga, Rik K ^a  

^a UNIVERSITY OF OULU   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL CARRIER PROTEIN; COENZYME A; FATTY ACID; THIOESTER;

CATALYSIS; CYTOSOL; ENZYMATIC DEGRADATION; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SYNTHESIS; EUKARYOTIC CELL; FATTY ACID OXIDATION; FATTY ACID SYNTHESIS; LIPID METABOLISM; MITOCHONDRION; NONHUMAN; PEROXISOME; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW; STRUCTURE ANALYSIS;

ACYL CARRIER PROTEIN; ANIMALS; COENZYME A; CYTOSOL; ENOYL-COA HYDRATASE; FATTY ACID SYNTHETASE COMPLEX; FATTY ACIDS; HUMANS; MITOCHONDRIA; MODELS, MOLECULAR; MULTIENZYME COMPLEXES; OXIDATION-REDUCTION; PEROXISOMES; PROTEIN CONFORMATION; SULFHYDRYL COMPOUNDS;

EUKARYOTA;

EID: 27944432550     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.10.010     Document Type: Review

References (48)

1. N. Gregersen, P. Bross, and B.S. Andresen Genetic defects in fatty acid β-oxidation and acyl-CoA dehydrogenases. Molecular pathogenesis and genotype-phenotype relationships Eur J Biochem 271 2004 470 482
2. R.J. Wanders Peroxisomes, lipid metabolism, and peroxisomal disorders Mol Genet Metab 83 2004 16 27
3. R.J. Heath, and C.O. Rock Fatty acid biosynthesis as a target for novel antibacterials Curr Opin Investig Drugs 5 2004 146 153
4. Y.M. Zhang, Y.J. Lu, and C.O. Rock The reductase steps of the type II fatty acid synthase as antimicrobial targets Lipids 39 2004 1055 1060
5. C.K. Matthews K.E. van Holde K.G. Ahern Biochemistry 2000 Addison Wesley Longman
6. H.M. Holden, M.M. Benning, T. Haller, and J.A. Gerlt The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme A thioesters Acc Chem Res 34 2001 145 157
7. P. Kursula, J. Ojala, A.-M. Lambeir, and R.K. Wierenga The catalytic cycle of biosynthetic thiolase: a conformational journey of an acetyl group through four binding modes and two oxyanion holes Biochemistry 41 2002 15543 15556
8. X. Qiu, and C.A. Janson Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions Acta Crystallogr D Biol Crystallogr 60 2004 1545 1554
9. M.A. Reed, M. Schweizer, A.E. Szafranska, C. Arthur, T.P. Nicholson, R.J. Cox, J. Crosby, M.P. Crump, and T.J. Simpson The type I rat fatty acid synthase ACP shows structural homology and analogous biochemical properties to type II ACPs Org Biomol Chem 1 2003 463 471
10. J.-J.P. Kim, and K.P. Battaile Burning fat: the structural basis of fatty acid β-oxidation Curr Opin Struct Biol 12 2002 721 728
11. K. Bartlett, and S. Eaton Mitochondrial β-oxidation Eur J Biochem 271 2004 462 469
12. J.K. Hiltunen, A.M. Mursula, H. Rottensteiner, R.K. Wierenga, A.J. Kastaniotis, and A. Gurvitz The biochemistry of peroxisomal β-oxidation in the yeast Saccharomyces cerevisiae FEMS Microbiol Rev 27 2003 35 64
13. C.W.T. van Roermund, H.R. Waterham, L. Ijlst, and R.J.A. Wanders Fatty acid metabolism in Saccharomyces cerevisiae Cell Mol Life Sci 60 2003 1838 1851
14. W.H. Kunau, V. Dommes, and H. Schulz β-Oxidation of fatty acids in mitochondria, peroxisomes, and bacteria: a century of continued progress Prog Lipid Res 34 1995 267 342
15. J.K. Hiltunen, and Y.-M. Qin β-Oxidation - strategies for the metabolism of a wide variety of acyl-CoA esters Biochim Biophys Acta 1484 2000 117 128
16. Y. Modis, S.A. Filppula, D.K. Novikov, B. Norledge, J.K. Hiltunen, and R.K. Wierenga The crystal structure of dienoyl-CoA isomerase at 1.5 Å resolution reveals the importance of aspartate and glutamate side chains for catalysis Structure 6 1998 957 970
17. P.A. Hubbard, X. Liang, H. Schulz, and J.-J.P. Kim The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase J Biol Chem 278 2003 37553 37560
18. M.S. Alphey, W. Yu, E. Byres, D. Li, and W.N. Hunter 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
19. 2-enoyl-CoA isomerase shows a novel mode of binding for the fatty acyl group J Mol Biol 342 2004 1197 1208
20. 2-enoyl-CoA isomerase Protein Sci 14 2005 1545 1555
21. D.W. Russell The enzymes, regulation, and genetics of bile acid synthesis Annu Rev Biochem 72 2003 137 174
22. K. Savolainen, P. Bhaumik, W. Schmitz, T.J. Kotti, E. Conzelmann, R.K. Wierenga, and J.K. Hiltunen α-Methylacyl-CoA racemase from Mycobacterium tuberculosis - mutational and structural characterization of the active site and the fold J Biol Chem 280 2005 12611 12620
23. S. Smith, A. Witkowski, and A.K. Joshi Structural and functional organization of the animal fatty acid synthase Prog Lipid Res 42 2003 289 317
24. S.W. White, J. Zheng, Y.-M. Zhang, and C.O. Rock The structural biology of type II fatty acid biosynthesis Annu Rev Biochem 74 2005 791 831 The known structures of bacterial FAS-II enzymes are extensively reviewed.
25. J.-J.P. Kim, and R. Miura Acyl-CoA dehydrogenases and acyl-CoA oxidases. Structural basis for mechanistic similarities and differences Eur J Biochem 271 2004 483 493 The X-ray structures and different substrate specificities of acyl-CoA dehydrogenases and acyl-CoA oxidases are discussed in this review article.
26. H.S. Toogood, A. van Thiel, J. Basran, M.J. Sutcliffe, N.S. Scrutton, and D. Leys Extensive domain motion and electron transfer in the human electron transferring flavoprotein-medium chain acyl-CoA dehydrogenase complex J Biol Chem 279 2004 32904 32912 The structure of the complex between the electron transferring flavoprotein and medium-chain acyl-CoA dehydrogenase highlights the importance of structural disorder of the FAD-containing ETF domain. It is speculated that this disorder allows the efficient sampling of a range of conformations, some of which are compatible with efficient interprotein electron transfer.
27. Y. Nakajima, I. Miyahara, K. Hirotsu, Y. Nishina, K. Shiga, C. Setoyama, H. Tamaoki, and R. Miura Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase J Biochem (Tokyo) 131 2002 365 374
28. L. Pedersen, and A. Henriksen Acyl-CoA oxidase 1 from Arabidopsis thaliana. Structure of a key enzyme in plant lipid metabolism J Mol Biol 345 2005 487 500
29. T.-R. Kiema, J.P. Taskinen, P.L. Pirilä, K.T. Koivuranta, R.K. Wierenga, and J.K. Hiltunen Organization of the multifunctional enzyme type 1: interaction between N- and C-terminal domains is required for the hydratase-1/isomerase activity Biochem J 367 2002 433 441
30. M.K. Koski, A.M. Haapalainen, J.K. Hiltunen, and T. Glumoff A two-domain structure of one subunit explains unique features of eukaryotic hydratase 2 J Biol Chem 279 2004 24666 24672
31. M.K. Koski, A.M. Haapalainen, J.K. Hiltunen, and T. Glumoff Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2 J Mol Biol 345 2005 1157 1169 The crystal structure of the hydratase-2 domain of human MFE-2, together with previously published structures of the dehydrogenase domains of mammalian MFE-2, suggests the quaternary structure of the mammalian MFE-2 dimer.
32. S.C. Dillon, and A. Bateman The hotdog fold: wrapping up a superfamily of thioesterase and dehydratases BMC Bioinformatics 5 2004 109
33. J.J. Barycki, L.K. O'Brien, A.W. Strauss, and L.J. Banaszak 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
34. J.J. Barycki, L.K. O'Brien, A.W. Strauss, and L.J. Banaszak Glutamate 170 of human L-3-hydroxyacyl-CoA dehydrogenase is required for proper orientation of the catalytic histidine and structural integrity of the enzyme J Biol Chem 276 2001 36718 36726
35. A.M. Haapalainen, M.K. Koski, Y.-M. Qin, J.K. Hiltunen, and T. Glumoff Binary structure of the two-domain (3R)-hydroxyacyl-CoA dehydrogenase from rat peroxisomal multifunctional enzyme type 2 at 2.38 Å resolution Structure 11 2003 87 97
36. U. Oppermann, C. Filling, M. Hult, N. Shafqat, X. Wu, M. Lindh, J. Shafqat, E. Nordling, Y. Kallberg, B. Persson, and H. Jörnvall Short-chain dehydrogenases/reductases (SDR): the 2002 update Chem Biol Interact 143-144 2003 247 253
37. R.J. Heath, and C.O. Rock The Claisen condensation in biology Nat Prod Rep 19 2002 581 596
38. J.G. Olsen, A.V. Rasmussen, P. von Wettstein-Knowles, and A. Henriksen Structure of the mitochondrial β-ketoacyl-[acyl carrier protein] synthase from Arabidopsis and its role in fatty acid synthesis FEBS Lett 577 2004 170 174 The first structure of a mitochondrial KAS enzyme is reported. Sequence identity to E. coli KAS-II is as high as 50% and the structure also shows that it belongs to the KAS-I/KAS-II family of the thiolase superfamily.
39. D. Kostrewa, F.K. Winkler, G. Folkers, L. Scapozza, and R. Perozzo The crystal structure of PfFabZ, the unique β-hydroxyacyl-ACP dehydratase involved in fatty acid biosynthesis of Plasmodium falciparum Protein Sci 14 2005 1570 1580
40. T.T. Airenne, J.M. Torkko, S. Van den plas, R.T. Sormunen, A.J. Kastaniotis, R.K. Wierenga, and J.K. Hiltunen Structure-function analysis of enoyl thioester reductase involved in mitochondrial maintenance J Mol Biol 327 2003 47 59 The first structure of a mitochondrial enoyl thioester reductase is discussed. It is shown to belong to the MDR superfamily.
41. H. Jörnvall, E. Nordling, and B. Persson Multiplicity of eukaryotic ADH and other MDR forms Chem Biol Interact 143-144 2003 255 261
42. A.M. Haapalainen, D.M. van Aalten, G. Meriläinen, J.E. Jalonen, P. Pirilä, R.K. Wierenga, J.K. Hiltunen, and T. Glumoff Crystal structure of the liganded SCP-2-like domain of human peroxisomal multifunctional enzyme type 2 at 1.75 Å resolution J Mol Biol 313 2001 1127 1138
43. 2 complex, which handles large, polar substrates. The active sites face a common polar cavity; the possible channelling mechanism is referred to as a substrate-anchored diffusion mechanism.
44. B. Chakravarty, Z. Gu, S.S. Chirala, S.J. Wakil, and F.A. Quiocho Human fatty acid synthase: structure and substrate selectivity of the thioesterase domain Proc Natl Acad Sci USA 101 2004 15567 15572
45. A. Witkowski, A. Ghosal, A.K. Joshi, H.E. Witkowska, F.J. Asturias, and S. Smith Head-to-head coiled arrangement of the subunits of the animal fatty acid synthase Chem Biol 11 2004 1667 1676
46. J. Brink, S.J. Ludtke, C.Y. Yang, Z.W. Gu, S.J. Wakil, and W. Chiu Quaternary structure of human fatty acid synthase by electron cryomicroscopy Proc Natl Acad Sci USA 99 2002 138 143
47. F.J. Asturias, J.Z. Chadick, I.K. Cheung, H. Stark, A. Witkowski, A.K. Joshi, and S. Smith Structure and molecular organization of mammalian fatty acid synthase Nat Struct Mol Biol 12 2005 225 232 This EM structure is the highest resolution structure available for the animal FAS-I dimer. It reveals a coiled structure of the two subunits, which dimerize via the KAS domains.
48. R. Yasuno, P. von Wettstein-Knowles, and H. Wada Identification and molecular characterization of the β-ketoacyl-[acyl carrier protein] synthase component of the Arabidopsis mitochondrial fatty acid synthase J Biol Chem 279 2004 8242 8251