1ivh › Citations

Structure of human isovaleryl-CoA dehydrogenase at 2.6 A resolution: structural basis for substrate specificity,.

Tiffany KA, Roberts DL, Wang M, Paschke R, Mohsen AW, Vockley J, Kim JJ
Biochemistry 36 8455-64 (1997)
Cited: 69 times
EuropePMC logo PMID: 9214289

Abstract

Isovaleryl-CoA dehydrogenase (IVD) belongs to an important flavoprotein family of acyl-CoA dehydrogenases that catalyze the alpha,beta-dehydrogenation of their various thioester substrates. Although enzymes from this family share similar sequences, catalytic mechanisms, and structural properties, the position of the catalytic base in the primary sequence is not conserved. E376 has been confirmed to be the catalytic base in medium-chain (MCAD) and short-chain acyl-CoA dehydrogenases and is conserved in all members of the acyl-CoA dehydrogenase family except for IVD and long-chain acyl-CoA dehydrogenase. To understand this dichotomy and to gain a better understanding of the factors important in determining substrate specificity in this enzyme family, the three-dimensional structure of human IVD has been determined. Human IVD expressed in Escherichia coli crystallizes in the orthorhombic space group P212121 with unit cell parameters a = 94.0 A, b = 97.7 A, and c = 181.7 A. The structure of IVD was solved at 2.6 A resolution by the molecular replacement method and was refined to an R-factor of 20.7% with an Rfree of 28.8%. The overall polypeptide fold of IVD is similar to that of other members of this family for which structural data are available. The tightly bound ligand found in the active site of the structure of IVD is consistent with that of CoA persulfide. The identity of the catalytic base was confirmed to be E254, in agreement with previous molecular modeling and mutagenesis studies. The location of the catalytic residue together with a glycine at position 374, which is a tyrosine in all other members of the acyl-CoA dehydrogenase family, is important for conferring branched-chain substrate specificity to IVD.

Articles - 1ivh mentioned but not cited (17)

  1. Identification of the human mitochondrial linoleoyl-coenzyme A monolysocardiolipin acyltransferase (MLCL AT-1). Taylor WA, Hatch GM. J Biol Chem 284 30360-30371 (2009)
  2. Mycobacterium tuberculosis utilizes a unique heterotetrameric structure for dehydrogenation of the cholesterol side chain. Thomas ST, Sampson NS. Biochemistry 52 2895-2904 (2013)
  3. Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover. Nagpal A, Valley MP, Fitzpatrick PF, Orville AM. Biochemistry 45 1138-1150 (2006)
  4. Different spectrum of mutations of isovaleryl-CoA dehydrogenase (IVD) gene in Korean patients with isovaleric acidemia. Lee YW, Lee DH, Vockley J, Kim ND, Lee YK, Ki CS. Mol Genet Metab 92 71-77 (2007)
  5. Structure and DNA binding of alkylation response protein AidB. Bowles T, Metz AH, O'Quin J, Wawrzak Z, Eichman BF. Proc Natl Acad Sci U S A 105 15299-15304 (2008)
  6. Characterization of novel acyl coenzyme A dehydrogenases involved in bacterial steroid degradation. Ruprecht A, Maddox J, Stirling AJ, Visaggio N, Seah SY. J Bacteriol 197 1360-1367 (2015)
  7. Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization. Rajgaria R, McAllister SR, Floudas CA. Proteins 74 929-947 (2009)
  8. Evidence for involvement of medium chain acyl-CoA dehydrogenase in the metabolism of phenylbutyrate. Kormanik K, Kang H, Cuebas D, Vockley J, Mohsen AW. Mol Genet Metab 107 684-689 (2012)
  9. Insights into Thiotemplated Pyrrole Biosynthesis Gained from the Crystal Structure of Flavin-Dependent Oxidase in Complex with Carrier Protein. Thapa HR, Robbins JM, Moore BS, Agarwal V. Biochemistry 58 918-929 (2019)
  10. The common K333Q polymorphism in long-chain acyl-CoA dehydrogenase (LCAD) reduces enzyme stability and function. Beck ME, Zhang Y, Bharathi SS, Kosmider B, Bahmed K, Dahmer MK, Nogee LM, Goetzman ES. Mol Genet Metab 131 83-89 (2020)
  11. Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis. Duan X, Zhang L, Zhou D, Ji K, Ma T, Shui W, Li G, Li X. Acta Crystallogr Sect F Struct Biol Cryst Commun 69 597-601 (2013)
  12. Kinetic and spectral properties of isovaleryl-CoA dehydrogenase and interaction with ligands. Mohsen AW, Vockley J. Biochimie 108 108-119 (2015)
  13. 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7(T): crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Schürmann M, Meijers R, Schneider TR, Steinbüchel A, Cianci M. Acta Crystallogr D Biol Crystallogr 71 1360-1372 (2015)
  14. Characterization of variants of uncertain significance in isovaleryl-CoA dehydrogenase identified through newborn screening: An approach for faster analysis. D'Annibale OM, Koppes EA, Alodaib AN, Kochersperger C, Karunanidhi A, Mohsen AW, Vockley J. Mol Genet Metab 134 29-36 (2021)
  15. Structural basis for substrate specificity of methylsuccinyl-CoA dehydrogenase, an unusual member of the acyl-CoA dehydrogenase family. Schwander T, McLean R, Zarzycki J, Erb TJ. J Biol Chem 293 1702-1712 (2018)
  16. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)
  17. Benzylmalonyl-CoA dehydrogenase, an enzyme involved in bacterial auxin degradation. Schühle K, Saft M, Vögeli B, Erb TJ, Heider J. Arch Microbiol 203 4149-4159 (2021)


Reviews citing this publication (6)

  1. Sequence-structure analysis of FAD-containing proteins. Dym O, Eisenberg D. Protein Sci 10 1712-1728 (2001)
  2. Acyl-CoA dehydrogenases and acyl-CoA oxidases. Structural basis for mechanistic similarities and differences. Kim JJ, Miura R. Eur J Biochem 271 483-493 (2004)
  3. Enzymes involved in branched-chain amino acid metabolism in humans. Adeva-Andany MM, López-Maside L, Donapetry-García C, Fernández-Fernández C, Sixto-Leal C. Amino Acids 49 1005-1028 (2017)
  4. Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response. Zhao L. Enzymes 45 311-341 (2019)
  5. Structure and function of plant acyl-CoA oxidases. Arent S, Pye VE, Henriksen A. Plant Physiol Biochem 46 292-301 (2008)
  6. Two crystal structures of N-acetyltransferases reveal a new fold for CoA-dependent enzymes. Modis Y, Wierenga R. Structure 6 1345-1350 (1998)

Articles citing this publication (46)

  1. Conversion of L-proline to pyrrolyl-2-carboxyl-S-PCP during undecylprodigiosin and pyoluteorin biosynthesis. Thomas MG, Burkart MD, Walsh CT. Chem Biol 9 171-184 (2002)
  2. Deciphering tuberactinomycin biosynthesis: isolation, sequencing, and annotation of the viomycin biosynthetic gene cluster. Thomas MG, Chan YA, Ozanick SG. Antimicrob Agents Chemother 47 2823-2830 (2003)
  3. Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct. Busquets C, Merinero B, Christensen E, Gelpí JL, Campistol J, Pineda M, Fernández-Alvarez E, Prats JM, Sans A, Arteaga R, Martí M, Campos J, Martínez-Pardo M, Martínez-Bermejo A, Ruiz-Falcó ML, Vaquerizo J, Orozco M, Ugarte M, Coll MJ, Ribes A. Pediatr Res 48 315-322 (2000)
  4. Acyl-CoA dehydrogenases: Dynamic history of protein family evolution. Swigonová Z, Mohsen AW, Vockley J. J Mol Evol 69 176-193 (2009)
  5. The mitochondrial isovaleryl-coenzyme a dehydrogenase of arabidopsis oxidizes intermediates of leucine and valine catabolism. Däschner K, Couée I, Binder S. Plant Physiol 126 601-612 (2001)
  6. Structural basis for substrate fatty acyl chain specificity: crystal structure of human very-long-chain acyl-CoA dehydrogenase. McAndrew RP, Wang Y, Mohsen AW, He M, Vockley J, Kim JJ. J Biol Chem 283 9435-9443 (2008)
  7. Human acyl-CoA dehydrogenase-9 plays a novel role in the mitochondrial beta-oxidation of unsaturated fatty acids. Ensenauer R, He M, Willard JM, Goetzman ES, Corydon TJ, Vandahl BB, Mohsen AW, Isaya G, Vockley J. J Biol Chem 280 32309-32316 (2005)
  8. Functional analysis of substrate and cofactor complex structures of a thymidylate synthase-complementing protein. Mathews II, Deacon AM, Canaves JM, McMullan D, Lesley SA, Agarwalla S, Kuhn P. Structure 11 677-690 (2003)
  9. Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with acetoacetyl-CoA: comparison with other acyl-CoA dehydrogenases. Battaile KP, Molin-Case J, Paschke R, Wang M, Bennett D, Vockley J, Kim JJ. J Biol Chem 277 12200-12207 (2002)
  10. Identification of isobutyryl-CoA dehydrogenase and its deficiency in humans. Nguyen TV, Andresen BS, Corydon TJ, Ghisla S, Abd-El Razik N, Mohsen AW, Cederbaum SD, Roe DS, Roe CR, Lench NJ, Vockley J. Mol Genet Metab 77 68-79 (2002)
  11. Structures of isobutyryl-CoA dehydrogenase and enzyme-product complex: comparison with isovaleryl- and short-chain acyl-CoA dehydrogenases. Battaile KP, Nguyen TV, Vockley J, Kim JJ. J Biol Chem 279 16526-16534 (2004)
  12. Shrinking the FadE proteome of Mycobacterium tuberculosis: insights into cholesterol metabolism through identification of an α2β2 heterotetrameric acyl coenzyme A dehydrogenase family. Wipperman MF, Yang M, Thomas ST, Sampson NS. J Bacteriol 195 4331-4341 (2013)
  13. Human METTL20 is a mitochondrial lysine methyltransferase that targets the β subunit of electron transfer flavoprotein (ETFβ) and modulates its activity. Małecki J, Ho AY, Moen A, Dahl HA, Falnes PØ. J Biol Chem 290 423-434 (2015)
  14. Expression and characterization of mutations in human very long-chain acyl-CoA dehydrogenase using a prokaryotic system. Goetzman ES, Wang Y, He M, Mohsen AW, Ninness BK, Vockley J. Mol Genet Metab 91 138-147 (2007)
  15. The chemistry of protein catalysis. Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. J Mol Biol 372 1261-1277 (2007)
  16. Acyl-CoA oxidase 1 from Arabidopsis thaliana. Structure of a key enzyme in plant lipid metabolism. Pedersen L, Henriksen A. J Mol Biol 345 487-500 (2005)
  17. Purification, characterization and cloning of isovaleryl-CoA dehydrogenase from higher plant mitochondria. Faivre-Nitschke SE, Couée I, Vermel M, Grienenberger JM, Gualberto JM. Eur J Biochem 268 1332-1339 (2001)
  18. A novel approach to the characterization of substrate specificity in short/branched chain Acyl-CoA dehydrogenase. He M, Burghardt TP, Vockley J. J Biol Chem 278 37974-37986 (2003)
  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. Genetic mutation profile of isovaleric acidemia patients in Taiwan. Lin WD, Wang CH, Lee CC, Lai CC, Tsai Y, Tsai FJ. Mol Genet Metab 90 134-139 (2007)
  21. Characterization of new ACADSB gene sequence mutations and clinical implications in patients with 2-methylbutyrylglycinuria identified by newborn screening. Alfardan J, Mohsen AW, Copeland S, Ellison J, Keppen-Davis L, Rohrbach M, Powell BR, Gillis J, Matern D, Kant J, Vockley J. Mol Genet Metab 100 333-338 (2010)
  22. Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases. Shen YQ, Lang BF, Burger G. Nucleic Acids Res 37 5619-5631 (2009)
  23. Impact of Branched-Chain Amino Acid Catabolism on Fatty Acid and Alkene Biosynthesis in Micrococcus luteus. Surger MJ, Angelov A, Stier P, Übelacker M, Liebl W. Front Microbiol 9 374 (2018)
  24. The METTL20 Homologue from Agrobacterium tumefaciens Is a Dual Specificity Protein-lysine Methyltransferase That Targets Ribosomal Protein L7/L12 and the β Subunit of Electron Transfer Flavoprotein (ETFβ). Małecki J, Dahl HA, Moen A, Davydova E, Falnes PØ. J Biol Chem 291 9581-9595 (2016)
  25. Pathogenic mutations in the carboxyl-terminal domain of glutaryl-CoA dehydrogenase: effects on catalytic activity and the stability of the tetramer. Westover JB, Goodman SI, Frerman FE. Mol Genet Metab 79 245-256 (2003)
  26. Identification of Caenorhabditis elegans isovaleryl-CoA dehydrogenase and structural comparison with other acyl-CoA dehydrogenases. Mohsen AW, Navarette B, Vockley J. Mol Genet Metab 73 126-137 (2001)
  27. Role of isovaleryl-CoA dehydrogenase and short branched-chain acyl-CoA dehydrogenase in the metabolism of valproic acid: implications for the branched-chain amino acid oxidation pathway. Luís PB, Ruiter JP, Ijlst L, Tavares de Almeida I, Duran M, Mohsen AW, Vockley J, Wanders RJ, Silva MF. Drug Metab Dispos 39 1155-1160 (2011)
  28. Crystallization and preliminary analysis of active nitroalkane oxidase in three crystal forms. Nagpal A, Valley MP, Fitzpatrick PF, Orville AM. Acta Crystallogr D Biol Crystallogr 60 1456-1460 (2004)
  29. MoIVD-Mediated Leucine Catabolism Is Required for Vegetative Growth, Conidiation and Full Virulence of the Rice Blast Fungus Magnaporthe oryzae. Li Y, Zheng X, Zhu M, Chen M, Zhang S, He F, Chen X, Lv J, Pei M, Zhang Y, Zhang Y, Wang W, Zhang J, Wang M, Wang Z, Li G, Lu G. Front Microbiol 10 444 (2019)
  30. Flavin-induced oligomerization in Escherichia coli adaptive response protein AidB. Hamill MJ, Jost M, Wong C, Elliott SJ, Drennan CL. Biochemistry 50 10159-10169 (2011)
  31. Structural insights into the stabilization of active, tetrameric DszC by its C-terminus. Zhang L, Duan X, Zhou D, Dong Z, Ji K, Meng W, Li G, Li X, Yang H, Ma T, Rao Z. Proteins 82 2733-2743 (2014)
  32. Structure of the prolyl-acyl carrier protein oxidase involved in the biosynthesis of the cyanotoxin anatoxin-a. Moncoq K, Regad L, Mann S, Méjean A, Ploux O. Acta Crystallogr D Biol Crystallogr 69 2340-2352 (2013)
  33. Arginine 387 of human isovaleryl-CoA dehydrogenase plays a crucial role in substrate/product binding. Volchenboum SL, Mohsen AW, Kim JJ, Vockley J. Mol Genet Metab 74 226-237 (2001)
  34. Functional characterization of rat glutaryl-CoA dehydrogenase and its comparison with straight-chain acyl-CoA dehydrogenase. Wu L, Qiao Y, Gao J, Deng G, Yu W, Chen G, Li D. Bioorg Med Chem Lett 21 6667-6673 (2011)
  35. Identification and functional analysis of genes required for desulfurization of alkyl dibenzothiophenes of Mycobacterium sp. G3. Nomura N, Takada M, Okada H, Shinohara Y, Nakajima-Kambe T, Nakahara T, Uchiyama H. J Biosci Bioeng 100 398-402 (2005)
  36. The roles of threonine-136 and glutamate-137 of human medium chain acyl-CoA dehydrogenase in FAD binding and peptide folding using site-directed mutagenesis: creation of an FAD-dependent mutant, T136D. Saijo T, Kim JJ, Kuroda Y, Tanaka K. Arch Biochem Biophys 358 49-57 (1998)
  37. A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket. Chai AF, Bulloch EM, Evans GL, Lott JS, Baker EN, Johnston JM. Acta Crystallogr D Biol Crystallogr 71 862-872 (2015)
  38. Two novel isovaleryl-CoA dehydrogenase gene mutations in a Chinese infant. Bei F, Sun JH, Yu YG, Jia J, Zheng ZJ, Fu QH, Cai W. Gene 524 396-400 (2013)
  39. Cloning of genomic and cDNA for mouse isovaleryl-CoA dehydrogenase (IVD) and evolutionary comparison to other known IVDs. Willard JM, Reinard T, Mohsen A, Vockley J. Gene 270 253-257 (2001)
  40. Functional analysis of acyl-CoA dehydrogenase catalytic residue mutants using surface plasmon resonance and circular dichroism. Goetzman ES, He M, Nguyen TV, Vockley J. Mol Genet Metab 87 233-242 (2006)
  41. Molecular defect of isovaleryl-CoA dehydrogenase in the skunk mutant of silkworm, Bombyx mori. Urano K, Daimon T, Banno Y, Mita K, Terada T, Shimizu K, Katsuma S, Shimada T. FEBS J 277 4452-4463 (2010)
  42. Comparative studies of Acyl-CoA dehydrogenases for monomethyl branched chain substrates in amino acid metabolism. Liu X, Wu L, Deng G, Chen G, Li N, Chu X, Li D. Bioorg Chem 47 1-8 (2013)
  43. Mechanism-based inactivation of human glutaryl-CoA dehydrogenase by 2-pentynoyl-CoA: rationale for enhanced reactivity. Rao KS, Albro M, Vockley J, Frerman FE. J Biol Chem 278 26342-26350 (2003)
  44. Case Reports Analysis of the genotype-phenotype correlation in isovaleric acidaemia: A case report of long-term follow-up of a chinese patient and literature review. Liu X, Liu X, Fan W, Zhang Z, Zhang P, Liu X, Lei M, Li Q, Yu X, Li D. Front Neurol 13 928334 (2022)
  45. FT-IR spectroscopic studies on the molecular mechanism for substrate specificity/activation of medium-chain acyl-CoA dehydrogenase. Nishina Y, Sato K, Tamaoki H, Setoyama C, Miura R, Shiga K. J Biochem 146 351-357 (2009)
  46. High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. Zhang Z, Tringides ML, Morgan CE, Miyagi M, Mears JA, Hoppel CL, Yu EW. Mol Cell Proteomics 22 100666 (2023)


Quick links