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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 12200-7 (2002)
Cited: 54 times
EuropePMC logo PMID: 11812788

Abstract

The acyl-CoA dehydrogenases are a family of flavin adenine dinucleotide-containing enzymes that catalyze the first step in the beta-oxidation of fatty acids and catabolism of some amino acids. They exhibit high sequence identity and yet are quite specific in their substrate binding. Short chain acyl-CoA dehydrogenase has maximal activity toward butyryl-CoA and negligible activity toward substrates longer than octanoyl-CoA. The crystal structure of rat short chain acyl-CoA dehydrogenase complexed with the inhibitor acetoacetyl-CoA has been determined at 2.25 A resolution. Short chain acyl-CoA dehydrogenase is a homotetramer with a subunit mass of 43 kDa and crystallizes in the space group P321 with a = 143.61 A and c = 77.46 A. There are two monomers in the asymmetric unit. The overall structure of short chain acyl-CoA dehydrogenase is very similar to those of medium chain acyl-CoA dehydrogenase, isovaleryl-CoA dehydrogenase, and bacterial short chain acyl-CoA dehydrogenase with a three-domain structure composed of N- and C-terminal alpha-helical domains separated by a beta-sheet domain. Comparison to other acyl-CoA dehydrogenases has provided additional insight into the basis of substrate specificity and the nature of the oxidase activity in this enzyme family. Ten reported pathogenic human mutations and two polymorphisms have been mapped onto the structure of short chain acyl-CoA dehydrogenase. None of the mutations directly affect the binding cavity or intersubunit interactions.

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  2. 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)
  3. The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein. Rohankhedkar MS, Mulrooney SB, Wedemeyer WJ, Hausinger RP. J Bacteriol 188 223-230 (2006)
  4. In silico identification of epitopes in Mycobacterium avium subsp. paratuberculosis proteins that were upregulated under stress conditions. Gurung RB, Purdie AC, Begg DJ, Whittington RJ. Clin Vaccine Immunol 19 855-864 (2012)
  5. Structure and mechanism of ORF36, an amino sugar oxidizing enzyme in everninomicin biosynthesis . Vey JL, Al-Mestarihi A, Hu Y, Funk MA, Bachmann BO, Iverson TM. Biochemistry 49 9306-9317 (2010)
  6. Potential of mean force calculation for the proton and hydride transfer reactions catalyzed by medium-chain acyl-CoA dehydrogenase: effect of mutations on enzyme catalysis. Bhattacharyya S, Ma S, Stankovich MT, Truhlar DG, Gao J. Biochemistry 44 16549-16562 (2005)
  7. Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs. Butler BM, Kazan IC, Kumar A, Ozkan SB. PLoS Comput Biol 14 e1006626 (2018)
  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. PatchSurfers: Two methods for local molecular property-based binding ligand prediction. Shin WH, Bures MG, Kihara D. Methods 93 41-50 (2016)
  10. 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)
  11. Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria. Chen X, Chen J, Yan B, Zhang W, Guddat LW, Liu X, Rao Z. Proc Natl Acad Sci U S A 117 16324-16332 (2020)
  12. 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)
  13. Kinetic and spectral properties of isovaleryl-CoA dehydrogenase and interaction with ligands. Mohsen AW, Vockley J. Biochimie 108 108-119 (2015)
  14. 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)
  15. 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)


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  2. Genetic defects in fatty acid beta-oxidation and acyl-CoA dehydrogenases. Molecular pathogenesis and genotype-phenotype relationships. Gregersen N, Bross P, Andresen BS. Eur J Biochem 271 470-482 (2004)
  3. Short-chain acyl-coenzyme A dehydrogenase deficiency. Jethva R, Bennett MJ, Vockley J. Mol Genet Metab 95 195-200 (2008)
  4. Nitroalkane oxidase, a carbanion-forming flavoprotein homologous to acyl-CoA dehydrogenase. Fitzpatrick PF, Orville AM, Nagpal A, Valley MP. Arch Biochem Biophys 433 157-165 (2005)
  5. Structure and function of plant acyl-CoA oxidases. Arent S, Pye VE, Henriksen A. Plant Physiol Biochem 46 292-301 (2008)
  6. Short-chain acyl-CoA dehydrogenase deficiency: from gene to cell pathology and possible disease mechanisms. Nochi Z, Olsen RKJ, Gregersen N. J Inherit Metab Dis 40 641-655 (2017)

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  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. Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism. Yeh JI, Chinte U, Du S. Proc Natl Acad Sci U S A 105 3280-3285 (2008)
  4. Acyl-CoA dehydrogenases: Dynamic history of protein family evolution. Swigonová Z, Mohsen AW, Vockley J. J Mol Evol 69 176-193 (2009)
  5. Misfolding, degradation, and aggregation of variant proteins. The molecular pathogenesis of short chain acyl-CoA dehydrogenase (SCAD) deficiency. Pedersen CB, Bross P, Winter VS, Corydon TJ, Bolund L, Bartlett K, Vockley J, Gregersen N. J Biol Chem 278 47449-47458 (2003)
  6. Acyl-CoA Dehydrogenase Drives Heat Adaptation by Sequestering Fatty Acids. Ma DK, Li Z, Lu AY, Sun F, Chen S, Rothe M, Menzel R, Sun F, Horvitz HR. Cell 161 1152-1163 (2015)
  7. 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)
  8. 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)
  9. (2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation. Erb TJ, Fuchs G, Alber BE. Mol Microbiol 73 992-1008 (2009)
  10. Genetic basis for correction of very-long-chain acyl-coenzyme A dehydrogenase deficiency by bezafibrate in patient fibroblasts: toward a genotype-based therapy. Gobin-Limballe S, Djouadi F, Aubey F, Olpin S, Andresen BS, Yamaguchi S, Mandel H, Fukao T, Ruiter JP, Wanders RJ, McAndrew R, Kim JJ, Bastin J. Am J Hum Genet 81 1133-1143 (2007)
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  14. Diet-sensitive sources of reactive oxygen species in liver mitochondria: role of very long chain acyl-CoA dehydrogenases. Cardoso AR, Kakimoto PA, Kowaltowski AJ. PLoS One 8 e77088 (2013)
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  17. A single acyl-CoA dehydrogenase is required for catabolism of isoleucine, valine and short-chain fatty acids in Aspergillus nidulans. Maggio-Hall LA, Lyne P, Wolff JA, Keller NP. Fungal Genet Biol 45 180-189 (2008)
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  20. 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)
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  22. 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)
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  25. 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)
  26. Two novel variants of human medium chain acyl-CoA dehydrogenase (MCAD). K364R, a folding mutation, and R256T, a catalytic-site mutation resulting in a well-folded but totally inactive protein. O'Reilly LP, Andresen BS, Engel PC. FEBS J 272 4549-4557 (2005)
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  28. 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)
  29. 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)
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  31. 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)
  32. Structural Basis of Cyclic 1,3-Diene Forming Acyl-Coenzyme A Dehydrogenases. Kung JW, Meier AK, Willistein M, Weidenweber S, Demmer U, Ermler U, Boll M. Chembiochem 22 3173-3177 (2021)
  33. 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)


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