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Solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii.

Berg A, Vervoort J, de Kok A
J Mol Biol 261 432-42 (1996)
Cited: 25 times
EuropePMC logo PMID: 8780784

Abstract

The three-dimensional solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii has been determined from nuclear magnetic resonance data by using distance geometry and dynamical simulated annealing refinement. The structure determination is based on a total of 580 experimentally derived distance constraints and 65 dihedral angle constraints. The solution structure is represented by an ensemble of 25 structures with an average root-mean-square deviation between the individual structures of the ensemble and the mean coordinates of 0.71 A for backbone atoms and 1.08 A for all heavy atoms. The overall fold of the lipoyl domain is that of a beta-barrel-sandwich hybrid. It consists of two almost parallel four-stranded anti-parallel beta-sheets formed around a well-defined hydrophobic core, with a central position of the single tryptophan 21. The lipoylation site, lysine 42, is found in a beta-turn at the far end of one of the sheets, and is close in space to a solvent-exposed loop comprising residues 7 to 15. The lipoyl domain displays a remarkable internal symmetry that projects one beta-sheet onto the other beta-sheet after rotation of approximately 180 degrees about a 2-fold rotational symmetry axis. There is close structural similarity between the structure of this 2-oxoglutarate dehydrogenase complex lipoyl domain and the structures of the lipoyl domains of pyruvate dehydrogenase complexes from Bacillus stearothermophilus and Escherichia coli, and conformational differences occur primarily in a solvent-exposed loop close in space to the lipoylation site. The lipoyl domain structure is discussed in relation to the process of molecular recognition of lipoyl domains by their parent 2-oxo acid dehydrogenase.

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  3. Structure and selectivity in post-translational modification: attaching the biotinyl-lysine and lipoyl-lysine swinging arms in multifunctional enzymes. Reche P, Perham RN. EMBO J. 18 2673-2682 (1999)
  4. Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex. Knapp JE, Mitchell DT, Yazdi MA, Ernst SR, Reed LJ, Hackert ML. J. Mol. Biol. 280 655-668 (1998)
  5. Three-dimensional structure in solution of the N-terminal lipoyl domain of the pyruvate dehydrogenase complex from Azotobacter vinelandii. Berg A, Vervoort J, de Kok A. Eur. J. Biochem. 244 352-360 (1997)
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  9. Protein-protein interaction revealed by NMR T(2) relaxation experiments: the lipoyl domain and E1 component of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Howard MJ, Chauhan HJ, Domingo GJ, Fuller C, Perham RN. J. Mol. Biol. 295 1023-1037 (2000)
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  12. Reaction mechanism for mammalian pyruvate dehydrogenase using natural lipoyl domain substrates. Liu S, Gong X, Yan X, Peng T, Baker JC, Li L, Robben PM, Ravindran S, Andersson LA, Cole AB, Roche TE. Arch. Biochem. Biophys. 386 123-135 (2001)
  13. Structural characterization of the entire 1.3S subunit of transcarboxylase from Propionibacterium shermanii. Reddy DV, Rothemund S, Shenoy BC, Carey PR, Sönnichsen FD. Protein Sci. 7 2156-2163 (1998)
  14. Solution structure and dynamics of the lipoic acid-bearing domain of human mitochondrial branched-chain alpha-keto acid dehydrogenase complex. Chang CF, Chou HT, Chuang JL, Chuang DT, Huang TH. J. Biol. Chem. 277 15865-15873 (2002)
  15. Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation. Cronan JE. EcoSal Plus 6 (2014)
  16. Cloning, overexpression and mutagenesis of cDNA encoding dihydrolipoamide succinyltransferase component of the porcine 2-oxoglutarate dehydrogenase complex. Koike K, Suematsu T, Ehara M. Eur. J. Biochem. 267 3005-3016 (2000)
  17. Pyruvate dehydrogenase from Azotobacter vinelandii. Properties of the N-terminally truncated enzyme. Hengeveld AF, Schoustra SE, Westphal AH, de Kok A. Eur. J. Biochem. 265 1098-1107 (1999)
  18. Solution structure of the lipoyl domain of the chimeric dihydrolipoyl dehydrogenase P64K from Neisseria meningitidis. Tozawa K, Broadhurst RW, Raine AR, Fuller C, Alvarez A, Guillen G, Padron G, Perham RN. Eur. J. Biochem. 268 4908-4917 (2001)
  19. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P. Nat Commun 12 5277 (2021)
  20. Overproduction of α-Lipoic Acid by Gene Manipulated Escherichia coli. Sun Y, Zhang W, Ma J, Pang H, Wang H. PLoS ONE 12 e0169369 (2017)


Related citations provided by authors (1)

  1. Sequential 1H and 15N nuclear magnetic resonance assignments and secondary structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. Evidence for high structural similarity with the lipoyl domain of the pyruvate dehydrogenase complex.. Berg A, Smits O, de Kok A, Vervoort J Eur J Biochem 234 148-59 (1995)

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