1GHJ

SOLUTION STRUCTURE OF THE LIPOYL DOMAIN OF THE 2-OXOGLUTARATE DEHYDROGENASE COMPLEX FROM AZOTOBACTER VINELAND II, NMR, MINIMIZED AVERAGE STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

Berg, A.Vervoort, J.de Kok, A.

(1996) J Mol Biol 261: 432-442

  • DOI: 10.1006/jmbi.1996.0474
  • Structures With Same Primary Citation

  • PubMed 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 annealin ...

    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.


    Related Citations: 
    • 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.
      (1995) Eur J Biochem 234: 148

    Organizational Affiliation

    Department of Biochemistry Agricultural University, Wageningen, The Netherlands.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E2, THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEXA79Azotobacter vinelandiiMutation(s): 0 
Gene Names: sucBodhB
EC: 2.3.1.61
Find proteins for P20708 (Azotobacter vinelandii)
Explore P20708 
Go to UniProtKB:  P20708
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • OLDERADO: 1GHJ Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other