1GHK

SOLUTION STRUCTURE OF THE LIPOYL DOMAIN OF THE 2-OXOGLUTARATE DEHYDROGENASE COMPLEX FROM AZOTOBACTER VINELAND II, NMR, 25 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 25 

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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
  • Primary Citation of Related Structures:  1GHJ

  • 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 COMPLEX
A
79Azotobacter vinelandiiGene Names: sucB (odhB)
EC: 2.3.1.61
Find proteins for P20708 (Azotobacter vinelandii)
Go to UniProtKB:  P20708
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 25 
  • Olderado: 1GHK Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other