1GHK

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

Summary for 1GHK

• Entry DOI: 10.2210/pdb1ghk/pdb
• Descriptor: E2, THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX (1 entity in total)
• Functional Keywords: glycolysis, transferase, acyltransferase, lipoyl
• Biological source: Azotobacter vinelandii
• Total number of polymer chains: 1
• Total formula weight: 8353.44

Authors

Berg, A.,Vervoort, J.,De Kok, A. (deposition date: 1996-01-16, release date: 1997-01-11, Last modification date: 2024-05-01)

Primary citation

Berg, A.,Vervoort, J.,de Kok, A.
Solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii.
J.Mol.Biol., 261:432-442, 1996

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 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.

PubMed: 8780784
DOI: 10.1006/jmbi.1996.0474

Experimental method

SOLUTION NMR