1OJT

STRUCTURE OF DIHYDROLIPOAMIDE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.232 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular structure of the lipoamide dehydrogenase domain of a surface antigen from Neisseria meningitidis.

Li de la Sierra, I.Pernot, L.Prange, T.Saludjian, P.Schiltz, M.Fourme, R.Padron, G.

(1997) J Mol Biol 269: 129-141

  • DOI: 10.1006/jmbi.1997.1009
  • Primary Citation of Related Structures:  
    1OJT

  • PubMed Abstract: 
  • The protein p64k from the surface of the Neisseria meningitidis bacteria has been characterized as a two-domain protein. It contains a dihydrolipoamide dehydrogenase domain of 482 residues, involving a FAD prosthetic group as a cofactor, and a smalle ...

    The protein p64k from the surface of the Neisseria meningitidis bacteria has been characterized as a two-domain protein. It contains a dihydrolipoamide dehydrogenase domain of 482 residues, involving a FAD prosthetic group as a cofactor, and a smaller lipoic acid binding domain of 86 residues. The two domains are joined by a flexible segment rich in alanine and proline residues. The structure of the dihydrolipoamide dehydrogenase domain was determined by X-ray diffraction. It was solved by a combination of molecular replacement and multiple isomorphous replacement techniques and refined to 2.7 A resolution. In the crystal, the recombinant p64k mimics the functional homo-dimer by using one of the crystallographic 2-fold axes. The reactive disulphide bridge Cys161-Cys166 is in the oxidised state and the FAD is bound in an extended conformation. This main domain contains the major antigenic determinant of the protein, an extended loop of 32 residues at the surface of the protein. A mis-attribution at residue 553 in the sequence has been detected by inspection of electron density maps and the geometry. However, when compared to the other dihydrolipoamide dehydrogenases, there are some significant differences: (1) an unusual number of cis-proline residues and (2) a new motif built around a 2-fold axis by the sulphur atoms of residues Met558, Cys560 and their symmetry related equivalents.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Investigation of a Recombinant Outer Membrane Protein from Neisseria Meningitidis
      Li De La Sierra, I., Prange, T., Fourme, R., Padron, G., Fuentes, P., Musacchio, A., Madrazo, J.
      (1994) J Mol Biol 235: 1154
    • The Refined Crystal Structure of Pseudomonas Putida Lipoamide Dehydrogenase Complexed with Nad+ at 2.45 A Resolution
      Mattevi, A., Obmolova, G., Sokatch, J.R., Betzel, C., Hol, W.G.
      (1992) Proteins 13: 336
    • Refined Crystal Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii at 2.2 A Resolution. A Comparison with the Structure of Glutathione Reductase
      Mattevi, A., Schierbeek, A.J., Hol, W.G.
      (1991) J Mol Biol 220: 975

    Organizational Affiliation

    CIGB, Cubanacan, La Habana, Cuba.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SURFACE PROTEINA482Neisseria meningitidisMutation(s): 0 
Gene Names: M-6 OBTAINED FROM A GENOMICm-6
EC: 1.8.1.4
Find proteins for Q51225 (Neisseria meningitidis)
Explore Q51225 
Go to UniProtKB:  Q51225
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.232 
  • R-Value Observed: 0.173 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.05α = 90
b = 138.05β = 90
c = 79.77γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEITdata reduction
SHARPphasing
PROLSQrefinement
CCP4data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance