3LAD

REFINED CRYSTAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM AZOTOBACTER VINELANDII AT 2.2 ANGSTROMS RESOLUTION. A COMPARISON WITH THE STRUCTURE OF GLUTATHIONE REDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 975-994


  • PubMed Abstract: 
  • The structure of lipoamide dehydrogenase from Azotobacter vinelandii has been refined by the molecular dynamics technique to an R-factor of 19.8% at 2.2 A resolution. In the final model, the root-mean-square deviation from ideality is 0.02 A for bond ...

    The structure of lipoamide dehydrogenase from Azotobacter vinelandii has been refined by the molecular dynamics technique to an R-factor of 19.8% at 2.2 A resolution. In the final model, the root-mean-square deviation from ideality is 0.02 A for bond lengths and 3.2 degrees for bond angles. The asymmetric unit comprises two subunits, each consisting of 466 amino acid residues and the prosthetic group FAD, plus 512 solvent molecules. The last ten amino acid residues of both chains are not visible in the electron density distribution and they are probably disordered. The operation required to superimpose the two chains forming the dimer is a rotation of exactly 180 degrees with no translation component. The final model shows the two independently refined subunits to be very similar, except for six loops located at the surface of the molecule. The structure of each subunit of the enzyme consists of four domains with the catalytic centre located at the subunit interface. The reactive disulphide bridge, 48-53, is oxidized with S gamma of Cys53 located 3.5 A away from carbon C-4a of the isoalloxazine ring. The side-chain of His450' points its N epsilon 2 towards S gamma of Cys48 and is hydrogen bonded to the carboxylate of Glu455'. The FAD is bound in an extended conformation and the isoalloxazine ring is not completely planar with an angle between the pteridine and the benzene ring of 7.3 degrees in the first subunit and of 12.1 degrees in the second one. The overall folding of lipoamide dehydrogenase is very similar to that of glutathione reductase. However, a comparison of the two enzymes, which have only 26% sequence identity, reveals significant conformational differences. These concern the tertiary as well as the quaternary structure of the two molecules. In each subunit of lipoamide dehydrogenase the NAD-binding domain and the interface domain appear to be differently oriented with respect to the FAD-binding domain by 7.1 degrees and 7.8 degrees, respectively. The interface domain contains, in addition, major changes in tertiary structure. Furthermore, the two subunits forming the dimer appear to be shifted with respect to each other by more than 4 A, when the lipoamide dehydrogenase dimer is compared with that of glutathione reductase. In spite of all these changes at the tertiary and quaternary level the active sites of the enzymes, which occur at the dimer interface, appear to be remarkably similar.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • X-Ray Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii Determined by a Combination of Molecular and Isomorphous Replacement Techniques
      Schierbeek, A.J.,Swarte, M.B.A.,Dijkstra, B.W.,Vriend, G.,Read, R.J.,Hol, W.G.J.,Drenth, J.,Betzel, C.
      (1989) J.Mol.Biol. 206: 365
    • Crystallization and Preliminary X-Ray Investigation of Lipoamide Dehydrogenase from Azotobacter Vinelandii
      Schierbeek, A.J.,Van Derlaan, J.M.,Groendijk, H.,Wierenga, R.K.,Drenth, J.
      (1983) J.Mol.Biol. 165: 563
    • Lipoamide Dehydrogenase from Azotobacter Vinelandii: Molecular Cloning, Organization and Sequence Analysis of the Gene
      Westphal, A.H.,Dekok, A.
      (1988) Eur.J.Biochem. 172: 299


    Organizational Affiliation

    Department of Chemistry, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROLIPOAMIDE DEHYDROGENASE
A, B
476Azotobacter vinelandiiMutation(s): 0 
EC: 1.8.1.4
Find proteins for P18925 (Azotobacter vinelandii)
Go to UniProtKB:  P18925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.130α = 90.00
b = 83.860β = 90.00
c = 191.960γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
GROMOSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance