1LPF

THREE-DIMENSIONAL STRUCTURE OF LIPOAMIDE DEHYDROGENASE FROM PSEUDOMONAS FLUORESCENS AT 2.8 ANGSTROMS RESOLUTION. ANALYSIS OF REDOX AND THERMOSTABILITY PROPERTIES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of lipoamide dehydrogenase from Pseudomonas fluorescens at 2.8 A resolution. Analysis of redox and thermostability properties.

Mattevi, A.Obmolova, G.Kalk, K.H.van Berkel, W.J.Hol, W.G.

(1993) J.Mol.Biol. 230: 1200-1215

  • DOI: 10.1006/jmbi.1993.1236

  • PubMed Abstract: 
  • The structure of Pseudomonas fluorescens lipoamide dehydrogenase, a dimeric flavoenzyme with a molecular mass of 106,000 daltons, was solved by the molecular replacement method and refined to an R-factor of 19.4% at 2.8 A resolution. The root-mean-sq ...

    The structure of Pseudomonas fluorescens lipoamide dehydrogenase, a dimeric flavoenzyme with a molecular mass of 106,000 daltons, was solved by the molecular replacement method and refined to an R-factor of 19.4% at 2.8 A resolution. The root-mean-square difference from ideal values for bonds and angles is 0.019 A and 3.8 degrees, respectively. The structure is closely related to that of the same flavoprotein from Azotobacter vinelandii. The root-mean-square difference for 932 C alpha atoms is 0.64 A, with 84% sequence identity. The residues in the active site are identical, while 89% of the interface residues are the same in the two enzymes. A few structural variations provide the basis for the differences in thermostability and redox properties between the two homologous proteins. Particularly, in the A. vinelandii molecule a threonine to alanine (T452A) mutation leaves a buried carbonyl oxygen, located at the subunit interface and in proximity of the flavin ring, unpaired to any H-bond donor, probably providing an explanation for the lower stability of the A. vinelandii enzyme with respect to the P. fluorescens enzyme. Six surface loops, which previously could not be accurately positioned in the A. vinelandii structure, are well defined in P. fluorescens lipoamide dehydrogenase. On the basis of the P. fluorescens structure, the six loops could be correctly defined also in the A. vinelandii enzyme. This is an unusual case where similar refinement methodologies applied to two crystal forms of closely related proteins led to electron density maps of substantially different quality. The correct definition of these surface residues is likely to be an essential step for revealing the structural basis of the interactions between lipoamide dehydrogenase and the other members of the pyruvate dehydrogenase multienzyme complex.


    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
    • Molecular Cloning and Sequence Determination of the Gene Encoding Lipoamide Dehydrogenase from Pseudomonas Fluorescens
      Benen, J.A.E.,Van Berkel, W.J.H.,Van Dongen, W.M.A.M.,Muller, F.,Dekok, A.
      (1989) J.Gen.Microbiol. 135: 1787
    • The Refined Crystal Structure of Lipoamide Dehydrogenase from Azotobacter Vinelandii at 2.2 Angstroms Resolution. A Comparison with the Structure of Glutathione Reductase
      Mattevi, A.,Schierbeek, A.J.,Hol, W.G.J.
      (1991) J.Mol.Biol. 220: 975


    Organizational Affiliation

    BIOSON Research Institute, Department of Chemistry, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROLIPOAMIDE DEHYDROGENASE
A, B
477Pseudomonas fluorescensGene Names: lpd
EC: 1.8.1.4
Find proteins for P14218 (Pseudomonas fluorescens)
Go to UniProtKB:  P14218
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: 2.8 Å
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 113.600α = 90.00
b = 66.400β = 99.20
c = 164.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1992-10-26 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Mattevi, A., Hol, W.

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance