1F0X

CRYSTAL STRUCTURE OF D-LACTATE DEHYDROGENASE, A PERIPHERAL MEMBRANE RESPIRATORY ENZYME.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme.

Dym, O., Pratt, E.A., Ho, C., Eisenberg, D.

(2000) Proc.Natl.Acad.Sci.USA 97: 9413-9418

  • DOI: 10.1073/pnas.97.17.9413

  • PubMed Abstract: 

    • d-Lactate dehydrogenase (d-LDH) of Escherichia coli is a peripheral membrane respiratory enzyme involved in electron transfer, located on the cytoplasmic side of the inner membrane. d-LDH catalyzes the oxidation of d-lactate to pyruvate, which is cou ...

    d-Lactate dehydrogenase (d-LDH) of Escherichia coli is a peripheral membrane respiratory enzyme involved in electron transfer, located on the cytoplasmic side of the inner membrane. d-LDH catalyzes the oxidation of d-lactate to pyruvate, which is coupled to transmembrane transport of amino acids and sugars. Here we describe the crystal structure at 1.9 A resolution of the three domains of d-LDH: the flavin adenine dinucleotide (FAD)-binding domain, the cap domain, and the membrane-binding domain. The FAD-binding domain contains the site of d-lactate reduction by a noncovalently bound FAD cofactor and has an overall fold similar to other members of a recently discovered FAD-containing family of proteins. This structural similarity extends to the cap domain as well. The most prominent difference between d-LDH and the other members of the FAD-containing family is the membrane-binding domain, which is either absent in some of these proteins or differs significantly. The d-LDH membrane-binding domain presents an electropositive surface with six Arg and five Lys residues, which presumably interacts with the negatively charged phospholipid head groups of the membrane. Thus, d-LDH appears to bind the membrane through electrostatic rather than hydrophobic forces.

    Organizational Affiliation: 

    Department of Energy Laboratory of Structural Biology and Molecular Medicine, University of California, Los Angeles 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-LACTATE DEHYDROGENASE
A, B
571Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dld
EC: 1.1.5.12
Find proteins for P06149 (Escherichia coli (strain K12))
Go to UniProtKB:  P06149
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: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.006α = 90.00
b = 74.187β = 95.73
c = 101.997γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SOLVEphasing
SCALEPACKdata scaling
DENZOdata reduction
SnBphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description