1FW3

OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.

Snijder, H.J.Kingma, R.L.Kalk, K.H.Dekker, N.Egmond, M.R.Dijkstra, B.W.

(2001) J.Mol.Biol. 309: 477-489

  • DOI: 10.1006/jmbi.2001.4675
  • Primary Citation of Related Structures:  1FW2

  • PubMed Abstract: 
  • Outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of phospholipids. Enzymatic activity is regulated by reversible dimerisation and calcium-binding. We have investigated the role of calcium by X-ray cr ...

    Outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of phospholipids. Enzymatic activity is regulated by reversible dimerisation and calcium-binding. We have investigated the role of calcium by X-ray crystallography. In monomeric OMPLA, one calcium ion binds between two external loops (L3L4 site) at 10 A from the active site. After dimerisation, a new calcium-binding site (catalytic site) is formed at the dimer interface in the active site of each molecule at 6 A from the L3L4 calcium site. The close spacing and the difference in calcium affinity of both sites suggests that the L3L4 site may function as a storage site for a calcium ion, which relocates to the catalytic site upon dimerisation. A sequence alignment demonstrates conservation of the catalytic calcium site but evolutionary variation of the L3L4 site. The residues in the dimer interface are conserved as well, suggesting that all outer membrane phospholipases require dimerisation and calcium in the catalytic site for activity. For this family of phospholipases, we have characterised a consensus sequence motif (YTQ-X(n)-G-X(2)-H-X-SNG) that contains conserved residues involved in dimerisation and catalysis.


    Related Citations: 
    • Structural Evidence for Dimerization-Regulated Activation of an Integral Membrane Phospholipase
      Snijder, H.J.,Ubarretxena-Belandia, I.,Blaauw, M.,Kalk, K.H.,Verheij, H.M.,Egmond, M.R.,Dekker, N.,Dijkstra, B.W.
      (1999) Nature 401: 717
    • Bacterial phospholipase A: structure and function of an integral membrane phospholipase
      Snijder, H.J.,Dijkstra, B.W.
      (2000) Biochim.Biophys.Acta 1488: 91
    • Crystallization and Preliminary X-Ray Analysis of Outer Membrane Phospholipase a from Escherichia Coli
      Blaauw, M.,Dekker, N.,Kalk, K.H.,Verheij, H.M.,Dijkstra, B.W.
      (1995) FEBS Lett. 373: 10


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, BIOSON Research Institute, University of Groningen, Nijenborgh 4 9747 AG, Groningen, The Netherlands. bauke@chem.rug.nl




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OUTER MEMBRANE PHOSPHOLIPASE A
A, B
275Escherichia coli (strain K12)Gene Names: pldA
EC: 3.1.1.4, 3.1.1.32
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
Protein: 
OmpLA (PldA) outer membrane phospholipase A monomer
Find proteins for P0A921 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A921
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
S1H
Query on S1H
A, B
L-PEPTIDE LINKINGC19 H39 N O5 SSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.540α = 90.00
b = 84.970β = 90.00
c = 95.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance