1QD5

OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

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: 717-721

  • DOI: 10.1038/44890
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dimerization is a biological regulatory mechanism employed by both soluble and membrane proteins. However, there are few structural data on the factors that govern dimerization of membrane proteins. Outer membrane phospholipase A (OMPLA) is an integr ...

    Dimerization is a biological regulatory mechanism employed by both soluble and membrane proteins. However, there are few structural data on the factors that govern dimerization of membrane proteins. Outer membrane phospholipase A (OMPLA) is an integral membrane enzyme which participates in secretion of colicins in Escherichia coli. In Campilobacter and Helicobacter pylori strains, OMPLA is implied in virulence. Its activity is regulated by reversible dimerization. Here we report X-ray structures of monomeric and dimeric OMPLA from E. coli. Dimer interactions occur almost exclusively in the apolar membrane-embedded parts, with two hydrogen bonds within the hydrophobic membrane area being key interactions. Dimerization results in functional oxyanion holes and substrate-binding pockets, which are absent in monomeric OMPLA. These results provide a detailed view of activation by dimerization of a membrane protein.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli
      Blaauw, M.,Dekker, N.,Verheij, H.M.,Kalk, K.H.,Dijkstra, B.W.
      (1995) FEBS Lett. 373: 10


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, BIOSON Research Institute, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OUTER MEMBRANE PHOSPHOLIPASE A
A
275Escherichia coli (strain K12)Gene Names: pldA
EC: 3.1.1.32, 3.1.1.4
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
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download SDF File 
Download CCD File 
A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.550α = 90.00
b = 78.550β = 90.00
c = 101.520γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
XDSdata scaling
DMphasing
MLPHAREphasing
SCALEPACKdata scaling
XDSdata reduction
DMmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-25
    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
  • Version 1.4: 2018-01-31
    Type: Experimental preparation
  • Version 1.5: 2018-04-04
    Type: Data collection
  • Version 1.6: 2018-04-11
    Type: Data collection