1QD6

OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1038/44890
  • Primary Citation of Related Structures:  
    1QD5, 1QD6

  • 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 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.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)
A, B
13Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pldA
Membrane Entity: Yes 
UniProt
Find proteins for P0A921 (Escherichia coli (strain K12))
Explore P0A921 
Go to UniProtKB:  P0A921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A921
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))
C, D
240Escherichia coliMutation(s): 0 
EC: 3.1.1.32
Membrane Entity: Yes 
UniProt
Find proteins for P0A921 (Escherichia coli (strain K12))
Explore P0A921 
Go to UniProtKB:  P0A921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A921
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.067α = 90
b = 84.038β = 90
c = 95.245γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-25
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Advisory, Structure summary
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2023-08-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description