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 1.4 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:  
    1QD6, 1QD5

  • 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 ...

    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., 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, The Netherlands.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)A, B13N/AMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A921 (Escherichia coli (strain K12))
Explore P0A921 
Go to UniProtKB:  P0A921
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))C, D240Escherichia coliMutation(s): 0 
EC: 3.1.1.32 (PDB Primary Data), 3.1.1.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0A921 (Escherichia coli (strain K12))
Explore P0A921 
Go to UniProtKB:  P0A921
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HDS (Subject of Investigation/LOI)
Query on HDS

Download Ideal Coordinates CCD File 
G [auth C], H [auth D]1-HEXADECANOSULFONIC ACID
C16 H34 O3 S
SSILHZFTFWOUJR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth C], F [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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