3PE7

Oligogalacturonate lyase in complex with manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination.

Abbott, D.W.Gilbert, H.J.Boraston, A.B.

(2010) J.Biol.Chem. 285: 39029-39038

  • DOI: 10.1074/jbc.M110.153981

  • PubMed Abstract: 
  • Oligogalacturonate lyases (OGLs; now also classified as pectate lyase family 22) are cytoplasmic enzymes found in pectinolytic members of Enterobacteriaceae, such as the enteropathogen Yersinia enterocolitica. OGLs utilize a β-elimination mechanism t ...

    Oligogalacturonate lyases (OGLs; now also classified as pectate lyase family 22) are cytoplasmic enzymes found in pectinolytic members of Enterobacteriaceae, such as the enteropathogen Yersinia enterocolitica. OGLs utilize a β-elimination mechanism to preferentially catalyze the conversion of saturated and unsaturated digalacturonate into monogalacturonate and the 4,5-unsaturated monogalacturonate-like molecule, 5-keto-4-deoxyuronate. To provide mechanistic insights into the specificity of this enzyme activity, we have characterized the OGL from Y. enterocolitica, YeOGL, on oligogalacturonides and determined its three-dimensional x-ray structure to 1.65 Å. The model contains a Mn(2+) atom in the active site, which is coordinated by three histidines, one glutamine, and an acetate ion. The acetate mimics the binding of the uronate group of galactourono-configured substrates. These findings, in combination with enzyme kinetics and metal supplementation assays, provide a framework for modeling the active site architecture of OGL. This enzyme appears to contain a histidine for the abstraction of the α-proton in the -1 subsite, a residue that is highly conserved throughout the OGL family and represents a unique catalytic base among pectic active lyases. In addition, we present a hypothesis for an emerging relationship observed between the cellular distribution of pectate lyase folding and the distinct metal coordination chemistries of pectate lyases.


    Organizational Affiliation

    Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA. wabbott@ccrc.uga.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligogalacturonate lyase
A
388Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)Mutation(s): 0 
Gene Names: ogl
Find proteins for A1JMA5 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081))
Go to UniProtKB:  A1JMA5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.650α = 90.00
b = 75.510β = 90.00
c = 78.510γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance