2V8K

Structure of a Family 2 Pectate Lyase in Complex with Trigalacturonic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Family 2 Pectate Lyase Displays a Rare Fold and Transition Metal-Assisted Beta-Elimination.

Abbott, D.W.Boraston, A.B.

(2007) J.Biol.Chem. 282: 35328

  • DOI: 10.1074/jbc.M705511200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The family 2 pectate lyase from Yersinia enterocolitica (YePL2A), solved to 1.5A, reveals it to be the first prokaryotic protein reported to display the rare (alpha/alpha)(7) barrel fold. In addition to its apo form, we have also determined the struc ...

    The family 2 pectate lyase from Yersinia enterocolitica (YePL2A), solved to 1.5A, reveals it to be the first prokaryotic protein reported to display the rare (alpha/alpha)(7) barrel fold. In addition to its apo form, we have also determined the structure of a metal-bound form of YePL2A (to 2.0A) and a trigalacturonic acid-bound substrate complex (to 2.1A) Although its fold is rare, the catalytic center of YePL2A can be superimposed with structurally unrelated families, underlining the conserved catalytic amino acid architecture of the beta-elimination mechanism. In addition to its overall structure, YePL2A also has two other unique features: 1) it utilizes a metal atom other than calcium for catalysis, and 2) its Brønstead base is in an alternate conformation and directly interacts with the uronate group of the substrate.


    Organizational Affiliation

    Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PECTATE LYASE
A
543Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)Mutation(s): 0 
Gene Names: pelY
Find proteins for A1JSS8 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081))
Go to UniProtKB:  A1JSS8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTR
Query on GTR

Download SDF File 
Download CCD File 
A
Beta-D-Galactopyranuronic acid
Galacturonic acid
C6 H10 O7
AEMOLEFTQBMNLQ-DTEWXJGMSA-N
 Ligand Interaction
ADA
Query on ADA

Download SDF File 
Download CCD File 
A
ALPHA-D-GALACTOPYRANURONIC ACID
ALPHA D-GALACTURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-BKBMJHBISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.486α = 90.00
b = 95.642β = 90.00
c = 126.608γ = 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: 2007-09-18
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2016-01-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description