Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.38 kDa 
• Atom Count: 1737 
• Residue Count: 210 
• Unique protein chains: 1

2XF4

Crystal structure of Salmonella enterica serovar typhimurium YcbL

• DOI: 10.2210/pdb2XF4/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-20 Released: 2010-07-28 
• Deposition Author(s): Stamp, A., Owen, P., El Omari, K., Nichols, C., Lockyer, M., Lamb, H., Charles, I., Hawkins, A.R., Stammers, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structural and Functional Characterization of Salmonella Enterica Serovar Typhimurium Ycbl: An Unusual Type II Glyoxalase

Stamp, A., Owen, P., El Omari, K., Nichols, C., Lockyer, M., Lamb, H., Charles, I., Hawkins, A.R., Stammers, D.K.

(2010) Protein Sci 19: 1897

• PubMed: 20669241 
• DOI: 10.1002/pro.475
• Primary Citation of Related Structures:  
  2XF4


• PubMed Abstract: 
  

YcbL has been annotated as either a metallo-β-lactamase or glyoxalase II (GLX2), both members of the zinc metallohydrolase superfamily, that contains many enzymes with a diverse range of activities. Here, we report crystallographic and biochemical data for Salmonella enterica serovar Typhimurium YcbL that establishes it as GLX2, which differs in certain structural and functional properties compared with previously known examples. These features include the insertion of an α-helix after residue 87 in YcbL and truncation of the C-terminal domain, which leads to the loss of some recognition determinants for the glutathione substrate. Despite these changes, YcbL has robust GLX2 activity. A further difference is that the YcbL structure contains only a single bound metal ion rather than the dual site normally observed for GLX2s. Activity assays in the presence of various metal ions indicate an increase in activity above basal levels in the presence of manganous and ferrous ions. Thus, YcbL represents a novel member of the GLX2 family.

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Organizational Affiliation: 

Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYACYLGLUTATHIONE HYDROLASE	A	210	Salmonella enterica	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	A	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.363	α = 90
b = 124.363	β = 90
c = 35.594	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-20 
• Released Date: 2010-07-28 
Deposition Author(s): Stamp, A., Owen, P., El Omari, K., Nichols, C., Lockyer, M., Lamb, H., Charles, I., Hawkins, A.R., Stammers, D.K.

Revision History 

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2012-09-12
  Changes: Database references, Structure summary, Version format compliance