Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 23378.77 
• Atom Count: 1640 
• Residue Count: 210 
• Unique protein chains: 1

2XF4

Crystal structure of Salmonella enterica serovar typhimurium YcbL

• DOI: 10.2210/pdb2XF4/pdb

• Classification: HYDROLASE
• Expression System: Escherichia coli


• 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: 2.3 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 

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


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HYDROXYACYLGLUTATHIONE HYDROLASE	A	210	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.229 
• R-Value Work: 0.193 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 124.363	α = 90.00
b = 124.363	β = 90.00
c = 35.594	γ = 90.00

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
  Type: Database references, Structure summary, Version format compliance