2VEC image
Deposition Date 2007-10-18
Release Date 2008-07-01
Last Version Date 2024-11-20
Entry Detail
PDB ID:
2VEC
Title:
The crystal structure of the protein YhaK from Escherichia coli
Biological Source:
Source Organism:
ESCHERICHIA COLI (Taxon ID: 562)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.20
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:PIRIN-LIKE PROTEIN YHAK
Gene (Uniprot):yhaK
Chain IDs:A
Chain Length:256
Number of Molecules:1
Biological Source:ESCHERICHIA COLI
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CSO A CYS S-HYDROXYCYSTEINE
Ligand Molecules
Primary Citation
The Crystal Structure of the Protein Yhak from Escherichia Coli Reveals a New Subclass of Redox Sensitive Enterobacterial Bicupins.
Proteins 74 18 ? (2008)
PMID: 18561187 DOI: 10.1002/PROT.22128

Abstact

YhaK is a protein of unknown function found in low abundance in the cytosol of Escherichia coli. DNA array studies have revealed that YhaK is strongly up-regulated by nitroso-glutathione (GSNO) and also displays a 12-fold increase in expression during biofilm growth of E. coli 83972 and VR50 in human urine. We have determined the YhaK crystal structure and demonstrated that in vitro YhaK is a good marker for monitoring oxidative stresses in E. coli. The YhaK protein structure shows a bicupin fold where the two cupin domains are crosslinked with one intramolecular disulfide bond (Cys10 to Cys204). We found that the third cysteine in YhaK, Cys122, is oxidized to a sulfenic acid. Two chloride ions are found in the structure, one close to the reactive Cys122, and the other on a hydrophobic surface close to a symmetry-related molecule. There are major structural differences at the N-terminus of YhaK compared with similar structures that also display the bicupin fold (YhhW and hPirin). YhaK showed no quercetinase and peroxidase activity. However, reduced YhaK was very sensitive to reactive oxygen species (ROS). The complete, functional E. coli glutaredoxin or thioredoxin systems protected YhaK from oxidation. E. coli thioredoxin reductase and NADPH produced ROS and caused oxidation and oligomerization of reduced YhaK. Taken together, we propose that YhaK is the first of a new sub-class of bicupins that lack the canonical cupin metal-binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria.

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Primary Citation of related structures