Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 28.69 kDa 
• Atom Count: 1901 
• Modelled Residue Count: 227 
• Deposited Residue Count: 256 
• Unique protein chains: 1

2VEC

The crystal structure of the protein YhaK from Escherichia coli

• PDB DOI: 10.2210/pdb2VEC/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-18 Released: 2008-07-01 
• Deposition Author(s): Gurmu, D., Lu, J., Johnson, K.A., Nordlund, P., Holmgren, A., Erlandsen, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.209 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Literature

The Crystal Structure of the Protein Yhak from Escherichia Coli Reveals a New Subclass of Redox Sensitive Enterobacterial Bicupins.

Gurmu, D., Lu, J., Johnson, K.A., Nordlund, P., Holmgren, A., Erlandsen, H.

(2008) Proteins 74: 18

• PubMed: 18561187 
• DOI: 10.1002/prot.22128
• Primary Citation of Related Structures:  
  2VEC


• PubMed Abstract: 
  

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.

---

Organizational Affiliation: 

Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PIRIN-LIKE PROTEIN YHAK	A	256	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P42624 (Escherichia coli (strain K12)) Explore P42624  Go to UniProtKB:  P42624

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.209 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.648	α = 90
b = 57.648	β = 90
c = 162.092	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-10-18 
• Released Date: 2008-07-01 
Deposition Author(s): Gurmu, D., Lu, J., Johnson, K.A., Nordlund, P., Holmgren, A., Erlandsen, H.

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance