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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.21 kDa 
• Atom Count: 2145 
• Modelled Residue Count: 247 
• Deposited Residue Count: 262 
• Unique protein chains: 1

3QY6

Crystal structures of YwqE from Bacillus subtilis and CpsB from Streptococcus pneumoniae, unique metal-dependent tyrosine phosphatases

• PDB DOI: 10.2210/pdb3QY6/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-03 Released: 2011-06-08 
• Deposition Author(s): Kim, H.S., Lee, S.J., Yoon, H.J., An, D.R., Kim, D.J., Kim, S.-J., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Crystal structures of YwqE from Bacillus subtilis and CpsB from Streptococcus pneumoniae, unique metal-dependent tyrosine phosphatases.

Kim, H.S., Lee, S.J., Yoon, H.J., An, D.R., Kim, D.J., Kim, S.J., Suh, S.W.

(2011) J Struct Biol 175: 442-450

• PubMed: 21605684 
• DOI: 10.1016/j.jsb.2011.05.007
• Primary Citation of Related Structures:  
  3QY6, 3QY7, 3QY8


• PubMed Abstract: 
  

Unique metal-dependent protein tyrosine phosphatases that belong to the polymerase and histindinol phosphatase (PHP) family are present in Gram-positive bacteria. They are distinct from the Cys-based, low-molecular-weight phosphotyrosine protein phosphatases (LMPTPs). Two representative members of the PHP family tyrosine phosphatases are YwqE from Bacillus subtilis and CpsB from Streptococcus pneumoniae. YwqE is involved in polysaccharide biosynthesis, bacterial DNA metabolism, and DNA damage response in B. subtilis. CpsB regulates capsular polysaccharide biosynthesis via tyrosine dephosphorylation of CpsD, its cognate tyrosine kinase, in S. pneumoniae. To gain insights into the active site and possible conformational changes of the metal-dependent tyrosine phosphatases from Gram-positive bacteria, we have determined the crystal structures of B. subtilis YwqE (in both the apo form and the phosphate-bound form) and S. pneumoniae CpsB (in the sulfate-bound form). Comparisons of the three structures reveal conformational plasticity of two active site loops. Furthermore, in both structures of the phosphate-bound YwqE and the sulfate-bound CpsB, the phosphate (or sulfate) ion is bound to a cluster of three metal ions in the active site, thus providing insight into the pre-catalytic state.

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Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, South Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase YwqE	A	262	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU36240, ywqE EC: 3.1.3.48
UniProt
Find proteins for P96717 (Bacillus subtilis (strain 168)) Explore P96717  Go to UniProtKB:  P96717

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A], C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.256 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.624	α = 90
b = 59.641	β = 101.08
c = 57.53	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-03 
• Released Date: 2011-06-08 
Deposition Author(s): Kim, H.S., Lee, S.J., Yoon, H.J., An, D.R., Kim, D.J., Kim, S.-J., Suh, S.W.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-17
  Changes: Database references