3U96

Crystal Structure of YopHQ357F(Catalytic Domain, Residues 163-468) in complex with pNCS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Investigation of catalytic loop structure, dynamics, and function relationship of Yersinia protein tyrosine phosphatase by temperature-jump relaxation spectroscopy and X-ray structural determination.

Ke, S.Ho, M.C.Zhadin, N.Deng, H.Callender, R.

(2012) J Phys Chem B 116: 6166-6176

  • DOI: 10.1021/jp3037846
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Yersinia protein tyrosine phosphatase (YopH) is the most efficient enzyme among all PTPases. YopH is hyperactive compared to human PTPases, interfering with mammalian cellular pathways to achieve the pathogenicity of Yersinia. Two properties related ...

    Yersinia protein tyrosine phosphatase (YopH) is the most efficient enzyme among all PTPases. YopH is hyperactive compared to human PTPases, interfering with mammalian cellular pathways to achieve the pathogenicity of Yersinia. Two properties related to the catalytic loop structure differences have been proposed to affect its dynamics and enzyme efficiency. One is the ability of the loop to form stabilizing interactions to bound ligand after loop closure, which has long been recognized. In addition, the loop flexibility/mobility was suggested in a previous study to be a factor as well, based on the observation that incremental changes in PTPase loop structure by single point mutations to alanine often induce incremental changes in enzyme catalytic efficiency. In this study, the temperature jump relaxation spectroscopy (T-jump) has been used to discern the subtle changes of the loop dynamics due to point loop mutations. As expected, our results suggest a correlation between loop dynamics and the size of the residue on the catalytic loop. The stabilization of the enzyme-ligand complex is often enthalpy driven, achieved by formation of additional favorable hydrogen bonding/ionic interactions after loop closure. Interestingly, our T-jump and X-ray crystallography studies on YopH suggest that the elimination of some ligand-protein interactions by mutation does not necessarily destabilize the ligand-enzyme complex after loop closure, since the increased entropy in the forms of more mobile protein residues may be sufficient to compensate the free energy loss due to lost interactions and may even lead to enhanced efficiency of the enzyme catalysis. How these competing loop properties may affect loop dynamics and enzyme function are discussed.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase yopHA, B306Yersinia enterocoliticaMutation(s): 2 
Gene Names: yop51yopH
EC: 3.1.3.48
Find proteins for P15273 (Yersinia enterocolitica)
Explore P15273 
Go to UniProtKB:  P15273
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CSN
Query on CSN

Download CCD File 
A, B
N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
C6 H5 N O7 S
XMCCOOONGGUOLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.863α = 104.78
b = 53.993β = 108.79
c = 65.759γ = 97.83
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-10-17 
  • Released Date: 2012-08-29 
  • Deposition Author(s): Ho, M.C., Ke, S.

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description