2Q8Y

Structural insight into the enzymatic mechanism of the phophothreonine lyase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase

Zhu, Y.Li, H.Long, C.Hu, L.Xu, H.Liu, L.Chen, S.Wang, D.C.Shao, F.

(2007) Mol.Cell 28: 899-913

  • DOI: 10.1016/j.molcel.2007.11.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The OspF family of phosphothreonine lyase, including SpvC from Salmonella, irreversibly inactivates the dual-phosphorylated host MAPKs (pT-X-pY) through beta elimination. We determined crystal structures of SpvC and its complex with a phosphopeptide ...

    The OspF family of phosphothreonine lyase, including SpvC from Salmonella, irreversibly inactivates the dual-phosphorylated host MAPKs (pT-X-pY) through beta elimination. We determined crystal structures of SpvC and its complex with a phosphopeptide substrate. SpvC adopts a unique fold of alpha/beta type. The disordered N terminus harbors a canonical D motif for MAPK substrate docking. The enzyme-substrate complex structure indicates that recognition of the phosphotyrosine followed by insertion of the threonine phosphate into an arginine pocket places the phosphothreonine into the enzyme active site. This requires the conformational flexibility of pT-X-pY, which suggests that p38 (pT-G-pY) is likely the preferred physiological substrate. Structure-based biochemical and enzymatic analysis allows us to propose a general acid/base mechanism for beta elimination reaction catalyzed by the phosphothreonine lyase. The mechanism described here provides a structural understanding of MAPK inactivation by a family of pathogenic effectors conserved in plant and animal systems and may also open a new route for biological catalysis.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing, 102206, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
27.5 kDa virulence protein
A
241Salmonella enteritidisMutation(s): 1 
Gene Names: spvC (mkaD, vsdD)
EC: 4.2.3.-
Find proteins for P0A2N1 (Salmonella enteritidis)
Go to UniProtKB:  P0A2N1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 7
B
9Homo sapiensMutation(s): 0 
Gene Names: MAPK7 (BMK1, ERK5, PRKM7)
EC: 2.7.11.24
Find proteins for Q13164 (Homo sapiens)
Go to Gene View: MAPK7
Go to UniProtKB:  Q13164
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
TPO
Query on TPO
B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.367α = 90.00
b = 71.842β = 90.00
c = 96.060γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance