Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 28.93 kDa 
• Atom Count: 2025 
• Residue Count: 222 
• Unique protein chains: 2

2Q8Y

Structural insight into the enzymatic mechanism of the phophothreonine lyase

• DOI: 10.2210/pdb2Q8Y/pdb

• Classification: LYASE/TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Enteritidis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-06-12 Released: 2007-12-11 
• Deposition Author(s): Zhu, Y.-Q., Wang, D.-C., Shao, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 

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

• PubMed: 18060821 
• DOI: 10.1016/j.molcel.2007.11.011
• Primary Citation of Related Structures:  
  2P1W, 2Q8Y


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
27.5 kDa virulence protein	A	241	Salmonella enterica subsp. enterica serovar Enteritidis	Mutation(s): 1  Gene Names: mkaD, spvC, vsdD EC: 4.2 (PDB Primary Data), 4.2.3 (UniProt)
Find proteins for P0A2N1 (Salmonella enteritidis) Explore P0A2N1  Go to UniProtKB:  P0A2N1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 7	B	9	N/A	Mutation(s): 2  EC: 2.7.11.24
Find proteins for Q13164 (Homo sapiens) Explore Q13164  Go to UniProtKB:  Q13164
NIH Common Fund Data Resources
PHAROS  Q13164 GTEx  ENSG00000166484

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.367	α = 90
b = 71.842	β = 90
c = 96.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-06-12 
• Released Date: 2007-12-11 
Deposition Author(s): Zhu, Y.-Q., Wang, D.-C., Shao, F.

Revision History 

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