2Z8O | pdb_00002z8o

Structural basis for the catalytic mechanism of phosphothreonine lyase

• PDB DOI: https://doi.org/10.2210/pdb2Z8O/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-09-07 Released: 2007-12-18 
• Deposition Author(s): Chen, L., Wang, H., Gu, L., Huang, N., Zhou, J.M., Chai, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.253 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

Structural basis for the catalytic mechanism of phosphothreonine lyase.

Chen, L., Wang, H., Zhang, J., Gu, L., Huang, N., Zhou, J.M., Chai, J.

(2008) Nat Struct Mol Biol 15: 101-102

• PubMed: 18084305 
• DOI: https://doi.org/10.1038/nsmb1329
• Primary Citation Related Structures: 
  2Z8M, 2Z8N, 2Z8O, 2Z8P


• PubMed Abstract: 
  

  Salmonella SpvC belongs to a new enzyme family designated phosphothreonine lyases that irreversibly inactivate mitogen-activated protein kinases. The crystal structure of SpvC reported here reveals that the two phosphorylated residues in the substrate peptide predominantly mediate its recognition by SpvC. Substrate-induced conformational changes in SpvC sequester the phosphothreonine in a completely solvent-free environment, preventing the hydrolysis of the phosphate group and facilitating the elimination reaction.

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Organizational Affiliation: 
• Graduate Program in Chinese Academy of Medical Sciences and Beijing Union Medical College, Beijing 100730, China.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.36 kDa 
• Atom Count: 3,581 
• Modeled Residue Count: 416 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
27.5 kDa virulence protein	A, B	241	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: mkaD, spvC, vsdD EC: 4.2.3
UniProt
Find proteins for P0A2M9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2M9  Go to UniProtKB:  P0A2M9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	C [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.253 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.755	α = 90
b = 70.755	β = 90
c = 200.71	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Chen, L., Wang, H., Gu, L., Huang, N., Zhou, J.M., Chai, J.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary