PDBsum entry 2z8p

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Lyase PDB id
Protein chain
217 a.a.
Waters ×259
PDB id:
Name: Lyase
Title: Structural basis for the catalytic mechanism of phosphothreo
Structure: 27.5 kda virulence protein. Chain: a. Synonym: spvc, phosphothreonine lyase. Engineered: yes. Mutation: yes. (Gly)(glu)(ala)(tpo)(val)(ptr)(ala). Chain: b. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: the peptide was chemically synthesized.
1.80Å     R-factor:   0.211     R-free:   0.229
Authors: L.Chen,H.Wang,L.Gu,N.Huang,J.M.Zhou,J.Chai
Key ref:
L.Chen et al. (2008). Structural basis for the catalytic mechanism of phosphothreonine lyase. Nat Struct Mol Biol, 15, 101-102. PubMed id: 18084305 DOI: 10.1038/nsmb1329
07-Sep-07     Release date:   18-Dec-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0A2M9  (VRP3_SALTY) -  MAPK phosphothreonine lyase
241 a.a.
217 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     lyase activity     1 term  


DOI no: 10.1038/nsmb1329 Nat Struct Mol Biol 15:101-102 (2008)
PubMed id: 18084305  
Structural basis for the catalytic mechanism of phosphothreonine lyase.
L.Chen, H.Wang, J.Zhang, L.Gu, N.Huang, J.M.Zhou, J.Chai.
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.
  Selected figure(s)  
Figure 1.
(a) Overall structure of free SpvC in space group P2[1]2[1]2[1]. (b) Electron density (at 1.3 ) for the peptide. SpvC is shown in the same orientation as in a. (c) Specific recognition of the phosphothreonine. The side chains of those residues of SpvC interacting with the phosphothreonine are colored yellow. (d) Specific recognition of the phosphotyrosine. (e) Effects on enzymatic activity of mutations in the residues of SpvC recognizing the phosphothreonine (the residues shown in c). Phosphorylated ERK2 was used as the substrate for various SpvC mutants. The residual phosphorylated ERK2 was detected by anti-pERK antibody. (f) Effects on enzymatic activity of mutations in the residues of SpvC shown in d.
Figure 2.
(a) Structural alignment of the free and substrate-bound forms of SpvC. (b) Binding of the substrate triggers conformational changes around the phosphothreonine binding site in SpvC. The peptide is colored cyan. Residues from the free and substrate-bound SpvC are shown in pink and orange, respectively. The solvent-accessible surface area of pThr183 in the SpvC-peptide complex is 0.0 Å^2.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2008, 15, 101-102) copyright 2008.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20143948 A.P.Bhavsar, S.D.Auweter, and B.B.Finlay (2010).
Proteomics as a probe of microbial pathogenesis and its molecular boundaries.
  Future Microbiol, 5, 253-265.  
20071215 C.A.Broberg, and K.Orth (2010).
Tipping the balance by manipulating post-translational modifications.
  Curr Opin Microbiol, 13, 34-40.  
20351769 Y.Goto, B.Li, J.Claesen, Y.Shi, M.J.Bibb, and W.A.van der Donk (2010).
Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights.
  PLoS Biol, 8, e1000339.  
19233656 D.F.Brennan, and D.Barford (2009).
Eliminylation: a post-translational modification catalyzed by phosphothreonine lyases.
  Trends Biochem Sci, 34, 108-114.  
18372208 J.M.Zhou, and J.Chai (2008).
Plant pathogenic bacterial type III effectors subdue host responses.
  Curr Opin Microbiol, 11, 179-185.  
18692770 M.A.Hamon, and P.Cossart (2008).
Histone modifications and chromatin remodeling during bacterial infections.
  Cell Host Microbe, 4, 100-109.  
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