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Structure of IDP90224

Structure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri

Edit deposit information
CSGID target
IDP90224 
PDB Id
3I0U (NCBI MMDB
Authors
A.U.Singer,T.Skarina,B.Nocek,R.Gordon,R.Lam,O.Kagan,A.M.Edwards,A.Joachimiak,N.Y.Chirgadze,W.F.Anderson,A.Savchenko 
Responsible person
Alexander Singer 
Responsible lab
University of Calgary 
Deposition Date
Jun 25, 2009 
Release Date
Sep 01, 2009 

Annotation

Description
Gram-negative pathogens exert virulence to a significant degree by the secretion of toxins, termed effectors, through the type III secretion system. One effector from Salmonella sp., SpvC, was found to have a highly novel enzymatic function, irreversibly dephosphorylating an activating threonine residue on MAP kinase proteins via a lyase activity (phosphothreonine lyase), leaving a double bond between the alpha and beta carbon (Science. 2007 315:1000-3.). We have solved the structure of the homologue of SpvC from Shigella flexneri, termed OspF, to 2.7 Å, from residue 23 to the C-terminus. This structure shows a very similar overall fold to Salmonella enterica SpvC, to which it shares 64% sequence identity. The principal difference involves a change in direction in the most N-terminal helix, which folds around the structure in SpvC but which remains straight in OspF. The overall significance of this finding has yet to be determined. Although 2 molecules of OspF can be found in an asymmetric unit in crystals, the protein is predicted to be monomeric. 
Functional assignment
phosphothreonince lyase 

Ligands

Ligand code Name Ligand type
MPD

Structure information

Unit cell parameters

Space Group
P 41 21 2  
Unit Cell

a=62.12Å, b=62.12Å, c=239.59Å
α=90.00, β=90.00, γ=90.00 
Solvent content
45.9  
Matthews coefficient
2.27  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
43.94-2.70Å (2.77-2.70Å)  
Rall(%)
25.2 
Rwork(%)
25.0 (26.4) 
Rfree(%)
28.7 (33.3) 
Num. observed reflections
13700 (963) 
Num. Rfree reflections
671 (43) 
Completeness(%)
99.8 (100.0) 

Model parameters

Num Atoms
3193  
Num Waters
6  
Num Hetatoms
14  
Model mean isotropic B factor
71.020Å2  
RMSD bond length
0.017Å  
RMSD bond angle
1.713°  
Filename uploaded
rcsb053822_final.pdb (uploaded on Oct 05, 2009 11:47 AM)  
Inserted
Oct 05, 2009