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Structure of IDP00167

Crystal structure of pre-cleavage form of cysteine protease domain from Vibrio cholerae RtxA toxin

Edit deposit information
CSGID target
IDP00167 
PDB Id
3FZY (NCBI MMDB
Authors
L.Shuvalova,G.Minasov,K.Prochazkova,K.J.F.Satchell,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Ludmilla Shuvalova 
Responsible lab
Northwestern University 
Deposition Date
Jan 26, 2009 
Release Date
Feb 17, 2009 

Annotation

Description
Vibrio cholerae produces a large multifunctional protein that undergoes autoproteolytic processing catalyzed by its cysteine protease domain (CPD) to release the cytopathic domains within the eukaryotic host cell cytoplasm. The CPD is activated after translocation into the host cell by the binding of inositol hexaphosphate (InsP6, red in the picture). One of the sites of proteolysis is at the N-terminus of the CPD. X-Ray crystallographic structure determination of the pro-form of a catalytically inactive mutant (C3568S) CPD reveals the structural basis for the InsP6 activation and the mechanism of proteolytic processing. The 1.8Å crystal structure shows that the CPD is a caspase-like protein that has the leucine (purple) of its N-terminal cleavage site bound in a hydrophobic specificity pocket and the scissile peptide bond located between the serine that was substituted for the essential cysteine and the conserved histidine residue (both shown with magenta carbon atoms). The InsP6 activating ligand is bound by a number of positively charged lysine and arginine residues from the N-terminal region (blue), the main body of the CDP (yellow) and the C-terminal region (green). Related toxins with Cysteine Protease Domains, but other cytopathic domains, occur in a number of other gram-negative bacteria. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
IHP inositol hexakisphosphate biological
CL
UNX unknown atom or ion

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=46.05Å, b=66.37Å, c=137.96Å
α=90.00, β=90.00, γ=90.00 
Solvent content
40.38  
Matthews coefficient
2.06  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
23.67-1.95Å (2.00-1.95Å)  
Rall(%)
17.1 
Rwork(%)
16.9 (22.0) 
Rfree(%)
21.6 (25.7) 
Num. observed reflections
31516 (2248) 
Num. Rfree reflections
1575 (109) 
Completeness(%)
99.6 (98.1) 

Model parameters

Num Atoms
3484  
Num Waters
313  
Num Hetatoms
406  
Model mean isotropic B factor
32.050Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.696°  
Filename uploaded
rcsb051248.pdb (uploaded on Feb 13, 2009 11:58 AM)  
Inserted
Feb 13, 2009