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Structure of IDP00573

Predicted insulinase family protease from Yersinia pestis.

Edit deposit information
CSGID target
IDP00573 
PDB Id
3GO9 (NCBI MMDB
Authors
J.Osipiuk,N.Maltseva,O.Onopriyenko,S.Peterson,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 18, 2009 
Release Date
Apr 07, 2009 

Annotation

Description
The YPO3991 gene product from Yersinia pestis is predicted to be an enzyme of the insulinase family of proteases which are involved in degradation of insulin, glucagon and other polypeptides. Insulinases are metallopeptidases belonging to the MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues that have been found either to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity. Our protein does not have a common HEXXH amino-acid motif found in about half of metalloproteases. The structure shows a putative substrate binding site in a region where the N-terminal part of the protein is placed outside the main body of the molecule and buried in a cavity of a neighbor molecule in the crystal. There are 6 zinc ions in the structure. Zinc 604 possibly represents a metal site necessary for protein activity.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
PEG
ZN
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=42.89Å, b=80.23Å, c=66.62Å
α=90.00, β=99.34, γ=90.00 
Solvent content
39.93  
Matthews coefficient
2.05  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
42.30-1.62Å (1.66-1.62Å)  
Rall(%)
16.8 
Rwork(%)
16.6 (24.6) 
Rfree(%)
20.3 (31.2) 
Num. observed reflections
59533 (4056) 
Num. Rfree reflections
3036 (191) 
Completeness(%)
99.6 (96.5) 

Model parameters

Num Atoms
3616  
Num Waters
493  
Num Hetatoms
615  
Model mean isotropic B factor
17.840Å2  
RMSD bond length
0.019Å  
RMSD bond angle
1.693°  
Filename uploaded
rcsb052108.pdb (uploaded on Apr 09, 2009 6:02 PM)  
Inserted
Apr 09, 2009