Structure of IDP91384

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with citrulline and inorganic phosphate

Edit deposit information
CSGID target
IDP91384 
PDB Id
4JQO (NCBI MMDB
Authors
I.G.Shabalin,J.Winsor,S.Grimshaw,M.J.Domagalski,W.F.Anderson,W.Minor,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Ivan Shabalin 
Responsible lab
University of Virginia 
Deposition Date
Mar 20, 2013 
Release Date
Apr 17, 2013 

Annotation

Description
Ornithine carbamoyltransferase (OTC) catalyzes the reversible transfer of the carbamoyl group from carbamoyl phosphate (CP) to the Nε atom of L-ornithine (ORN) to produce L-citrulline. There are two types of the enzyme – anabolic (aOTC) and catabolic (cOTC). Anabolic OTCs participate in the urea cycle and L-arginine biosynthesis. Catabolic OTCs are part of the catabolic arginine deiminase pathway found in a number of microorganisms. The reported structure is for the anabolic enzyme from pathogen Vibrio vulnificus. The structure has three monomers in the asymmetric unit which form the physiologically active trimer. All three enzyme subunits are entrapped in a complex with the products of the enzymatic reaction – L-citrulline and inorganic phosphate. The structure shows that binding of both products together causes closure of interdomain cleft and brings catalytic loops K*STRTR, B2–H3 and SMG into the catalytic site that adopt conformations same as in the the Michaelis complex. 
Functional assignment
transferase 

Ligands

Ligand code Name Ligand type
CIR citrulline biological
CL crystallization
PEG crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=81.42Å, b=82.60Å, c=171.97Å
α=90.00, β=90.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
36.04-2.08Å (2.14-2.08Å)  
Rall(%)
16.3 
Rwork(%)
16.2 (22.7) 
Rfree(%)
18.9 (24.5) 
Num. observed reflections
68264 (4094) 
Num. Rfree reflections
3481 (213) 
Completeness(%)
97.2 (80.0) 

Model parameters

Num Atoms
7768  
Num Waters
430  
Num Hetatoms
529  
Model mean isotropic B factor
36.140Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.758°  
Filename uploaded
hkl_refine_33_ter_tls.pdb (uploaded on Mar 20, 2013 4:41 PM)  
Inserted
Mar 20, 2013