Structure of IDP91384

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoylphosphate and arginine

Edit deposit information
CSGID target
IDP91384 
PDB Id
4JHX (NCBI MMDB
Authors
I.G.Shabalin,P.Bacal,J.Winsor,S.Grimshaw,M.Grabowski,M.D.Chordia,L.Shuvalova,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 05, 2013 
Release Date
Mar 20, 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. One of the three enzyme subunits is entrapped in a complex with its first substrate carbamoyl phosphate and its inhibitor arginine. That complex provides additional structural insights into mechanism of inhibition by arginine. It shows that binding of CP together with arginine 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. However, binding mode of arginine is substantially different from binding of citrulline, which is the product of the enzymatic reaction. 
Functional assignment
Anabolic ornithine carbamoyltransferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=76.03Å, b=79.39Å, c=147.17Å
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
36.61-1.85Å (1.90-1.85Å)  
Rall(%)
15.6 
Rwork(%)
15.4 (20.1) 
Rfree(%)
19.0 (23.7) 
Num. observed reflections
76638 (5609) 
Num. Rfree reflections
3831 (290) 
Completeness(%)
99.8 (99.9) 

Model parameters

Num Atoms
7669  
Num Waters
571  
Num Hetatoms
600  
Model mean isotropic B factor
32.710Å2  
RMSD bond length
0.019Å  
RMSD bond angle
1.773°  
Filename uploaded
hkl_refine_80_TLS_ters.pdb (uploaded on Mar 05, 2013 1:01 PM)  
Inserted
Mar 05, 2013