Structure of IDP91384

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate

Edit deposit information
CSGID target
IDP91384 
PDB Id
4JFR (NCBI MMDB
Authors
I.G.Shabalin,J.Winsor,S.Grimshaw,T.Osinski,J.Bajor,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
Feb 28, 2013 
Release Date
Mar 13, 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. Two of the three enzyme subunits are entrapped in a complex with its first substrate carbamoyl phosphate. That complex provides additional structural insights in the enzyme mechanism of action because it proves that binding of CP causes closure of interdomain cleft and change of 55-60 catalytic loop conformation, whereas catalytic loops B2–H3 and SMG can adopt conformations different from the Michaelis complex of be disordered. 
Functional assignment
Anabolic ornithine carbamoyltransferase 

Ligands

Ligand code Name Ligand type
CP carbamoyl phosphate biological
MG 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=81.34Å, b=80.92Å, c=177.64Å
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
38.96-2.17Å (2.23-2.17Å)  
Rall(%)
17.3 
Rwork(%)
17.1 (26.9) 
Rfree(%)
20.5 (33.0) 
Num. observed reflections
62539 (4494) 
Num. Rfree reflections
3189 (240) 
Completeness(%)
99.5 (99.1) 

Model parameters

Num Atoms
7793  
Num Waters
272  
Num Hetatoms
293  
Model mean isotropic B factor
58.170Å2  
RMSD bond length
0.016Å  
RMSD bond angle
1.669°  
Filename uploaded
hkl_refine_60_ter_TLS.pdb (uploaded on Mar 01, 2013 3:38 PM)  
Inserted
Mar 01, 2013