Structure of IDP91384

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate and L-norvaline

Edit deposit information
CSGID target
IDP91384 
PDB Id
4H31 (NCBI MMDB
Authors
I.G.Shabalin,J.Winsor,S.Grimshaw,T.Osinski,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
Sep 13, 2012 
Release Date
Sep 26, 2012 

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. The enzyme is entrapped in a triple complex with its substrate carbamoyl phosphate and L-norvaline, which is analogue of the second substrate incapable to perform the reaction due to the absence of Nε atom. That complex mimics the Michaelis complex of the enzymatic reaction and provides additional structural insights in its mechanism of action because it has both catalytic loops B2–H3 loop and SMG loop ordered, which are usually discorded in the apo forms of the enzyme. Moreover, more rigid triple complexes allowed for getting the structure at much better resolution than the apo-form (3UPD) 
Functional assignment
transferase 

Ligands

Ligand code Name Ligand type
CL CHLORIDE ION crystallization
CP carbamoyl phosphate biological
PE5 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol 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=74.26Å, b=80.91Å, c=152.73Å
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
50.00-1.70Å (1.74-1.70Å)  
Rall(%)
13.7 
Rwork(%)
13.5 (19.6) 
Rfree(%)
16.7 (20.7) 
Num. observed reflections
101790 (7041) 
Num. Rfree reflections
5089 (364) 
Completeness(%)
100.0 (100.0) 

Model parameters

Num Atoms
8512  
Num Waters
495  
Num Hetatoms
0  
Model mean isotropic B factor
25.750Å2  
RMSD bond length
0.017Å  
RMSD bond angle
1.799°  
Filename uploaded
hkl_refine_43_TLS_TER.pdb (uploaded on Sep 19, 2012 11:59 AM)  
Inserted
Sep 19, 2012