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 

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)  

R_all(%)

13.7 

R_work(%)

13.5 (19.6) 

R_free(%)

16.7 (20.7) 

Num. observed reflections

101790 (7041) 

Num. R_free reflections

5089 (364) 

Completeness(%)

100.0 (100.0) 

Model parameters

Num Atoms

8512  

Num Waters

495  

Num Hetatoms

0  

Model mean isotropic B factor

25.750Ų  

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