Structure of IDP90525

1.77 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961

Annotation

Description

Orotidine 5′-monophosphate decarboxylase catalyses the decarboxylation of orotidine 5′-monophosphate to uridine 5′-monophosphate (UMP) without the aid of any metal ions or cofactors. This reaction is the last step in the de novo synthesis of pyrimidine nucleotides. We have determined an apo-structure of orotidine 5′-monophosphate decarboxylase from Vibrio cholerae. Two chains of the protein in the asymmetric unit form a closely bound homodimer. Each subunit of the dimer folds as an alpha/beta-barrel with eight central beta-strands flanked by eleven alpha helices. There is one active sites per subunit located at the C termini of the beta-strands of the barrel. Residues from both chains contribute to formation of each active site. A conserved unique motif Lys-Asp-Lys-Asp of the active site is present in the V. cholerae decarboxylase. Structures of binary complexes with UMP and known inhibitor 1-(5′-phospho-beta-D-ribofuranosyl)barbituric acid (BMP) can help to elucidate the mechanism of the reaction catalyzed by the protein.  

Functional assignment

Lyase  

Ligands

Ligand code	Name	Ligand type

Structure information

Unit cell parameters

Space Group

P 21 21 21  

Unit Cell

a=47.30Å, b=94.67Å, c=99.18Å
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

68.48-1.77Å (1.82-1.77Å)  

R_all(%)

15.5  

R_work(%)

15.4 (22.9)  

R_free(%)

18.5 (26.2)  

Num. observed reflections

43729 (3076)  

Num. R_free reflections

2186 (164)  

Completeness(%)

99.4 (95.8)  

Model parameters

Num Atoms

4245  

Num Waters

593  

Num Hetatoms

5  

Model mean isotropic B factor

14.580Ų  

RMSD bond length

0.010Å  

RMSD bond angle

1.383°  

Filename uploaded

final-deposit-idp90525a.pdb (uploaded on 2010-01-14 10:41:27-05)