Structure of IDP90525

1.80 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with uridine-5'-monophosphate (UMP)

Edit deposit information
CSGID target
IDP90525 
PDB Id
3UWQ (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,J.Winsor,L.Shuvalova,M.Kuhn,E.V.Filippova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Dec 02, 2011 
Release Date
Dec 14, 2011 

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. Here we present the second structure of the orotidine 5'-phosphate decarboxylase (IDP90525) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with its product uridine-5'-monophosphate (UMP). The protein exhibits (α8/β8)-TIM-barrel topology with three additional helices flanking the TIM-barrel core. Structurally, apo and product bound form structures are very similar with the RMSD between 0.4 and 0.7 Å. UMP makes direct polar interactions with residues in strand β8, β7, β5, β2, and β1 and water mediated contacts with some residues residing at the C-termini of the strands.  
Functional assignment
LYASE 

Ligands

Ligand code Name Ligand type
PEG crystallization
U5P uridine-5'-monophosphate biological
TRS Tris(hydroxymethyl)aminomethane crystallization
XPE 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol 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=52.14Å, b=96.94Å, c=104.08Å
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
29.33-1.80Å (1.85-1.80Å)  
Rall(%)
15.2 
Rwork(%)
15.0 (17.9) 
Rfree(%)
17.8 (22.2) 
Num. observed reflections
49639 (3585) 
Num. Rfree reflections
2531 (194) 
Completeness(%)
100.0 (100.0) 

Model parameters

Num Atoms
3649  
Num Waters
468  
Num Hetatoms
605  
Model mean isotropic B factor
28.190Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.631°  
Filename uploaded
3UWQ.pdb (uploaded on Dec 26, 2011 7:46 PM)  
Inserted
Dec 26, 2011