ISDA: 2ZA3

Deposition Date 2007-09-26

Release Date 2007-12-04

Last Version Date 2023-11-01

Entry Detail

PDB ID:

2ZA3

Keywords:

LYASE

Title:

Crystal Structure of orotidine 5'-monophosphate decarboxylase complexed with uridine 5'-monophosphate from P.falciparum

Biological Source:

Source Organism:

Plasmodium falciparum (Taxon ID: 5833)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.65 Å

R-Value Free:

0.28

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

H 3

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Orotidine 5'-phosphate decarboxylase
Gene (Uniprot):ompdc
Chain IDs:A, B
Chain Length:323
Number of Molecules:2
Biological Source:Plasmodium falciparum

UniProt ID:Q8T6J6 Pfam ID:PF00215 EC:2.4.2.10

Ligand Molecules

U5P

Primary Citation

Structural Basis for the Decarboxylation of Orotidine 5'-Monophosphate (OMP) by Plasmodium Falciparum OMP Decarboxylase

Tokuoka, K, Kusakari, Y, Krungkrai, S.R, Matsumura, H, Kai, Y, Krungkrai, J, Horii, T, Inoue, T.Show

J.Biochem.(Tokyo) 143 69 78 (2008)

PMID: 17981823 DOI: 10.1093/jb/mvm193

Abstact

Orotidine 5'-monophoshate decarboxylase (OMPDC) catalyses the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP). Here, we report the X-ray analysis of apo, substrate or product-complex forms of OMPDC from Plasmodium falciparum (PfOMPDC) at 2.7, 2.65 and 2.65 A, respectively. The structural analysis provides the substrate recognition mechanism with dynamic structural changes, as well as the rearrangement of the hydrogen bond array at the active site. The structural basis of substrate or product binding to PfOMPDC will help to uncover the decarboxylation mechanism and facilitate structure-based optimization of antimalarial drugs.

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Primary Citation of related structures

Abstact

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