2ZA3

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

• PDB DOI: https://doi.org/10.2210/pdb2ZA3/pdb

• Classification: LYASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-26 Released: 2007-12-04 
• Deposition Author(s): Tokuoka, K., Inoue, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.287 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6DSS

Literature

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.

(2008) J Biochem 143: 69-78

• PubMed: 17981823 
• DOI: https://doi.org/10.1093/jb/mvm193
• Primary Citation of Related Structures:  
  2ZA1, 2ZA2, 2ZA3


• PubMed Abstract: 
  

  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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Organizational Affiliation: 

Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.38 kDa 
• Atom Count: 5,187 
• Modelled Residue Count: 631 
• Deposited Residue Count: 646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	323	Plasmodium falciparum	Mutation(s): 0  EC: 4.1.1.23
UniProt
Find proteins for Q8T6J6 (Plasmodium falciparum) Explore Q8T6J6  Go to UniProtKB:  Q8T6J6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	C [auth A], D [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
U5P	PDBBind:  2ZA3	Ki: 2.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.287 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.5	α = 90
b = 202.5	β = 90
c = 44.7	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Tokuoka, K., Inoue, T.

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description