2ZA2

Crystal Structure of the apo-form of orotidine-5'-monophosphate decarboxylase from P.falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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.(Tokyo) 143: 69-78

  • DOI: 10.1093/jb/mvm193
  • Primary Citation of Related Structures:  
  • Also Cited By: 6DSS, 6DSR, 6DSQ

  • 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 Plasmodiu ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orotidine 5'-phosphate decarboxylase
A, B
323Plasmodium falciparumMutation(s): 0 
Gene Names: ompdc
EC: 4.1.1.23
Find proteins for Q8T6J6 (Plasmodium falciparum)
Go to UniProtKB:  Q8T6J6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.210 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 201.800α = 90.00
b = 201.800β = 90.00
c = 44.000γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-09-26 
  • 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
    Type: Version format compliance