1EIX

STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase.

Harris, P., Poulsen, J.C.N., Jensen, K.F., Larsen, S.

(2000) Biochemistry 39: 4217-4224


  • PubMed Abstract: 

    • Orotidine 5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate, the last step in the de novo synthesis of uridine 5'-monophosphate. ODCase is a very proficient enzyme [Radzicka, A., and Wolfenden, R. (19 ...

    Orotidine 5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate, the last step in the de novo synthesis of uridine 5'-monophosphate. ODCase is a very proficient enzyme [Radzicka, A., and Wolfenden, R. (1995) Science 267, 90-93], enhancing the reaction rate by a factor of 10(17). This proficiency has been enigmatic, since it is achieved without metal ions or cofactors. Here we present a 2.5 A resolution structure of ODCase complexed with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid. It shows a closely packed dimer composed of two alpha/beta-barrels with two shared active sites. The orientation of the orotate moiety of the substrate is unambiguously deduced from the structure, and previously proposed catalytic mechanisms involving protonation of O2 or O4 can be ruled out. The proximity of the OMP carboxylate group with Asp71 appears to be instrumental for the decarboxylation of OMP, either through charge repulsion or through the formation of a very short O.H.O hydrogen bond between the two carboxylate groups.

    Organizational Affiliation: 

    Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE
A, B, C, D
245Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pyrF
EC: 4.1.1.23
Find proteins for P08244 (Escherichia coli (strain K12))
Go to UniProtKB:  P08244
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMQ
Query on BMQ
Download SDF File 
Download CCD File 
A, B, C, D
1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID
C9 H13 N2 O10 P
AODYJUNLDJOADV-YXZULKJRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BMQKi: 0.0088 nM BINDINGMOAD
BMQKi: 0.0088 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.280α = 90.00
b = 95.920β = 90.00
c = 145.020γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
CCP4data scaling
CNSrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection