1L2U

Orotidine 5'-monophosphate decarboxylase from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase

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

(2002) J.Mol.Biol. 18: 1019-1029

  • DOI: 10.1016/S0022-2836(02)00200-0

  • PubMed Abstract: 
  • Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate (UMP). We have earlier determined the structure of ODCase from Escherichia coli complexed with the inhibitor 1-( ...

    Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate (UMP). We have earlier determined the structure of ODCase from Escherichia coli complexed with the inhibitor 1-(5'-phospho-beta-d-ribofuranosyl)barbituric acid (BMP); here we present the 2.5 A structure of the uncomplexed apo enzyme, determined from twinned crystals. A structural analysis and comparison of the two structures of the E. coli enzyme show that binding of the inhibitor is accompanied by significant domain movements of approximately 12 degrees around a hinge that crosses the active site. Hence, the ODCase dimer, which contains two active sites, may be divided in three domains: a central domain that is fixed, and two lids which independently move 12 degrees upon binding. Corresponding analyses, presented herein, of the two Saccharomyces cerevisiae ODCase structures (with and without BMP) and the Methanobacterium thermoautotrophicum ODCase structures (with and without 6-aza UMP) show very similar, but somewhat smaller domain movements. The domain movements seem to be initiated by the phosphoryl binding to the enzyme and can explain why the binding of the phosphoryl group is essential for the catalytic function.


    Related Citations: 
    • Structural basis for the catalytic mechanism of a proficient enzyme: Orotidine 5'-monophosphate decarboxylase
      Harris, P.,Navarro Poulsen, J.C.,Jensen, K.F.,Larsen, S.
      (2000) Biochemistry 39: 4217
    • Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group
      Poulsen, J.C.,Harris, P.,Jensen, K.F.,Larsen, S.
      (2001) Acta Crystallogr.,Sect.D 57: 1251


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orotidine 5'-phosphate decarboxylase
A, B
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.159 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.690α = 90.00
b = 142.690β = 90.00
c = 105.370γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection