1DQX

CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.

Miller, B.G.Hassell, A.M.Wolfenden, R.Milburn, M.V.Short, S.A.

(2000) Proc.Natl.Acad.Sci.USA 97: 2011-2016

  • DOI: 10.1073/pnas.030409797
  • Primary Citation of Related Structures:  1DQW

  • PubMed Abstract: 
  • Orotidine 5'-phosphate decarboxylase produces the largest rate enhancement that has been reported for any enzyme. The crystal structure of the recombinant Saccharomyces cerevisiae enzyme has been determined in the absence and presence of the proposed ...

    Orotidine 5'-phosphate decarboxylase produces the largest rate enhancement that has been reported for any enzyme. The crystal structure of the recombinant Saccharomyces cerevisiae enzyme has been determined in the absence and presence of the proposed transition state analog 6-hydroxyuridine 5'-phosphate, at a resolution of 2.1 A and 2.4 A, respectively. Orotidine 5'-phosphate decarboxylase folds as a TIM-barrel with the ligand binding site near the open end of the barrel. The binding of 6-hydroxyuridine 5'-phosphate is accompanied by protein loop movements that envelop the ligand almost completely, forming numerous favorable interactions with the phosphoryl group, the ribofuranosyl group, and the pyrimidine ring. Lysine-93 appears to be anchored in such a way as to optimize electrostatic interactions with developing negative charge at C-6 of the pyrimidine ring, and to donate the proton that replaces the carboxylate group at C-6 of the product. In addition, H-bonds from the active site to O-2 and O-4 help to delocalize negative charge in the transition state. Interactions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphoribosyl group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.


    Organizational Affiliation

    Department of Biochemistry, University of North Carolina, Chapel Hill, NC 27599, USA. Research Triangle Park, NC 27709, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
A, B, C, D
267Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: URA3
EC: 4.1.1.23
Find proteins for P03962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P03962
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMP
Query on BMP

Download SDF File 
Download CCD File 
A, B, C, D
6-HYDROXYURIDINE-5'-PHOSPHATE
C9 H13 N2 O10 P
UDOBICLZEKUKCV-YXZULKJRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BMPKi: 0 nM (98) BINDINGDB
BMPKi: 0.009 nM BINDINGMOAD
BMPKi: 0.009 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.890α = 90.00
b = 79.970β = 108.59
c = 98.190γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-20
    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: 2017-10-04
    Type: Refinement description