1LOL

Crystal structure of orotidine monophosphate decarboxylase complex with XMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase.

Wu, N.Pai, E.F.

(2002) J.Biol.Chem. 277: 28080-28087

  • DOI: 10.1074/jbc.M202362200
  • Primary Citation of Related Structures:  1LOS, 1LOQ, 1LOR, 1LP6

  • PubMed Abstract: 
  • The crystal structures of the enzyme orotidine-5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with its product UMP and the inhibitors 6-hydroxyuridine 5'-phosphate (BMP), XMP, and CMP are reported. A mutant version ...

    The crystal structures of the enzyme orotidine-5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with its product UMP and the inhibitors 6-hydroxyuridine 5'-phosphate (BMP), XMP, and CMP are reported. A mutant version of the protein, in which four residues of the flexible phosphate-binding loop (180)Gly-Gly(190) were removed and Arg(203) was replaced by alanine, was also analyzed. The XMP and CMP complexes reveal a ligand-binding mode that is distinct from the one identified previously with the aromatic rings located outside the binding pocket. A potential pathway for ligand binding is discussed.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
orotidine 5'-monophosphate decarboxylase
A, B
229Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)Gene Names: pyrF
EC: 4.1.1.23
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Go to UniProtKB:  O26232
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU2
Query on BU2

Download SDF File 
Download CCD File 
A, B
1,3-BUTANEDIOL
C4 H10 O2
PUPZLCDOIYMWBV-BYPYZUCNSA-N
 Ligand Interaction
XMP
Query on XMP

Download SDF File 
Download CCD File 
A, B
XANTHOSINE-5'-MONOPHOSPHATE
5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE
C10 H14 N4 O9 P
DCTLYFZHFGENCW-UUOKFMHZSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XMPKi: 410 nM BINDINGMOAD
XMPKi: 410 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.570α = 90.00
b = 55.482β = 94.28
c = 66.129γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-05-06 
  • Released Date: 2002-08-07 
  • Deposition Author(s): Wu, N., Pai, E.F.

Revision History 

  • Version 1.0: 2002-08-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance