1LOL

Crystal structure of orotidine monophosphate decarboxylase complex with XMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


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:  
    1LOL, 1LOQ, 1LOR, 1LOS, 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 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
orotidine 5'-monophosphate decarboxylaseA, B229Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
Gene Names: pyrFMTH_129
EC: 4.1.1.23
UniProt
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26232 
Go to UniProtKB:  O26232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26232
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XMP
Query on XMP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
XANTHOSINE-5'-MONOPHOSPHATE
C10 H14 N4 O9 P
DCTLYFZHFGENCW-UUOKFMHZSA-O
 Ligand Interaction
BU2
Query on BU2

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
1,3-BUTANEDIOL
C4 H10 O2
PUPZLCDOIYMWBV-BYPYZUCNSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
XMP Binding MOAD:  1LOL Ki: 410 (nM) from 1 assay(s)
PDBBind:  1LOL Ki: 410 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.57α = 90
b = 55.482β = 94.28
c = 66.129γ = 90
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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