2QCF

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 5-fluoro-UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 

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This is version 1.2 of the entry. See complete history


Literature

Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design.

Wittmann, J.G.Heinrich, D.Gasow, K.Frey, A.Diederichsen, U.Rudolph, M.G.

(2008) Structure 16: 82-92

  • DOI: https://doi.org/10.1016/j.str.2007.10.020
  • Primary Citation of Related Structures:  
    2QCC, 2QCD, 2QCE, 2QCF, 2QCG, 2QCH, 2QCL, 2QCM, 2QCN

  • PubMed Abstract: 

    UMP synthase (UMPS) catalyzes the last two steps of de novo pyrimidine nucleotide synthesis and is a potential cancer drug target. The C-terminal domain of UMPS is orotidine-5'-monophosphate decarboxylase (OMPD), a cofactor-less yet extremely efficient enzyme. Studies of OMPDs from micro-organisms led to the proposal of several noncovalent decarboxylation mechanisms via high-energy intermediates. We describe nine crystal structures of human OMPD in complex with substrate, product, and nucleotide inhibitors. Unexpectedly, simple compounds can replace the natural nucleotides and induce a closed conformation of OMPD, defining a tripartite catalytic site. The structures outline the requirements drugs must meet to maximize therapeutic effects and minimize cross-species activity. Chemical mimicry by iodide identified a CO(2) product binding site. Plasticity of catalytic residues and a covalent OMPD-UMP complex prompt a reevaluation of the prevailing decarboxylation mechanism in favor of covalent intermediates. This mechanism can also explain the observed catalytic promiscuity of OMPD.


  • Organizational Affiliation

    Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine 5'-monophosphate synthase (UMP synthase)260Homo sapiensMutation(s): 1 
Gene Names: UMPS
EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11172 (Homo sapiens)
Explore P11172 
Go to UniProtKB:  P11172
PHAROS:  P11172
GTEx:  ENSG00000114491 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11172
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Binding Affinity Annotations 
IDSourceBinding Affinity
5FU BindingDB:  2QCF Ki: 9.80e+4 (nM) from 1 assay(s)
PDBBind:  2QCF IC50: 3.20e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.815α = 90
b = 115.512β = 90
c = 61.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Data collection, Database references, Derived calculations