2QCG

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to 5-bromo-UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2007.10.020
  • Primary Citation of Related Structures:  
    2QCC, 2QCH, 2QCG, 2QCF, 2QCE, 2QCD, 2QCN, 2QCM, 2QCL

  • 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 efficie ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uridine 5'-monophosphate synthase (UMP synthase)AB260Homo sapiensMutation(s): 0 
Gene Names: UMPSOK/SW-cl.21
EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (UniProt)
Find proteins for P11172 (Homo sapiens)
Explore P11172 
Go to UniProtKB:  P11172
NIH Common Fund Data Resources
PHAROS  P11172
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5BU
Query on 5BU

Download CCD File 
A, B
5-BROMO-URIDINE-5'-MONOPHOSPHATE
C9 H12 Br N2 O9 P
IDPVUMJNEZFMNU-UAKXSSHOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5BUIC50 :  100000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.184α = 90
b = 61.699β = 113.06
c = 69.169γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
COMOphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance