The structure of E. coli UMP kinase in complex with UMP

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

Starting Model: experimental
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Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation.

Briozzo, P.Evrin, C.Meyer, P.Assairi, L.Joly, N.Barzu, O.Gilles, A.M.

(2005) J Biol Chem 280: 25533

  • DOI: https://doi.org/10.1074/jbc.M501849200
  • Primary Citation of Related Structures:  
    2BND, 2BNE, 2BNF

  • PubMed Abstract: 

    Bacterial UMP kinases are essential enzymes involved in the multistep synthesis of nucleoside triphosphates. They are hexamers regulated by the allosteric activator GTP and inhibited by UTP. We solved the crystal structure of Escherichia coli UMP kinase bound to the UMP substrate (2.3 A resolution), the UDP product (2.6 A), or UTP (2.45 A). The monomer fold, unrelated to that of other nucleoside monophosphate kinases, belongs to the carbamate kinase-like superfamily. However, the phosphate acceptor binding cleft and subunit assembly are characteristic of UMP kinase. Interactions with UMP explain the high specificity for this natural substrate. UTP, previously described as an allosteric inhibitor, was unexpectedly found in the phosphate acceptor site, suggesting that it acts as a competitive inhibitor. Site-directed mutagenesis of residues Thr-138 and Asn-140, involved in both uracil recognition and active site interaction within the hexamer, decreased the activation by GTP and inhibition by UTP. These experiments suggest a cross-talk mechanism between enzyme subunits involved in cooperative binding at the phosphate acceptor site and in allosteric regulation by GTP. As bacterial UMP kinases have no counterpart in eukaryotes, the information provided here could help the design of new antibiotics.

  • Organizational Affiliation

    Unité de Chimie Biologique, UMR 206 Institut National de la Recherche Agronomique, Institut National Agronomique Paris-Grignon, 78850 Thiverval-Grignon, URA 2171 CNRS, Institut Pasteur, 75724 Paris Cedex 15. briozzo@grignon.inra.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
241Escherichia coli K-12Mutation(s): 1 
Find proteins for P0A7E9 (Escherichia coli (strain K12))
Explore P0A7E9 
Go to UniProtKB:  P0A7E9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7E9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on U5P

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
C9 H13 N2 O9 P
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.434α = 90
b = 140.434β = 90
c = 59.993γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description