2BNE

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

Summary for 2BNE

• Entry DOI: 10.2210/pdb2bne/pdb
• Related: 2BND 2BNF
• Descriptor: URIDYLATE KINASE, URIDINE-5'-MONOPHOSPHATE, GLYCEROL, ... (4 entities in total)
• Functional Keywords: transferase, nucleoside monophosphate kinase, pyrimidine biosynthesis
• Biological source: ESCHERICHIA COLI
• Cellular location: Cytoplasm: P29464
• Total number of polymer chains: 2
• Total formula weight: 53291.57

Authors

Briozzo, P.,Evrin, C.,Meyer, P.,Assairi, L.,Joly, N.,Barzu, O.,Gilles, A.M. (deposition date: 2005-03-23, release date: 2005-04-25, Last modification date: 2023-12-13)

Primary citation

Briozzo, P.,Evrin, C.,Meyer, P.,Assairi, L.,Joly, N.,Barzu, O.,Gilles, A.M.
Structure of Escherichia Coli Ump Kinase Differs from that of Other Nucleoside Monophosphate Kinases and Sheds New Light on Enzyme Regulation.
J.Biol.Chem., 280:25533-, 2005

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.

PubMed: 15857829
DOI: 10.1074/JBC.M501849200

Experimental method

X-RAY DIFFRACTION (2.3 Å)