4LRL

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dTTP

Summary for 4LRL

• Entry DOI: 10.2210/pdb4lrl/pdb
• Related: 2O6I 3IRH
• Descriptor: HD domain protein, NICKEL (II) ION, 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, ... (7 entities in total)
• Functional Keywords: structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, hd domain, phosphohydrolase, dntpase, allosteric regulation, metal binding protein, hydrolase
• Biological source: Enterococcus faecalis
• Total number of polymer chains: 4
• Total formula weight: 227342.39

Authors

Vorontsov, I.I.,Minasov, G.,Shuvalova, L.,Joachimiak, A.,Anderson, W.F.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2013-07-19, release date: 2013-11-20, Last modification date: 2023-09-20)

Primary citation

Vorontsov, I.I.,Wu, Y.,Delucia, M.,Minasov, G.,Mehrens, J.,Shuvalova, L.,Anderson, W.F.,Ahn, J.
Mechanisms of Allosteric Activation and Inhibition of the Deoxyribonucleoside Triphosphate Triphosphohydrolase from Enterococcus faecalis.
J.Biol.Chem., 289:2815-2824, 2014

PubMed Abstract: EF1143 from Enterococcus faecalis, a life-threatening pathogen that is resistant to common antibiotics, is a homo-tetrameric deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase (dNTPase), converting dNTPs into the deoxyribonucleosides and triphosphate. The dNTPase activity of EF1143 is regulated by canonical dNTPs, which simultaneously act as substrates and activity modulators. Previous crystal structures of apo-EF1143 and the protein bound to both dGTP and dATP suggested allosteric regulation of its enzymatic activity by dGTP binding at four identical allosteric sites. However, whether and how other canonical dNTPs regulate the enzyme activity was not defined. Here, we present the crystal structure of EF1143 in complex with dGTP and dTTP. The new structure reveals that the tetrameric EF1143 contains four additional secondary allosteric sites adjacent to the previously identified dGTP-binding primary regulatory sites. Structural and enzyme kinetic studies indicate that dGTP binding to the first allosteric site, with nanomolar affinity, is a prerequisite for substrate docking and hydrolysis. Then, the presence of a particular dNTP in the second site either enhances or inhibits the dNTPase activity of EF1143. Our results provide the first mechanistic insight into dNTP-mediated regulation of dNTPase activity.

PubMed: 24338016
DOI: 10.1074/jbc.M113.524207

Experimental method

X-RAY DIFFRACTION (2.35 Å)