7TU5

Structure of the L. blandensis dGTPase in the apo form

Summary for 7TU5

• Entry DOI: 10.2210/pdb7tu5/pdb
• EMDB information: 26126 26127 26128 26129
• Descriptor: dGTP triphosphohydrolase, MAGNESIUM ION (3 entities in total)
• Functional Keywords: dgtpase, nucleotide binding, hydrolase
• Biological source: Leeuwenhoekiella blandensis MED217
• Total number of polymer chains: 6
• Total formula weight: 316485.28

Authors

Klemm, B.P.,Sikkema, A.P.,Hsu, A.L.,Borgnia, M.J.,Schaaper, R.M. (deposition date: 2022-02-02, release date: 2022-06-01, Last modification date: 2024-02-21)

Primary citation

Klemm, B.P.,Sikkema, A.P.,Hsu, A.L.,Horng, J.C.,Hall, T.M.T.,Borgnia, M.J.,Schaaper, R.M.
High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP.
J.Biol.Chem., 298:102073-102073, 2022

PubMed Abstract: Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human sterile alpha motif and HD domain-containing protein 1 (SAMHD1), a tetrameric dNTPase, and the hexameric Escherichia coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 Å) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 Å) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.

PubMed: 35643313
DOI: 10.1016/j.jbc.2022.102073

Experimental method

ELECTRON MICROSCOPY (2.1 Å)