title: Histidine 114 Is Critical for ATP Hydrolysis by the Universally Conserved ATPase YchF.
abstract: GTPases perform a wide range of functions, ranging from protein synthesis to cell signaling. Of all known GTPases, only eight are conserved across all three domains of life. YchF is one of these eight universally conserved GTPases; however, its cellular function and enzymatic properties are poorly understood. YchF differs from the classical GTPases in that it has a higher affinity for ATP than for GTP and is a functional ATPase. As a hydrophobic amino acid-substituted ATPase, YchF does not possess the canonical catalytic Gln required for nucleotide hydrolysis. To elucidate the catalytic mechanism of ATP hydrolysis by YchF, we have taken a two-pronged approach combining classical biochemical and in silico techniques. The use of molecular dynamics simulations allowed us to complement our biochemical findings with information about the structural dynamics of YchF. We have thereby identified the highly conserved His-114 as critical for the ATPase activity of YchF from Escherichia coli. His-114 is located in a flexible loop of the G-domain, which undergoes nucleotide-dependent conformational changes. The use of a catalytic His is also observed in the hydrophobic amino acid-substituted GTPase RbgA and is an identifier of the translational GTPase family.
authors.affiliation: From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
authors.forename: Kirsten S
authors.initials: KS
authors.lastname: Rosler
authors.affiliation: From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
authors.forename: Evan
authors.initials: E
authors.lastname: Mercier
authors.affiliation: From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada.
authors.forename: Ian C
authors.initials: IC
authors.lastname: Andrews
authors.affiliation: From the Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada hj.wieden@uleth.ca.
authors.forename: Hans-Joachim
authors.initials: HJ
authors.lastname: Wieden
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D020816:Amino Acid Motifs / Q000235:genetics; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020558:GTP Phosphohydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D006639:Histidine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006868:Hydrolysis; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D014176:Protein Biosynthesis / Q000235:genetics; D011487:Protein Conformation; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins; D006639:Histidine; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases; D020558:GTP Phosphohydrolases; C559743:YchF protein, E. coli
keywords: ATPase; HAS-ATPase; YchF; catalytic mechanism; conformational change; molecular dynamics; molecular switch; nucleotide binding; pre-steady-state kinetics; ribosome