title: Nucleic acid polymerases use a general acid for nucleotidyl transfer.
abstract: Nucleic acid polymerases catalyze the formation of DNA or RNA from nucleoside-triphosphate precursors. Amino acid residues in the active site of polymerases are thought to contribute only indirectly to catalysis by serving as ligands for the two divalent cations that are required for activity or substrate binding. Two proton-transfer reactions are necessary for polymerase-catalyzed nucleotidyl transfer: deprotonation of the 3'-hydroxyl nucleophile and protonation of the pyrophosphate leaving group. Using model enzymes representing all four classes of nucleic acid polymerases, we show that the proton donor to pyrophosphate is an active-site amino acid residue. The use of general acid catalysis by polymerases extends the mechanism of nucleotidyl transfer beyond that of the well-established two-metal-ion mechanism. The existence of an active-site residue that regulates polymerase catalysis may permit manipulation of viral polymerase replication speed and/or fidelity for virus attenuation and vaccine development.
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Christian
authors.initials: C
authors.lastname: Castro
authors.forename: Eric D
authors.initials: ED
authors.lastname: Smidansky
authors.forename: Jamie J
authors.initials: JJ
authors.lastname: Arnold
authors.forename: Kenneth R
authors.initials: KR
authors.lastname: Maksimchuk
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Moustafa
authors.forename: Akira
authors.initials: A
authors.lastname: Uchida
authors.forename: Matthias
authors.initials: M
authors.lastname: Götte
authors.forename: William
authors.initials: W
authors.lastname: Konigsberg
authors.forename: Craig E
authors.initials: CE
authors.lastname: Cameron
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D002384:Catalysis; D008345:Manganese / Q000378:metabolism; D008958:Models, Molecular; D009696:Nucleic Acids / Q000378:metabolism; D009713:Nucleotidyltransferases / Q000737:chemistry / Q000378:metabolism*; D011522:Protons; D014780:Viruses / Q000201:enzymology*
chemical_list: D000596:Amino Acids; D009696:Nucleic Acids; D011522:Protons; D008345:Manganese; D009713:Nucleotidyltransferases