Nucleic acid polymerases use a general acid for nucleotidyl transfer

Christian Castro, Eric D. Smidansky, Jamie J. Arnold, Kenneth R. Maksimchuk, Ibrahim Moustafa, Akira Uchida, Matthias Götte, William Konigsberg, Craig E. Cameron

Research output: Contribution to journalArticlepeer-review

155 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)212-218
Number of pages7
JournalNature Structural and Molecular Biology
Volume16
Issue number2
DOIs
StatePublished - Feb 2009

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

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