title: Motif D of viral RNA-dependent RNA polymerases determines efficiency and fidelity of nucleotide addition.
abstract: Fast, accurate nucleotide incorporation by polymerases facilitates expression and maintenance of genomes. Many polymerases use conformational dynamics of a conserved α helix to permit efficient nucleotide addition only when the correct nucleotide substrate is bound. This α helix is missing in structures of RNA-dependent RNA polymerases (RdRps) and RTs. Here, we use solution-state nuclear magnetic resonance to demonstrate that the conformation of conserved structural motif D of an RdRp is linked to the nature (correct versus incorrect) of the bound nucleotide and the protonation state of a conserved, motif-D lysine. Structural data also reveal the inability of motif D to achieve its optimal conformation after incorporation of an incorrect nucleotide. Functional data are consistent with the conformational change of motif D becoming rate limiting during and after nucleotide misincorporation. We conclude that motif D of RdRps and, by inference, RTs is the functional equivalent to the fidelity helix of other polymerases.
authors: Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
authors: Xiaorong
authors: X
authors: Yang
authors: Eric D
authors: ED
authors: Smidansky
authors: Kenneth R
authors: KR
authors: Maksimchuk
authors: David
authors: D
authors: Lum
authors: Jesse L
authors: JL
authors: Welch
authors: Jamie J
authors: JJ
authors: Arnold
authors: Craig E
authors: CE
authors: Cameron
authors: David D
authors: DD
authors: Boehr
mesh_terms: D020816:Amino Acid Motifs; D020029:Base Pairing; D001483:Base Sequence; D055162:Biocatalysis; D020134:Catalytic Domain; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009711:Nucleotides / Q000737:chemistry*; D017955:Poliovirus / Q000201:enzymology*; D011485:Protein Binding; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry*; D014764:Viral Proteins
chemical_list: D009711:Nucleotides; D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase