Mechanism for the alteration of the substrate specificities of template-independent RNA polymerases

Structure. 2011 Feb 9;19(2):232-43. doi: 10.1016/j.str.2010.12.006.

Abstract

PolyA polymerase (PAP) adds a polyA tail onto the 3'-end of RNAs without a nucleic acid template, using adenosine-5'-triphosphate (ATP) as a substrate. The mechanism for the substrate selection by eubacterial PAP remains obscure. Structural and biochemical studies of Escherichia coli PAP (EcPAP) revealed that the shape and size of the nucleobase-interacting pocket of EcPAP are maintained by an intra-molecular hydrogen-network, making it suitable for the accommodation of only ATP, using a single amino acid, Arg(197). The pocket structure is sustained by interactions between the catalytic domain and the RNA-binding domain. EcPAP has a flexible basic C-terminal region that contributes to optimal RNA translocation for processive adenosine 5'-monophosphate (AMP) incorporations onto the 3'-end of RNAs. A comparison of the EcPAP structure with those of other template-independent RNA polymerases suggests that structural changes of domain(s) outside the conserved catalytic core domain altered the substrate specificities of the template-independent RNA polymerases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / metabolism*
  • Adenosine Triphosphate / metabolism*
  • Amino Acid Sequence
  • Arginine / chemistry
  • Arginine / genetics
  • Arginine / metabolism*
  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Protein Structure, Tertiary
  • RNA / metabolism*
  • Substrate Specificity
  • Templates, Genetic

Substances

  • Adenosine Monophosphate
  • RNA
  • Adenosine Triphosphate
  • Arginine
  • DNA-Directed RNA Polymerases

Associated data

  • PDB/3AQK
  • PDB/3AQL
  • PDB/3AQM
  • PDB/3AQN