title: Mechanism for the alteration of the substrate specificities of template-independent RNA polymerases.
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.
authors.affiliation: Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.
authors.forename: Yukimatsu
authors.initials: Y
authors.lastname: Toh
authors.forename: Daijiro
authors.initials: D
authors.lastname: Takeshita
authors.forename: Takashi
authors.initials: T
authors.lastname: Nagaike
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Numata
authors.forename: Kozo
authors.initials: K
authors.lastname: Tomita
mesh_terms: D000249:Adenosine Monophosphate / Q000378:metabolism*; D000255:Adenosine Triphosphate / Q000378:metabolism*; D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012313:RNA / Q000378:metabolism*; D013379:Substrate Specificity; D013698:Templates, Genetic
chemical_list: D000249:Adenosine Monophosphate; D012313:RNA; D000255:Adenosine Triphosphate; D001120:Arginine; D012321:DNA-Directed RNA Polymerases