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

Toh Y, Takeshita D, Nagaike T, Numata T, Tomita K
Structure 19 232-43 (2011)
Related entries: 3aql, 3aqm, 3aqn

Cited: 19 times
EuropePMC logo PMID: 21300291

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.

Articles - 3aqk mentioned but not cited (1)

  1. Tyrosine phosphorylation controlled poly(A) polymerase I activity regulates general stress response in bacteria. Francis N, Behera MR, Natarajan K, Laishram RS. Life Sci Alliance 6 e202101148 (2023)


Reviews citing this publication (4)

  1. The CCA-adding enzyme: A central scrutinizer in tRNA quality control. Betat H, Mörl M. Bioessays 37 975-982 (2015)
  2. Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases. Tomita K, Yamashita S. Front Genet 5 36 (2014)
  3. Function and Regulation of Human Terminal Uridylyltransferases. Yashiro Y, Tomita K. Front Genet 9 538 (2018)
  4. Structures and functions of Qβ replicase: translation factors beyond protein synthesis. Tomita K. Int J Mol Sci 15 15552-15570 (2014)

Articles citing this publication (14)

  1. Crystal structures of U6 snRNA-specific terminal uridylyltransferase. Yamashita S, Takagi Y, Nagaike T, Tomita K. Nat Commun 8 15788 (2017)
  2. Translocation and rotation of tRNA during template-independent RNA polymerization by tRNA nucleotidyltransferase. Yamashita S, Takeshita D, Tomita K. Structure 22 315-325 (2014)
  3. Measurement of Acceptor-TΨC Helix Length of tRNA for Terminal A76-Addition by A-Adding Enzyme. Yamashita S, Martinez A, Tomita K. Structure 23 830-842 (2015)
  4. FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells. Hu JL, Liang H, Zhang H, Yang MZ, Sun W, Zhang P, Luo L, Feng JX, Bai H, Liu F, Zhang T, Yang JY, Gao Q, Long Y, Ma XY, Chen Y, Zhong Q, Yu B, Liao S, Wang Y, Zhao Y, Zeng MS, Cao N, Wang J, Chen W, Yang HT, Gao S. Nucleic Acids Res 48 2733-2748 (2020)
  5. Mechanism for template-independent terminal adenylation activity of Qβ replicase. Takeshita D, Yamashita S, Tomita K. Structure 20 1661-1669 (2012)
  6. Mechanism of 3'-Matured tRNA Discrimination from 3'-Immature tRNA by Class-II CCA-Adding Enzyme. Yamashita S, Tomita K. Structure 24 918-925 (2016)
  7. Discovery of Three Toxic Proteins of Klebsiella Phage fHe-Kpn01. Spruit CM, Wicklund A, Wan X, Skurnik M, Pajunen MI. Viruses 12 E544 (2020)
  8. Structural and functional characterization of multiple myeloma associated cytoplasmic poly(A) polymerase FAM46C. Zhang H, Zhang SH, Hu JL, Wu YT, Ma XY, Chen Y, Yu B, Liao S, Huang H, Gao S. Cancer Commun (Lond) 41 615-630 (2021)
  9. Phylogeny and Evolution of RNA 3'-Nucleotidyltransferases in Bacteria. Jones GH. J Mol Evol 87 254-270 (2019)
  10. Acquisition of pcnB [poly(A) polymerase I] genes via horizontal transfer from the β, γ-Proteobacteria. Jones GH. Microb Genom 7 (2021)
  11. A cellular platform for production of C4 monomers. Davis MA, Yu VY, Fu B, Wen M, Koleski EJ, Silverman J, Berdan CA, Nomura DK, Chang MCY. Chem Sci 14 11718-11726 (2023)
  12. Base editor-mediated large-scale screening of functional mutations in bacteria for industrial phenotypes. Yuan Y, Liao X, Li S, Xing XH, Zhang C. Sci China Life Sci (2024)
  13. Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs. Błaszczyk E, Płociński P, Lechowicz E, Brzostek A, Dziadek B, Korycka-Machała M, Słomka M, Dziadek J. Sci Rep 13 20717 (2023)
  14. NMR reveals structural rearrangements associated to substrate insertion in nucleotide-adding enzymes. Mohanty B, Geralt M, Wüthrich K, Serrano P. Protein Sci 25 917-925 (2016)


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