3gyq Citations

Structure of the thiostrepton resistance methyltransferase.S-adenosyl-L-methionine complex and its interaction with ribosomal RNA.

OpenAccess logo J. Biol. Chem. 284 17013-20 (2009)
Cited: 14 times
EuropePMC logo PMID: 19369248

Abstract

The x-ray crystal structure of the thiostrepton resistance RNA methyltransferase (Tsr).S-adenosyl-L-methionine (AdoMet) complex was determined at 2.45-A resolution. Tsr is definitively confirmed as a Class IV methyltransferase of the SpoU family with an N-terminal "L30-like" putative target recognition domain. The structure and our in vitro analysis of the interaction of Tsr with its target domain from 23 S ribosomal RNA (rRNA) demonstrate that the active biological unit is a Tsr homodimer. In vitro methylation assays show that Tsr activity is optimal against a 29-nucleotide hairpin rRNA though the full 58-nucleotide L11-binding domain and intact 23 S rRNA are also effective substrates. Molecular docking experiments predict that Tsr.rRNA binding is dictated entirely by the sequence and structure of the rRNA hairpin containing the A1067 target nucleotide and is most likely driven primarily by large complementary electrostatic surfaces. One L30-like domain is predicted to bind the target loop and the other is near an internal loop more distant from the target site where a nucleotide change (U1061 to A) also decreases methylation by Tsr. Furthermore, a predicted interaction with this internal loop by Tsr amino acid Phe-88 was confirmed by mutagenesis and RNA binding experiments. We therefore propose that Tsr achieves its absolute target specificity using the N-terminal domains of each monomer in combination to recognize the two distinct structural elements of the target rRNA hairpin such that both Tsr subunits contribute directly to the positioning of the target nucleotide on the enzyme.

Articles - 3gyq mentioned but not cited (1)



Reviews citing this publication (3)

  1. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. Chem. Rev. 117 5389-5456 (2017)
  2. Methylthioadenosine/S-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism. Parveen N, Cornell KA. Mol. Microbiol. 79 7-20 (2011)
  3. Recent advances in thiopeptide antibiotic biosynthesis. Li C, Kelly WL. Nat Prod Rep 27 153-164 (2010)

Articles citing this publication (10)

  1. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kötter P, Engels JW, Heckel A, Karas M, Entian KD, Wöhnert J. Nucleic Acids Res. 38 2387-2398 (2010)
  2. Structural insights into the function of aminoglycoside-resistance A1408 16S rRNA methyltransferases from antibiotic-producing and human pathogenic bacteria. Macmaster R, Zelinskaya N, Savic M, Rankin CR, Conn GL. Nucleic Acids Res. 38 7791-7799 (2010)
  3. Expression, purification and crystallization of adenosine 1408 aminoglycoside-resistance rRNA methyltransferases for structural studies. Zelinskaya N, Rankin CR, Macmaster R, Savic M, Conn GL. Protein Expr. Purif. 75 89-94 (2011)
  4. A thiostrepton resistance gene and its mutants serve as selectable markers in Geobacillus kaustophilus HTA426. Wada K, Kobayashi J, Furukawa M, Doi K, Ohshiro T, Suzuki H. Biosci. Biotechnol. Biochem. 80 368-375 (2016)
  5. Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism. Singh RK, Feller A, Roovers M, Van Elder D, Wauters L, Droogmans L, Versées W. RNA 24 1080-1092 (2018)
  6. Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine. Koh CS, Madireddy R, Beane TJ, Zamore PD, Korostelev AA. Sci Rep 7 969 (2017)
  7. Functional roles in S-adenosyl-L-methionine binding and catalysis for active site residues of the thiostrepton resistance methyltransferase. Myers CL, Kuiper EG, Grant PC, Hernandez J, Conn GL, Honek JF. FEBS Lett. 589 3263-3270 (2015)
  8. Molecular interactions between thiostrepton and the TipAS protein from Streptomyces lividans. Myers CL, Harris J, Yeung JC, Honek JF. Chembiochem 15 681-687 (2014)
  9. Substrate recognition and modification by the nosiheptide resistance methyltransferase. Yin S, Jiang H, Chen D, Murchie AI. PLoS ONE 10 e0122972 (2015)
  10. A Family Divided: Distinct Structural and Mechanistic Features of the SpoU-TrmD (SPOUT) Methyltransferase Superfamily. Krishnamohan A, Jackman JE. Biochemistry 58 336-345 (2019)