Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Oct 1;61(Pt 10):867-74. doi: 10.1107/S1744309105029842. Epub 2005 Sep 30.

Abstract

The Thermus thermophilus hypothetical protein TTHA1280 belongs to a family of predicted S-adenosyl-L-methionine (AdoMet) dependent RNA methyltransferases (MTases) present in many bacterial and archaeal species. Inspection of amino-acid sequence motifs common to class I Rossmann-fold-like MTases suggested a specific role as an RNA 5-methyluridine MTase. Selenomethionine (SeMet) labelled and native versions of the protein were expressed, purified and crystallized. Two crystal forms of the SeMet-labelled apoprotein were obtained: SeMet-ApoI and SeMet-ApoII. Cocrystallization of the native protein with S-adenosyl-L-homocysteine (AdoHcy) yielded a third crystal form, Native-AdoHcy. The SeMet-ApoI structure was solved by the multiple anomalous dispersion method and refined at 2.55 A resolution. The SeMet-ApoII and Native-AdoHcy structures were solved by molecular replacement and refined at 1.80 and 2.60 A, respectively. TTHA1280 formed a homodimer in the crystals and in solution. Each subunit folds into a three-domain structure composed of a small N-terminal PUA domain, a central alpha/beta-domain and a C-terminal Rossmann-fold-like MTase domain. The three domains form an overall clamp-like shape, with the putative active site facing a deep cleft. The architecture of the active site is consistent with specific recognition of uridine and catalysis of methyl transfer to the 5-carbon position. The cleft is suitable in size and charge distribution for binding single-stranded RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites
  • Carbon / chemistry
  • Catalytic Domain
  • Cloning, Molecular
  • Crystallization
  • Dimerization
  • Escherichia coli / metabolism
  • Models, Chemical
  • Models, Molecular
  • Models, Statistical
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA / chemistry
  • S-Adenosylhomocysteine / chemistry
  • Sequence Homology, Amino Acid
  • Species Specificity
  • Thermus thermophilus / enzymology*
  • Ultracentrifugation
  • Uridine / chemistry
  • tRNA Methyltransferases / chemistry*

Substances

  • RNA
  • Carbon
  • S-Adenosylhomocysteine
  • tRNA Methyltransferases
  • tRNA(uracil-5)-methyltransferase
  • Uridine

Associated data

  • PDB/1WXW
  • PDB/1WXX
  • PDB/2CWW
  • PDB/R1WXWSF
  • PDB/R1WXXSF
  • PDB/R2CWWSF