Structural analyses of peptide release factor 1 from Thermotoga maritima reveal domain flexibility required for its interaction with the ribosome

Dong Hae Shin, Jeroen Brandsen, Jaru Jancarik, Hisao Yokota, Rosalind Kim, Sung Hou Kim

Research output: Contribution to journalArticlepeer-review

66 Scopus citations

Abstract

We have determined the crystal structure of peptide chain release factor 1 (RF1) from Thermotoga maritima (gi 4981173) at 2.65Å resolution by selenomethionine single-wavelength anomalous dispersion (SAD) techniques. RF1 is a protein that recognizes stop codons and promotes the release of a nascent polypeptide from tRNA on the ribosome. Selenomethionine-labeled RF1 crystallized in space group P21 with three monomers per asymmetric unit. It has approximate dimensions of 75Å×70Å×45Å and is composed of four domains. The overall fold of each RF1 domain shows almost the same topology with Escherichia coli RF2, except that the RF1 N-terminal domain is shorter and the C-terminal domain is longer than that of RF2. The N-terminal domain of RF1 indicates a rigid-body movement relative to that of RF2 with an angle of ∼90°. Including these features, RF1 has a tripeptide anticodon PVT motif instead of the SPF motif of RF2, which confers the specificity towards the stop codons. The analyses of three molecules in the asymmetric unit and comparison with RF2 revealed the presence of dynamic movement of domains I and III, which are anchored to the central domain by hinge loops. The crystal structure of RF1 elucidates the intrinsic property of this family of having large domain movements for proper function with the ribosome.

Original languageEnglish
Pages (from-to)227-239
Number of pages13
JournalJournal of Molecular Biology
Volume341
Issue number1
DOIs
StatePublished - 30 Jul 2004

Keywords

  • conformational change
  • crystal structure
  • DC, decoding center
  • gi 4981923
  • peptide release factor 1
  • PTC, peptidyl transferase center
  • RF, release factor
  • ribosome
  • SAD, single-wavelength anomalous dispersion

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