The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion

Nucleic Acids Res. 2018 Apr 6;46(6):3232-3244. doi: 10.1093/nar/gky115.

Abstract

Archaea and eukaryotes have ribosomal P stalks composed of anchor protein P0 and aP1 homodimers (archaea) or P1•P2 heterodimers (eukaryotes). These P stalks recruit translational GTPases to the GTPase-associated center in ribosomes to provide energy during translation. The C-terminus of the P stalk is known to selectively recognize GTPases. Here we investigated the interaction between the P stalk and elongation factor 2 by determining the structures of Pyrococcus horikoshii EF-2 (PhoEF-2) in the Apo-form, GDP-form, GMPPCP-form (GTP-form), and GMPPCP-form bound with 11 C-terminal residues of P1 (P1C11). Helical structured P1C11 binds to a hydrophobic groove between domain G and subdomain G' of PhoEF-2, where is completely different from that of aEF-1α in terms of both position and sequence, implying that such interaction characteristic may be requested by how GTPases perform their functions on the ribosome. Combining PhoEF-2 P1-binding assays with a structural comparison of current PhoEF-2 structures and molecular dynamics model of a P1C11-bound GDP form, the conformational changes of the P1C11-binding groove in each form suggest that in response to the translation process, the groove has three states: closed, open, and release for recruiting and releasing GTPases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaeal Proteins / chemistry
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism*
  • Guanosine Diphosphate / chemistry
  • Guanosine Diphosphate / metabolism
  • Guanosine Triphosphate / analogs & derivatives
  • Guanosine Triphosphate / chemistry
  • Guanosine Triphosphate / metabolism
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular
  • Peptide Elongation Factor 2 / chemistry
  • Peptide Elongation Factor 2 / genetics
  • Peptide Elongation Factor 2 / metabolism*
  • Protein Binding
  • Protein Conformation
  • Pyrococcus horikoshii / genetics
  • Pyrococcus horikoshii / metabolism*
  • Ribosomal Proteins / chemistry
  • Ribosomal Proteins / genetics
  • Ribosomal Proteins / metabolism*
  • Ribosomes / chemistry
  • Ribosomes / metabolism*
  • Sequence Homology, Amino Acid

Substances

  • Archaeal Proteins
  • Peptide Elongation Factor 2
  • Ribosomal Proteins
  • Guanosine Diphosphate
  • 5'-guanylylmethylenebisphosphonate
  • Guanosine Triphosphate