YNR046w: component of the eRF1 methyltransferase

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Structure of Ynr046w A. Ribbon representation of Ynr046w structure. The conserved and “insert” domains are coloured green and yellow, respectively. The Zn atom is shown as a black sphere and the Cys side chains chelating the Zn atoms are shown as sticks. B. Superimposition of the HIV-1 nucleocapsid protein (yellow, Zn atom in blue and residues labelled in grey) on to the Ynr046w Zn finger (green, Zn in black and residues labelled in black). C. Homodimer formation in the crystal structure. D. Close-up of Ynr046w monomer A (yellow) and monomer B (magenta) residues involved at the homodimer interface. Hydrogen bonds are depicted by black dotted lines. E. Molecular surface representation of the sequence conservation among the eukaryotic Ynr046w orthologues. The left panel has the same orientation as in A and the right panel is related by a 180° rotation. Colouring is from white (poorly conserved) to blue (highly conserved). F. Surface mapping of the residues from monomers A (green) and B (blue) involved in homodimer formation. G. Hydrophobic surface representation of the Ynr046w monomer. Polar and hydrophobic residues are coloured in white and red respectively.

Function eRF1 methyltransferase
Fold alpha beta
Resolution 1.7
Remarks Phased using SAD data at the Zn-edge
Biological unit Dimer
PDB code Not yet
Reference Valérie Heurgué-Hamard, Marc Graille, Nathalie Scrima, Nathalie Ulryck, Stéphanie Champ, Herman van Tilbeurgh, and Richard H. Buckingham The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. J. Biol. Chem., Sep 2006. [Epub ahead of print] Full text

Protein release factor eRF1 in Saccharomyces cerevisiae, in complex with eRF3 and GTP, is methylated on a functionally crucial Gln residue by the AdoMet-dependent methyltransferase Ydr140w. Here we show that eRF1 methylation, in addition to these previously characterised components, requires a 15 kDa zinc-binding protein, Ynr046w. Co-expression in E. coli of Ynr046w and Ydr140w allows the latter to be recovered in soluble form rather than as inclusion bodies, and the two proteins co-purify on Ni-NTA chromatography when Ydr140w alone carries a His-tag. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N-terminal and C-terminal sequences, and an inserted domain, absent from bacterial and archaeal orthologues of the protein, composed of three -helices. The active methyltransferase is the heterodimer Ydr140w*Ynr046w, but when alone, both in solution and in crystals, Ynr046w appears to be a homodimer. The Ynr046w eRF1 methyltransferase subunit is shared by the tRNA methyltransferase Trm11p and probably by two other enzymes containing a Rossman fold.