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NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor.

Mantsyzov AB, Ivanova EV, Birdsall B, Alkalaeva EZ, Kryuchkova PN, Kelly G, Frolova LY, Polshakov VI - FEBS J. (2010)

Bottom Line: The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal structure.Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor.The results provide new insights into the possible role of the C-domain in the process of translation termination.

View Article: PubMed Central - PubMed

Affiliation: Center for Magnetic Tomography and Spectroscopy, M. V. Lomonosov Moscow State University, Russia.

ABSTRACT
Termination of translation in eukaryotes is triggered by two polypeptide chain release factors, eukaryotic class 1 polypeptide chain release factor (eRF1) and eukaryotic class 2 polypeptide chain release factor 3. eRF1 is a three-domain protein that interacts with eukaryotic class 2 polypeptide chain release factor 3 via its C-terminal domain (C-domain). The high-resolution NMR structure of the human C-domain (residues 277-437) has been determined in solution. The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal structure. The structure of the minidomain (residues 329-372), which was ill-defined in the crystal structure, has been determined in solution. The protein backbone dynamics, studied using (15)N-relaxation experiments, showed that the C-terminal tail 414-437 and the minidomain are the most flexible parts of the human C-domain. The minidomain exists in solution in two conformational states, slowly interconverting on the NMR timescale. Superposition of this NMR solution structure of the human C-domain onto the available crystal structure of full-length human eRF1 shows that the minidomain is close to the stop codon-recognizing N-terminal domain. Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination.

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The topology of the zinc-binding domain of zinc finger protein Ynr046w, a component of the yeast eRF1 methyltransferase (A), and the minidomain (residues 329–372) of human eRF1 in the open (B) and closed (C) forms.
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fig08: The topology of the zinc-binding domain of zinc finger protein Ynr046w, a component of the yeast eRF1 methyltransferase (A), and the minidomain (residues 329–372) of human eRF1 in the open (B) and closed (C) forms.

Mentions: Despite the rather simple topology of the minidomain (three antiparallel β-strands and one α-helix on top of the β-sheet), a search of the CATH database (http://www.cathdb.info) [24] provided no direct structural homologs. The closest cluster of structures has the fold found in the factor Xα inhibitor (CATH code 4.10.410). An additional manual search based on these results highlighted a structural homology between the minidomain and the zinc-binding domain of the zinc finger protein Ynr046w [25] (Fig. 8). The fit of the heavy atoms (Cα, C, and N) from three β-strands and the α-helices of both the closed and the open conformer onto a corresponding set of atoms of Ynr046w gives rmsd values of 3.7 and 4.1 Å, respectively. Smaller rmsd values of 1.9 and 2.4 Å are obtained when the β-core residues only are used for the superposition. Interestingly, this protein is a component of yeast eRF1 methyltransferase, which is involved in methylation of the Glu from the strictly conserved GGQ tripeptide, and therefore it also, like human eRF1, plays an important role in translation termination.


NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor.

Mantsyzov AB, Ivanova EV, Birdsall B, Alkalaeva EZ, Kryuchkova PN, Kelly G, Frolova LY, Polshakov VI - FEBS J. (2010)

The topology of the zinc-binding domain of zinc finger protein Ynr046w, a component of the yeast eRF1 methyltransferase (A), and the minidomain (residues 329–372) of human eRF1 in the open (B) and closed (C) forms.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2984548&req=5

fig08: The topology of the zinc-binding domain of zinc finger protein Ynr046w, a component of the yeast eRF1 methyltransferase (A), and the minidomain (residues 329–372) of human eRF1 in the open (B) and closed (C) forms.
Mentions: Despite the rather simple topology of the minidomain (three antiparallel β-strands and one α-helix on top of the β-sheet), a search of the CATH database (http://www.cathdb.info) [24] provided no direct structural homologs. The closest cluster of structures has the fold found in the factor Xα inhibitor (CATH code 4.10.410). An additional manual search based on these results highlighted a structural homology between the minidomain and the zinc-binding domain of the zinc finger protein Ynr046w [25] (Fig. 8). The fit of the heavy atoms (Cα, C, and N) from three β-strands and the α-helices of both the closed and the open conformer onto a corresponding set of atoms of Ynr046w gives rmsd values of 3.7 and 4.1 Å, respectively. Smaller rmsd values of 1.9 and 2.4 Å are obtained when the β-core residues only are used for the superposition. Interestingly, this protein is a component of yeast eRF1 methyltransferase, which is involved in methylation of the Glu from the strictly conserved GGQ tripeptide, and therefore it also, like human eRF1, plays an important role in translation termination.

Bottom Line: The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal structure.Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor.The results provide new insights into the possible role of the C-domain in the process of translation termination.

View Article: PubMed Central - PubMed

Affiliation: Center for Magnetic Tomography and Spectroscopy, M. V. Lomonosov Moscow State University, Russia.

ABSTRACT
Termination of translation in eukaryotes is triggered by two polypeptide chain release factors, eukaryotic class 1 polypeptide chain release factor (eRF1) and eukaryotic class 2 polypeptide chain release factor 3. eRF1 is a three-domain protein that interacts with eukaryotic class 2 polypeptide chain release factor 3 via its C-terminal domain (C-domain). The high-resolution NMR structure of the human C-domain (residues 277-437) has been determined in solution. The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal structure. The structure of the minidomain (residues 329-372), which was ill-defined in the crystal structure, has been determined in solution. The protein backbone dynamics, studied using (15)N-relaxation experiments, showed that the C-terminal tail 414-437 and the minidomain are the most flexible parts of the human C-domain. The minidomain exists in solution in two conformational states, slowly interconverting on the NMR timescale. Superposition of this NMR solution structure of the human C-domain onto the available crystal structure of full-length human eRF1 shows that the minidomain is close to the stop codon-recognizing N-terminal domain. Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination.

Show MeSH