Molecular Morphology of Eukaryotic Class-1 Translation Termination Factor eRF1 in Solution

Av, Kononenko; Ka, Dembo; Ll, Kiselev; Vv, Volkov

doi:10.1023/b:mbil.0000023742.62903.ef

Cited by 18 publications

(9 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Replacement of the Gln residue by certain amino acids in either human (9) or E. coli (8) RFs allows significant release activity to be retained in in vitro termination assays, but no substitution has been found for the Gln residue in Saccharomyces cerevisiae (3) or E. coli (8) RFs that supports cell growth, even at low levels. The three-dimensional structure of eRF1 in solution is similar if not identical to that in the crystal (10), whereas the crystal structures of both E. coli RF2 (4) and Thermotoga maritima RF1 (11), which are thought to approximate to the structures of the factors free in the cytoplasm, are much more compact.…”

mentioning

confidence: 87%

The Glutamine Residue of the Conserved GGQ Motif in Saccharomyces cerevisiae Release Factor eRF1 Is Methylated by the Product of the YDR140w Gene

Heurgué-Hamard

Champ

Mora

et al. 2005

Journal of Biological Chemistry

View full text Add to dashboard Cite

Polypeptide release factors from eubacteria and eukaryotes, although similar in function, belong to different protein families. They share one sequence motif, a GGQ tripeptide that is vital to release factor (RF) activity in both kingdoms. In bacteria, the Gln residue of the motif in RF1 and RF2 is modified to N 5 -methylGln by the S-adenosyl L-methionine-dependent methyltransferase PrmC and the absence of Gln methylation decreases the release activity of Escherichia coli RF2 in vitro severalfold. We show here that the same modification is made to the GGQ motif of Saccharomyces cerevisiae release factor eRF1, the first time that N 5 -methyl-Gln has been found outside the bacterial kingdom. The product of the YDR140w gene is required for the methylation of eRF1 in vivo and for optimal yeast cell growth. YDR140w protein has significant homology to PrmC but lacks the N-terminal domain thought to be involved in the recognition of the bacterial release factors. Overproduced in S. cerevisiae, YDR140w can methylate eRF1 from yeast or man in vitro using S-adenosyl L-methionine as methyl donor provided that eRF3 and GTP are also present, suggesting that the natural substrate of the methyltransferase YDR140w is the ternary complex eRF1⅐eRF3⅐GTP.

show abstract

mentioning

confidence: 87%

The Glutamine Residue of the Conserved GGQ Motif in Saccharomyces cerevisiae Release Factor eRF1 Is Methylated by the Product of the YDR140w Gene

Heurgué-Hamard

Champ

Mora

et al. 2005

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…1D; Song et al 2000), as follows from smallangle X-ray scattering data (Kononenko et al 2004). If eRF1 structure in a ribosome-bound state remains the same, the GTx and YxCxxxF motifs close to each other but remote from the NIKS loop could not interact with the same A-site-bound stop codon.…”

Section: A Significant Conformational Change Of the A-site-bound Erf1mentioning

confidence: 99%

“…It is evident that the stop signal crossreacts with three distinct sites in the N domain of eRF1, two of which-oligopeptide 121-131 (including the YxCxxxF motif) and the 31-33 fragment-are remote from the third one, V66 (in the region of the NIKS motif), in spatial (both in crystal and in solution) structure ( Fig. 1C,D ;Song et al 2000;Kononenko et al 2004). The major cross-linking site for all mRNAs with the exception of mRNA I was in eRF1 positions 31-33.…”

Section: Mapping Of the Cross-linking Sites Corresponding To ''B'' Bandsmentioning

confidence: 99%

Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome

Bulygin¹,

Khairulina²,

Kolosov³

et al. 2010

RNA

View full text Add to dashboard Cite

To study positioning of the polypeptide release factor eRF1 toward a stop signal in the ribosomal decoding site, we applied photoactivatable mRNA analogs, derivatives of oligoribonucleotides. The human eRF1 peptides cross-linked to these short mRNAs were identified. Cross-linkers on the guanines at the second, third, and fourth stop signal positions modified fragment 31-33, and to lesser extent amino acids within region 121-131 (the ''YxCxxxF loop'') in the N domain. Hence, both regions are involved in the recognition of the purines. A cross-linker at the first uridine of the stop codon modifies Val66 near the NIKS loop (positions 61-64), and this region is important for recognition of the first uridine of stop codons. Since the N domain distinct regions of eRF1 are involved in a stop-codon decoding, the eRF1 decoding site is discontinuous and is not of ''protein anticodon'' type. By molecular modeling, the eRF1 molecule can be fitted to the A site proximal to the P-site-bound tRNA and to a stop codon in mRNA via a large conformational change to one of its three domains. In the simulated eRF1 conformation, the YxCxxxF motif and positions 31-33 are very close to a stop codon, which becomes also proximal to several parts of the C domain. Thus, in the A-site-bound state, the eRF1 conformation significantly differs from those in crystals and solution. The model suggested for eRF1 conformation in the ribosomal A site and cross-linking data are compatible.

show abstract

“…However, it remained unanswered if the compact crystal structure of prokaryotic RFs is functionally relevant and if it exists under physiological conditions since the recent small angle X-ray scattering investigations (SAXS) on E. coli RF1 (29) indicated the existence of the elongated conformation also at ambient temperatures similar to human eRF1 (30). …”

Section: Introductionmentioning

confidence: 99%

Release Factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies

Redecke

Svergun

Konarev

et al. 2007

Nucleic Acids Research

View full text Add to dashboard Cite

Prokaryotic class I release factors (RFs) respond to mRNA stop codons and terminate protein synthesis. They interact with the ribosomal decoding site and the peptidyl-transferase centre bridging these 75 Å distant ribosomal centres. For this an elongated RF conformation, with partially unfolded core domains II·III·IV is required, which contrasts the known compact RF crystal structures. The crystal structure of Thermus thermophilus RF2 was determined and compared with solution structure of T. thermophilus and Escherichia coli RF2 by microcalorimetry, circular dichroism spectroscopy and small angle X-ray scattering. The structure of T. thermophilus RF2 in solution at 20°C is predominantly compact like the crystal structure. Thermodynamic analysis point to an initial melting of domain I, which is independent from the melting of the core. The core domains II·III·IV melt cooperatively at the respective physiological temperatures for T. thermophilus and E. coli. Thermodynamic analyses and the X-ray scattering results for T. thermophilus RF2 in solution suggest that the compact conformation of RF2 resembles a physiological state in absence of the ribosome.

show abstract

Molecular Morphology of Eukaryotic Class-1 Translation Termination Factor eRF1 in Solution

Cited by 18 publications

References 21 publications

The Glutamine Residue of the Conserved GGQ Motif in Saccharomyces cerevisiae Release Factor eRF1 Is Methylated by the Product of the YDR140w Gene

The Glutamine Residue of the Conserved GGQ Motif in Saccharomyces cerevisiae Release Factor eRF1 Is Methylated by the Product of the YDR140w Gene

Three distinct peptides from the N domain of translation termination factor eRF1 surround stop codon in the ribosome

Release Factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies

Contact Info

Product

Resources

About