Helix unwinding in the effector region of elongation factor EF-Tu–GDP

Polekhina, Galina; Thirup, Søren; Kjeldgaard, Morten; Nissen, Poul; Lippmann, Corinna; Nyborg, Jens

doi:10.1016/s0969-2126(96)00122-0

Cited by 225 publications

(223 citation statements)

References 35 publications

(43 reference statements)

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“…This finding is confirmed by x-ray structural analysis (45)(46)(47). Because the C-domain of eRF3 is homologous to eEF1〈, it was speculated that the nucleotidedependent conformational change also occurs in the C-terminal region of eRF3.…”

Section: Discussionmentioning

confidence: 65%

The GTP-binding Release Factor eRF3 as a Key Mediator Coupling Translation Termination to mRNA Decay

Kobayashi

Funakoshi

Hoshino

et al. 2004

Journal of Biological Chemistry

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GTP is essential for eukaryotic translation termination, where the release factor 3 (eRF3) complexed with eRF1 is involved as the guanine nucleotide-binding protein. In addition, eRF3 regulates the termination-coupled events, eRF3 interacts with poly(A)-binding protein (Pab1) and the surveillance factor Upf1 to mediate normal and nonsense-mediated mRNA decay. However, the roles of GTP binding to eRF3 in these processes remain largely unknown. Here, we showed in yeast that GTP is essentially required for the association of eRF3 with eRF1, but not with Pab1 and Upf1. A mutation in the GTP-binding motifs of eRF3 impairs the eRF1-binding ability without altering the Pab1-or Upf1-binding activity. Interestingly, the mutation causes not only a defect in translation termination but also delay of normal and nonsense-mediated mRNA decay, suggesting that GTP/ eRF3-dependent termination exerts its influence on the subsequent mRNA degradation. The termination reaction itself is not sufficient, but eRF3 is essential for triggering mRNA decay. Thus, eRF3 is a key mediator that transduces termination signal to mRNA decay.

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Section: Discussionmentioning

confidence: 65%

The GTP-binding Release Factor eRF3 as a Key Mediator Coupling Translation Termination to mRNA Decay

Kobayashi

Funakoshi

Hoshino

et al. 2004

Journal of Biological Chemistry

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“…Our data show that this EF-Tu structure indeed corresponds to an activated state for the hydrolysis of the nucleotide, as detailed below. Several conserved regions playing prominent roles in the working cycle of GTPases, namely switch I (EF-Tu residues 40-62; E. coli numbering is used throughout this article), switch II (80-100) and P loop (18)(19)(20)(21)(22)(23), are found to undergo characteristic conformational changes in EF-Tu. We describe these changes in the context of the ribosome-bound state of EF-Tu captured by the map.…”

Section: Resultsmentioning

confidence: 99%

“…The other wing of the hydrophobic gate (Ile-60) is part of switch I (also known as effector loop), which assumes an ␣-helix conformation in the closed form of EF-Tu and changes to a ␤-hairpin conformation in the open form (17,18). The large flexibility of this region has prevented switch I from being resolved in EM density maps and some crystallographic structures.…”

Section: Resultsmentioning

confidence: 99%

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

Villa

Sengupta

Trabuco

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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219

186

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In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-Å cryo-electron microscopy map of the aminoacyl-tRNA⅐EF-Tu⅐GDP⅐kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.decoding ͉ GTPase ͉ flexible fitting ͉ cryo-EM ͉ ternary complex

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“…In the former, the C-terminal part of this region is a -hairpin, whereas in the latter it forms an R-helix. 31 This means that upon GTP binding, Thr62, which is exposed to the solvent in the GDP form (reference distances from OG1 of this residue to magnesium ion are 18.4 and 16.9 Å in EF1A‚GDP and eEF1A‚GDP: eEF1BR complexes, respectively), gets involved in the coordination of the Mg 2+ ion by means of its hydroxyl oxygen because the conserved sequence 60-GITI-63 ( Figure 5) comes close to both the phosphate-binding loop (P-loop) and helix B. Another consequence of exchanging GDP with GTP is that the conserved Ile61 gets close to Val20 in the P-loop in such a way that both residues form a "hydrophobic gate" that could be important for GTP hydrolysis.…”

Section: Resultsmentioning

confidence: 99%

Structural Basis for the Binding of Didemnins to Human Elongation Factor eEF1A and Rationale for the Potent Antitumor Activity of These Marine Natural Products

et al. 2004

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Didemnins and tamandarins are closely related marine natural products with potent inhibitory effects on protein synthesis and cell viability. On the basis of available biochemical and structural evidence and results from molecular dynamics simulations, a model is proposed that accounts for the strong and selective binding of these compounds to human elongation factor eEF1A in the presence of GTP. We suggest that the p-methoxyphenyl ring of these cyclic depsipeptides is inserted into the same pocket in eEF1A that normally lodges either the 3′ terminal adenine of aminoacylated tRNA, as inferred from two prokaryotic EF-Tu‚GTP‚tRNA complexes, or the aromatic side chain of Phe/Tyr-163 from the nucleotide exchange factor eEF1BR, as observed in several X-ray crystal structures of a yeast eEF1A:eEF1BR complex. This pocket, which has a strong hydrophobic character, is formed by two protruding loops on the surface of eEF1A domain 2. Further stabilization of the bound depsipeptide is brought about by additional crucial interactions involving eEF1A domain 1 in such a way that the molecule fits snugly at the interface between these two domains. In the GDP-bound form of eEF1A, this binding site exists only as two separate halves, which accounts for the much greater affinity of didemnins for the GTP-bound form of this elongation factor. This binding mode is entirely different from those seen in the complexes of the homologous prokaryotic EF-Tu with kirromycin-type antibiotics or the cyclic thiazolyl peptide antibiotic GE2270A. Interestingly, the set of interactions used by didemnins to bind to eEF1A is also distinct from that used by eEF1BR or eEF1B , thus establishing a competition for binding to a common site that goes beyond simple molecular mimicry. The model presented here is consistent with both available biochemical evidence and known structure-activity relationships for these two classes of natural compounds and synthetic analogues and provides fertile ground for future research.

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Helix unwinding in the effector region of elongation factor EF-Tu–GDP

Cited by 225 publications

References 35 publications

The GTP-binding Release Factor eRF3 as a Key Mediator Coupling Translation Termination to mRNA Decay

The GTP-binding Release Factor eRF3 as a Key Mediator Coupling Translation Termination to mRNA Decay

Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis

Structural Basis for the Binding of Didemnins to Human Elongation Factor eEF1A and Rationale for the Potent Antitumor Activity of These Marine Natural Products

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