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evolution
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LepA is a paralogue of elongation factor G found in all bacteria
evolution
unlike all other translational GTPases, the enzyme does not have an effecter domain that stably contacts the switch II region of the GTPase domain. The domain organization of enzyme IF2 is inconsistent with the articulated lever mechanism of communication between the GTPase and initiator tRNA binding domains that is proposed for the eukaryotic initiation factor 5B, eIF5B. The catalytic mechanism of enzyme IF2 appears to be unique among the translational GTPases of prokaryotes. Because the interaction of enzyme IF2 and initiator tRNA is strongest in the presence of the 30S ribosomal subunit, it is not GDP or GTP but the 30S ribosomal subunit that facilitates IF2 to interact with the initiator tRNA
evolution
BPI-inducible protein A (BipA) is a member of the family of ribosomedependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Comparison of domain arrangement and overall structure of EF-G, EF4, and BipA, overview
evolution
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different relationships between IF5B and IF1A exist in archaea and eukaryotes, overview
evolution
elongation factor G (EF-G) belongs to the subfamily of translational G-proteins in the GTPase superfamily. All G-proteins share a nucleotide binding G domain, which contains distinct and highly conserved elements (G1-G5). The G3 sequence motif, switch II, is highly flexible and contains a DXXG sequence
evolution
the translational GTPase LepA is a highly conserved bacterial protein
evolution
there are three major GTPase superfamilies: small Ras-like GTPase, heterotrimeric G protein alphasubunit (Galpha) and protein-synthesizing GTPase. Underlying this functional difference are the low sequence identity (below 20%) and overall different molecular shapes among these three types of GTPases. In particular, whereas small G protein consists of a single canonical Ras-like catalytic domain (RasD), Galpha has an extra alpha-helical domain (HD) inserted and elongation factor EF-Tu has two extra beta-barrel domains (D2 and D3) subsequent to the C-terminus. In addition, Galpha can form a complex with Gbetagamma and undergoes a cycle of altered oligomeric states during function. In contrast to the functional and structural diversity, GTPases display significant conservation in the core structure of the catalytic domain. Small GTPase, Galpha, and EF-Tu contain a RasD consisting of six beta strands (beta1-beta6) and five alpha helices (alpha1-alpha5) flanking on both sides of the beta sheet. Three highly conserved loops named P-loop (PL), switch I (SI), and switch II (SII) constitute the primary sites coordinating the nucleotide phosphates. This structural similarity suggests that at a fundamental level small GTPase, Galpha, and EF-Tu may utilize the same mode of structural dynamics for their allosteric regulation, which is likely inherited from their common evolutionary ancestor. Structural comparison of Ras, Galphat and EF-Tu reveals common canonical Ras-like domain, nucleotide-associated conformational dynamics, molecular dynamics simulations, overview. Identification of EF-Tu specific key residues. But the enzymes show distinct nucleotide-associated flexibility and cross-correlation near functional regions, molecular dynamics simulations
evolution
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different relationships between IF5B and IF1A exist in archaea and eukaryotes, overview
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evolution
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different relationships between IF5B and IF1A exist in archaea and eukaryotes, overview
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evolution
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different relationships between IF5B and IF1A exist in archaea and eukaryotes, overview
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evolution
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LepA is a paralogue of elongation factor G found in all bacteria
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evolution
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different relationships between IF5B and IF1A exist in archaea and eukaryotes, overview
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evolution
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unlike all other translational GTPases, the enzyme does not have an effecter domain that stably contacts the switch II region of the GTPase domain. The domain organization of enzyme IF2 is inconsistent with the articulated lever mechanism of communication between the GTPase and initiator tRNA binding domains that is proposed for the eukaryotic initiation factor 5B, eIF5B. The catalytic mechanism of enzyme IF2 appears to be unique among the translational GTPases of prokaryotes. Because the interaction of enzyme IF2 and initiator tRNA is strongest in the presence of the 30S ribosomal subunit, it is not GDP or GTP but the 30S ribosomal subunit that facilitates IF2 to interact with the initiator tRNA
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malfunction
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an EF-G mutant lacking domains 4 and 5 shows ribosome-stimulated GTP hydrolysis activity 2.5fold slower than that of wild-type full-length EF-G and is insensitive to the effects of thiostrepton on both GTPase activity and ribosome binding
malfunction
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in strains DEltadksA, DELTAmolR1, DELTArsgA, DELTAtatB, DELTAtonB, DELTAtolR, DELTAubiF, DELTAubiG or DELTAubiH the deletion of lepA confers a synthetic growth phenotype. The strains are compromised for gene regulation, ribosome assembly, transport and/or respiration. Loss of LepA alters the average ribosome density for hundreds of mRNA coding regions in the cell, substantially reducing average ribosome density in many cases, but only subtle and codon-specific changes in ribosome distribution along mRNA are seen. Global perturbation of gene expression in the DELTAlepA mutant likely explains most of its phenotypes. LepA variants lacking the active-site histidine or unique C-terminal domain fail to complement the synthetic phenotypes
malfunction
successive removal of the C-terminus impairs ribosome-dependent multiple turnover GTPase activity of enzyme EF4
malfunction
EF-G is inactivated upon formation of an intramolecular disulfide bond by Cys114 and Cys266. The enzyme is reactivated by thioredoxin, and replacement of Cys114 by serine allows H2O2-treated EF-G to support translation at the same rate as DTT-treated EF-G. Oxidation of EF-G inhibits the function of EF-G on the ribosome. The GTPase activity and the dissociation of EF-G from the ribosome are suppressed when EF-G is oxidized. With hydrogen peroxide, neither the insertion of EF-G into the ribosome nor single-cycle translocation activity in vitro is affected, while the GTPase activity and the dissociation of EF-G from the ribosome are suppressed when EF-G is oxidized. The synthesis of longer peptides is suppressed to a greater extent than that of a shorter peptide when EF-G is oxidized. The formation of the disulphide bond in EF-G might interfere with the hydrolysis of GTP that is coupled with dissociation of EF-G from the ribosome and might thereby retard the turnover of EF-G within the translational machinery
malfunction
EF-G mutant H91A hydrolyzes GTP at a substantially slower rate compared to wild-type EF-G
malfunction
in cells lacking LepA, immature 30S particles accumulate. Four proteins are specifically underrepresented in these particles (S3, S10, S14, and S21) all of which bind late in the assembly process and contribute to the folding of the 3' domain of 16S rRNA. Processing of 16S rRNA is also delayed in the mutant strain, as indicated by increased levels of precursor 17S rRNA in assembly intermediates. Mutation DELTAlepA confers a synthetic growth phenotype in absence of RsgA, another GTPase, well known to act in 30S subunit assembly. Analysis of the DELTArsgA strain reveals accumulation of intermediates that resemble those seen in the absence of LepA. The growth defect is rescued by plasmid pRSGA, which contains the rsgA gene and its native promoter region
malfunction
intrinsic GTP hydrolysis by EF-G is unaffected by the H91 and F94 mutations. H91 mutated EF-Gs show different degrees of defect in ribosome-stimulated GTP hydrolysis. H91 mutants show larger defects in Pi release than in GTP hydrolysis
malfunction
mutations of EF-Tu specific key residues significantly disrupt the couplings in EF-Tu
malfunction
mutations of the conservative histidine H715 residue located at the tip of domain IV decreases the rate of mRNA translocation. ADP-ribosylation of eEF2 domain IV blocks reverse translocation activity of eEF2. ADP-ribosylation may directly interrupt the ability of eEF2 to stabilize the intermediate conformation of the tRNA ends during their movement through the SSU in the course of translocation
malfunction
two cold-sensitive IF2 mutations cause the accumulation of immature ribosomal particles
malfunction
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an EF-G mutant lacking domains 4 and 5 shows ribosome-stimulated GTP hydrolysis activity 2.5fold slower than that of wild-type full-length EF-G and is insensitive to the effects of thiostrepton on both GTPase activity and ribosome binding
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malfunction
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in strains DEltadksA, DELTAmolR1, DELTArsgA, DELTAtatB, DELTAtonB, DELTAtolR, DELTAubiF, DELTAubiG or DELTAubiH the deletion of lepA confers a synthetic growth phenotype. The strains are compromised for gene regulation, ribosome assembly, transport and/or respiration. Loss of LepA alters the average ribosome density for hundreds of mRNA coding regions in the cell, substantially reducing average ribosome density in many cases, but only subtle and codon-specific changes in ribosome distribution along mRNA are seen. Global perturbation of gene expression in the DELTAlepA mutant likely explains most of its phenotypes. LepA variants lacking the active-site histidine or unique C-terminal domain fail to complement the synthetic phenotypes
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metabolism
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universal mechanism for GTPase activation and hydrolysis in translational GTPases on the ribosome
metabolism
IF1 and IF3 increase plays a role in translation regulation at low temperature (cold-shock-induced translational bias) while the increase in IF2 made after cold stress is associated with immature ribosomal subunits together with at least another nine proteins involved in assembly and/or maturation of ribosomal subunits. IF2 is endowed with GTPase-associated chaperone activity that promotes refolding of denatured GFP
metabolism
IF2alpha is phosphorylated at Ser51 by four kinases in what is collectively known as the integrated stress response (ISR)
metabolism
in human, eIF5B displacing eIF2 from Met-tRNAi upon subunit joining may be coupled to eIF1A displacing eIF5 from eIF5B, allowing the eIF5:eIF2-GDP complex to leave the ribosome
metabolism
RsgA and LepA play partially redundant roles to ensure efficient 30S assembly
metabolism
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universal mechanism for GTPase activation and hydrolysis in translational GTPases on the ribosome
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physiological function
archaeal initiation factor 2 is a protein involved in the initiation of protein biosynthesis. In its GTP-bound, ON conformation, aIF2 binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, OFF conformation, it dissociates from tRNA, molecular dynamics, overview. AIF2 is largely responsible for recruiting the first, initiator tRNA to the ribosome and positioning it correctly, in register with the start codon of the ribosome-bound mRNA
physiological function
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EF-G and EF4 perform ribosome-dependent GTP hydrolysis and bind to conserved bases in 23S rRNA and stabilize ribosomal ratcheting
physiological function
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elongation factor G, EF-G, is one of several GTP hydrolytic proteins that cycles repeatedly on and off the ribosome during protein synthesis in bacterial cells. In the functional cycle of EF-G, hydrolysis of GTP is coupled to tRNA-mRNA translocation in ribosomes. GTP hydrolysis induces conformational rearrangements in two switch elements in the G domain of EF-G and other GTPases. These switch elements are thought to initiate the cascade of events that lead to translocation and EF-G cycling between ribosomes, coupling mechanism, overview
physiological function
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importance of interdomain communication in IF2, importance of GTP as an IF2 ligand in the early initiation steps and the dispensability of the free energy generated by the IF2 GTPase in the late events of the translation initiation pathway
physiological function
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importance of interdomain communication in IF2, importance of GTP as an IF2 ligand in the early initiation steps and the dispensability of the free energy generated by the IF2 GTPase in the late events of the translation initiation pathway
physiological function
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protein synthesis requires several GTPase factors, including elongation factor Tu, EF-Tu, which delivers aminoacyl-tRNAs to the ribosome
physiological function
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the EF-G GTPase mediates the movement of the tRNA2-mRNA complex during translation
physiological function
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the universally conserved GTPase HflX is a putative translation factor whose GTPase activity is stimulated by the 70S ribosome as well as the 50S but not the 30S ribosomal subunit
physiological function
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LepA contributes mainly to the initiation phase of translation. The effect of LepA on average ribosome density is related to the sequence of the Shine-Dalgarno region. But the enzyme does not generally influence polypeptide chain elongation rate
physiological function
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synchronous tRNA movements during translocation on the ribosome are orchestrated by elongation factor G and GTP hydrolysis
physiological function
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synchronous tRNA movements during translocation on the ribosome are orchestrated by elongation factor G and GTP hydrolysis
physiological function
the enzyme, initiation factor 2, is a GTPase that positions the initiator tRNA on the 30S ribosomal initiation complex and stimulates its assembly to the 50S ribosomal subunit to make the 70S ribosome
physiological function
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the GTPase aIF5B is a universally conserved initiation factor that assists ribosome assembly
physiological function
the translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex and triggers GTP hydrolysis upon ribosomal subunit joining
physiological function
archaeal translation initiation processes, like eukaryotic, involve a heterotrimeric GTPase aIF2 (eIF2) crucial for accuracy of start codon selection. Enzyme aIF2 is peculiar in that it functions on the small ribosomal subunit, whereas other translational GTPases bind the same region of the assembled ribosome in all species and likely use the sarcin-ricin loop in the large subunit for activation of GTP hydrolysis
physiological function
BPI-inducible protein A (BipA) is a GTPase involved in bacterial stress response. BipA is working as a ribosome-dependent translational GTPase factor and interacts with the A-site tRNA
physiological function
EF-G-mediated tRNA translocation, mechanism, overview
physiological function
elongation factor G (EF-G) is a key protein in translational elongation. It interacts with 70S ribosomes
physiological function
elongation factor G (EF-G) is a translational GTPase responsible for tRNA-mRNA translocation
physiological function
elongation factor Tu (EF-Tu) is a central part of the bacterial translation machinery. During each round of translation elongation, EF-Tu delivers an aminoacyl-tRNA (aatRNA) to the ribosome in a ternary complex with GTP. The successful decoding of the messenger RNA codon by the aa-tRNA leads to a closing of the small ribosomal subunit (30S), which in turn docks EF-Tu at the sarcin-ricin loop of the large subunit (50S) in the GTPase-activated (GA) state. The transition of EF-Tu into a reorganized catalytic configuration in the GTPase-activated state catalyzes GTP hydrolysis to GDP, followed by the release of inorganic phosphate (Pi) and a conformational change of EF-Tu
physiological function
elongation factor Tu (EF-Tu) is a central part of the bacterial translation machinery. During each round of translation elongation, EF-Tu delivers an aminoacyl-tRNA (aatRNA) to the ribosome in a ternary complex with GTP. The successful decoding of the messenger RNA codon by the aa-tRNA leads to a closing of the small ribosomal subunit (30S), which in turn docks EF-Tu at the sarcin-ricin loop of the large subunit (50S) in the GTPase-activated (GA) state. The transition of EF-Tu into a reorganized catalytic configuration in the GTPase-activated state catalyzes GTP hydrolysis to GDP, followed by the release of inorganic phosphate (Pi) and a conformational change of EF-Tu
physiological function
eukaryotic translation initiation factor 2 (eIF2) is a heterotrimeric GTPase (cf. EC 3.6.5.1), which plays a critical role in protein synthesis regulation. eIF2-GTP binds MettRNAi to form the eIF2-GTP-Met-tRNAi ternary complex (TC), which is recruited to the 40S ribosomal subunit. Following GTP hydrolysis, eIF2-GDP is recycled back to TC by its guanine nucleotide exchange factor (GEF), eIF2B (i.e. eIF-2B GDP-GTP exchange factor). Mechanisms of eIF2B action and its regulation by phosphorylation of the substrate eIF2, overview. eIF2 consists of alpha, beta, and gamma subunits, with eIF2gamma being the actual GTPase, and eIF2alpha and beta serving accessory functions. eIF2B is inhibited by phosphorylated eIF2, eIF2(alpha-P)-GDP. Modeling of the structural and thermodynamic basis of the eIF2B/eIF2 and eIF2B/eIF2(alpha-P) interactions and the mechanism of catalysis, and modelling of the structural mechanism of IF2B inhibition by eIF2(alpha-P)-GDP, detailed overview
physiological function
eukaryotic translation initiation is a multistep process requiring a number of eukaryotic translation initiation factors (eIFs). Two GTPases play key roles in the process. EIF2 brings the initiator Met-tRNAi to the preinitiation complex (PIC). Upon start codon selection and GTP hydrolysis promoted by the GTPase-activating protein (GAP) eIF5, eIF2-GDP is displaced from Met-tRNAi by eIF5B-GTP and is released in complex with eIF5. EIF5B promotes ribosomal subunit joining, with the help of eIF1A. Upon subunit joining, eIF5B hydrolyzes GTP and is released together with eIF1A. EIF5 promotes GTP hydrolysis by eIF2, followed by phosphate release. eIF2-GDP has lower affinity for Met-tRNAi than eIF2-GTP, and is released together with its GAP, eIF5. Possible mechanism for coordination between the two steps in translation initiation controlled by GTPases: start codon selection and ribosomal subunit joining, overview
physiological function
eukaryotic translation initiation is a multistep process requiring a number of eukaryotic translation initiation factors (eIFs). Two GTPases play key roles in the process. EIF2 brings the initiator Met-tRNAi to the preinitiation complex (PIC). Upon start codon selection and GTP hydrolysis promoted by the GTPase-activating protein (GAP) eIF5, eIF2-GDP is displaced from Met-tRNAi by eIF5B-GTP and is released in complex with eIF5. EIF5B promotes ribosomal subunit joining, with the help of eIF1A. Upon subunit joining, eIF5B hydrolyzes GTP and is released together with eIF1A. Possible mechanism for coordination between the two steps in translation initiation controlled by GTPases: start codon selection and ribosomal subunit joining, overview
physiological function
GTP hydrolysis in mRNA-tRNA translocation is catalyzed by elongation factor G, EF-G. GTP hydrolysis cannot proceed with EF-G bound to the unrotated form of the ribosome
physiological function
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initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining
physiological function
LepA functions in ribosome biogenesis, analysis of the role of LepA in ribosome assembly, overview. LepA functions in biogenesis of the 30S subunit of the ribosome, rather than in translation elongation. The GTPase activity of LepA is stimulated by interactions with both subunits of the ribosome, implying that LepA acts at a late stage of assembly, in the context of the 70S ribosome
physiological function
one of the final maturation steps of the large ribosomal subunit requires the joint action of the elongation factor-like 1 (EFL1) GTPase and the Shwachman-Diamond syndrome protein (SBDS) to release the eukaryotic translation initiation factor 6 (eIF6) and allow the assembly of mature ribosomes. EFL1 function is driven by conformational changes
physiological function
one of the final maturation steps of the large ribosomal subunit requires the joint action of the elongation factor-like 1 (Efl1) GTPase and the Shwachman-Diamond syndrome protein (SDO1, UniProt ID Q07953) to release the eukaryotic translation initiation factor 6 (Tif6) and allow the assembly of mature ribosomes. EFL1 function is driven by conformational changes
physiological function
the eukaryotic elongation factor eEF2 catalyzes ribosomal reverse translocation at one mRNA triplet. This process requires a cognate tRNA in the ribosomal E-site and cannot occur spontaneously without eEF2. The efficiency of this reaction depends on the concentrations of eEF2 and cognate tRNAs and increases in the presence of nonhydrolyzable GTP analogues. Crucial role of interactions of domain IV of eEF2 with the ribosome for the catalysis of the reverse translocation reaction. eEF2 is able to induce ribosomal translocation in forward and backward directions, highlighting the universal mechanism of tRNA-mRNA movements within the ribosome. During forward translocation, eEF2 binds to the PRE complex, capable of undergoing spontaneous conformational changes, including an intersubunit rotation of the ribosomal subunits. During reverse translocation, eEF2 binds to the POST complex, which has a conformation of unrotated ribosomal subunits because no tRNAs with hybrid acceptor ends are present therein. Reverse translocation requires an excessive concentration of cognate deacylated tRNA
physiological function
the protein-synthesizing GTPases participate in initiation, elongation and termination of mRNA translation
physiological function
translation initiation factor IF2 contributes to ribosome assembly and maturation during cold adaptation. IF2 is endowed with GTPase-associated chaperone activity that promotes refolding of denatured GFP. IF2 is another GTPase protein that participates in ribosome assembly/maturation, especially at low temperatures, the GTPase activity takes part in the assembly and maturation of the ribosomal subunits. The functional role of IF2 cannot be regarded as being restricted to its well documented functions in translation initiation of bacterial mRNA. IF2 has protein chaperone activity. For assembly and maturation of the ribosomal subunits, the cell requires an increased number of IF2 molecules, it is essential during the cold acclimation phase which follows cold stress when this process becomes particularly critical
physiological function
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initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining
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physiological function
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initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining
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physiological function
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archaeal translation initiation processes, like eukaryotic, involve a heterotrimeric GTPase aIF2 (eIF2) crucial for accuracy of start codon selection. Enzyme aIF2 is peculiar in that it functions on the small ribosomal subunit, whereas other translational GTPases bind the same region of the assembled ribosome in all species and likely use the sarcin-ricin loop in the large subunit for activation of GTP hydrolysis
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physiological function
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initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining
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physiological function
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EF-G and EF4 perform ribosome-dependent GTP hydrolysis and bind to conserved bases in 23S rRNA and stabilize ribosomal ratcheting
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physiological function
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archaeal translation initiation processes, like eukaryotic, involve a heterotrimeric GTPase aIF2 (eIF2) crucial for accuracy of start codon selection. Enzyme aIF2 is peculiar in that it functions on the small ribosomal subunit, whereas other translational GTPases bind the same region of the assembled ribosome in all species and likely use the sarcin-ricin loop in the large subunit for activation of GTP hydrolysis
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physiological function
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LepA contributes mainly to the initiation phase of translation. The effect of LepA on average ribosome density is related to the sequence of the Shine-Dalgarno region. But the enzyme does not generally influence polypeptide chain elongation rate
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physiological function
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one of the final maturation steps of the large ribosomal subunit requires the joint action of the elongation factor-like 1 (Efl1) GTPase and the Shwachman-Diamond syndrome protein (SDO1, UniProt ID Q07953) to release the eukaryotic translation initiation factor 6 (Tif6) and allow the assembly of mature ribosomes. EFL1 function is driven by conformational changes
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physiological function
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initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining
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physiological function
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archaeal translation initiation processes, like eukaryotic, involve a heterotrimeric GTPase aIF2 (eIF2) crucial for accuracy of start codon selection. Enzyme aIF2 is peculiar in that it functions on the small ribosomal subunit, whereas other translational GTPases bind the same region of the assembled ribosome in all species and likely use the sarcin-ricin loop in the large subunit for activation of GTP hydrolysis
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physiological function
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protein synthesis requires several GTPase factors, including elongation factor Tu, EF-Tu, which delivers aminoacyl-tRNAs to the ribosome
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physiological function
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the translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex and triggers GTP hydrolysis upon ribosomal subunit joining
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physiological function
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the enzyme, initiation factor 2, is a GTPase that positions the initiator tRNA on the 30S ribosomal initiation complex and stimulates its assembly to the 50S ribosomal subunit to make the 70S ribosome
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physiological function
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archaeal translation initiation processes, like eukaryotic, involve a heterotrimeric GTPase aIF2 (eIF2) crucial for accuracy of start codon selection. Enzyme aIF2 is peculiar in that it functions on the small ribosomal subunit, whereas other translational GTPases bind the same region of the assembled ribosome in all species and likely use the sarcin-ricin loop in the large subunit for activation of GTP hydrolysis
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additional information
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cyclical movements of switch element I, sw1, within EF-G, Sw1 exposure depends on EF-G functional state, conformational changes in sw1 help to drive the unidirectional EF-G cycle during protein synthesis, intramolecular movements in EF-G, overview
additional information
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HflX-GTP exists in a structurally distinct 50S- and 70S-bound form that stabilizes GTP binding up to 70000fold and that may represent the GTPase-activated state. This activation is likely required for efficient GTP-hydrolysis, and may be similar to that observed in elongation factor G
additional information
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IF2 mutant E571K, modified in its 30S binding domain IF2-G3, can perform in vitro all individual translation initiation functions of wild-type IF2 and supports faithful messenger RNA translation, despite having a reduced affinity for the 30S subunit and being completely inactive in GTP hydrolysis
additional information
protein:ligand interactions and conformational changes by molecular dynamics and Monte Carlo simulations, overview
additional information
comparison of crystal structures of prokaryotic initiation factor 2, IF2, from Thermus thermophilus with eukaryotic initiation factor 5B, eIF5B from Methanobacterium thermoautotrophicum, structure homology modeling, overview. The structures are significantly different. Enzyme IF2 is not a classical GTPase and acts more as a conformational switch, although IF2 is not a conformational switch like EF-G and RF3 are proposed to be. Enzyme IF2 functions better with GTP but does not require it, and IF2 does not have an identified nucleotide exchange factor. Comparison of switch II regions of translational GTPases
additional information
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comparison of crystal structures of prokaryotic initiation factor 2, IF2, from Thermus thermophilus with eukaryotic initiation factor 5B, eIF5B from Methanobacterium thermoautotrophicum, structure homology modeling, overview. The structures are significantly different. Enzyme IF2 is not a classical GTPase and acts more as a conformational switch, although IF2 is not a conformational switch like EF-G and RF3 are proposed to be. Enzyme IF2 functions better with GTP but does not require it, and IF2 does not have an identified nucleotide exchange factor. Comparison of switch II regions of translational GTPases
additional information
conformational changes of enzyme IF2 upon nucleotide binding control switches I and II in the G domain, modeling, overview
additional information
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conformational changes of enzyme IF2 upon nucleotide binding control switches I and II in the G domain, modeling, overview
additional information
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histidine 81 is critical for GTPase activity, both the C-terminal domain and the GTPase activity of LepA are critical for its function in vivo
additional information
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overall scheme of translocation: in the pre-translocation state, deacylated tRNA is bound in the P site and peptidy-tRNAl in the A site, both bound to their cognate codons in the mRNA. Following the binding of EF-G-GTP to the pretranslocation complex, translocation takes place. In the post-translocation state, peptidyl-tRNA has moved to the P site, whereas deacylated tRNA has dissociated, as have inorganic phosphate and EF-G-GDP. A histidine residue in the switch II region, His84 in Thermus thermophilus EF-G, plays an essential role in the reaction, structure-function relationships, overview
additional information
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overall scheme of translocation: in the pre-translocation state, deacylated tRNA is bound in the P site and peptidy-tRNAl in the A site, both bound to their cognate codons in the mRNA. Following the binding of EF-G-GTP to the pretranslocation complex, translocation takes place. In the post-translocation state, peptidyl-tRNA has moved to the P site, whereas deacylated tRNA has dissociated, as have inorganic phosphate and EF-G-GDP. A histidine residue in the switch II region, His91 in Escherichia coli EF-G, plays an essential role in the reaction, structure-function relationships, overview
additional information
the last 44 C-terminal amino acids of elongation factor 4 form a subdomain within the C-terminal domain that is important for GTP-dependent function on the ribosome. Efficient nucleotide hydrolysis by the enzyme on the ribosome depends on its conserved residue His 81, which is essential for catalysis in EF4
additional information
a conserved histidine in switch-II of EF-G moderates release of inorganic phosphate. EF-G possesses a conserved histidine 91 at the apex of switch-II, which is implicated in GTPase activation and GTP hydrolysis, H91 facilitates phosphate release. In crystal structures of the ribosome bound EF-G-GTP a tight coupling between H91 and the gamma-phosphate of GTP can be seen. Following GTP hydrolysis, H91 flips about 140° in the opposite direction, probably with phosphate still coupled to it, promoting phosphate to detach from GDP and reach the inter-domain space of EF-G, which constitutes an exit path for the phosphate, molecular dynamics simulations, overview. Mg2+ ion plays a vital role in the process
additional information
analysis of the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form at 4.7 A resolution, the unique structural attributes of BipA interactions with the ribosome and A-site tRNA function in regulating translation, translational factor recruitment and GTPase activation mechanisms by the ribosome, overview
additional information
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archeal enzyme structure analysis with bound GDP, archaea-specific region of IF5B (helix alpha15) binds and occludes the groove of domain IV, comparison with eukaryotic IF5B enzymes, in which IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A). Archaeal IF5B cannot access IF1A in the same manner as eukaryotic IF5B. Structural comparison of crenarchaeal and euryarchaeal aIF5Bs with crenarchaeal and euryarchaeal, detailed overview
additional information
calorimetric energetic basis describing the recognition of Efl1 to GT(D)P, Sdo1 and their intercommunication in solution, overview. The structure based analysis of the binding signatures indicates that Efl1 has a large structural flexibility
additional information
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calorimetric energetic basis describing the recognition of Efl1 to GT(D)P, Sdo1 and their intercommunication in solution, overview. The structure based analysis of the binding signatures indicates that Efl1 has a large structural flexibility
additional information
cryogenic electron microscopy (cryo-EM) at near-atomic resolution at 4.0-5.7 A resolution is used to investigate two complexes formed by EF-G H91A in its GTP-bound state with the ribosome, distinguished by the presence or absence of the intersubunit rotation, overview. GTP hydrolysis cannot proceed with EF-G bound to the unrotated form of the ribosome. Contacts between EF-G, protein S12, and helices 43 and 44 of 23S ribosomal RNA
additional information
EF-G binds with GTP or GDP on the PRE ribosome. But only in the presence of the GDP nucleotide, and not GTP, does EF-G crystalize with the non-rotated ribosome under the experimental conditions
additional information
EF-Tu in the GTPase-activated conformation, three-dimensional structure. The gamma-phosphate of GTP interacts with EF-Tu via the P-loop (V20, D21), the switch 1 loop (T61), and the switch 2 loop (G83). The switch 1 loop in turn is involved in the binding of EF-Tu to the tRNA (nucleotides 1-3 and 73-75). The conformational changes of the ribosome-EF-Tu complex and the effect of GTP hydrolysis as well as of KIR are modeled by all-atom explicit-solvent molecular dynamics simulations with GTP and with GDP and KIR as well as with GDP in the absence of KIR
additional information
EF-Tu in the GTPase-activated conformation, three-dimensional structure. The gamma-phosphate of GTP interacts with EF-Tu via the P-loop (V20, D21), the switch 1 loop (T61), and the switch 2 loop (G83). The switch 1 loop in turn is involved in the binding of EF-Tu to the tRNA (nucleotides 1-3 and 73-75). The conformational changes of the ribosome-EF-Tu complex and the effect of GTP hydrolysis as well as of KIR are modeled by all-atom explicit-solvent molecular dynamics simulations with GTP and with GDP and KIR as well as with GDP in the absence of KIR
additional information
high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with a nonhydrolyzable guanosine triphosphate analogue and initiator fMet-tRNAi Met in the context of the Escherichia coli ribosome to 3.7 A resolution using cryo-electron microscopy. Analysis of the intrinsic conformational modes of the 70S initiation complex (IC), establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome, mechanism of the final steps of translation initiation, overview. IF2-induced subunit joining of the 30S IC with the 50S subunit occurs in a rotated conformation and leads to the formation of the 70S-IC I. The initiator tRNA is positioned in the P/ei state through interactions with the L1 stalk and domain IV of IF2. Partial back rotation and unswiveling facilitate the P/pi state of initiator tRNA and reorient the G-domain of IF2 to trigger GTP hydrolysis. To reach the elongation-competent 70S complex, the 30S subunit completes back rotation, IF2-GDP dissociates, and the initiator tRNA completes the partial reverse translocation on the 50S subunit to reach the P/P-site state
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high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with a nonhydrolyzable guanosine triphosphate analogue and initiator fMet-tRNAi Met in the context of the Escherichia coli ribosome to 3.7 A resolution using cryo-electron microscopy. Analysis of the intrinsic conformational modes of the 70S initiation complex (IC), establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome, mechanism of the final steps of translation initiation, overview. IF2-induced subunit joining of the 30S IC with the 50S subunit occurs in a rotated conformation and leads to the formation of the 70S-IC I. The initiator tRNA is positioned in the P/ei state through interactions with the L1 stalk and domain IV of IF2. Partial back rotation and unswiveling facilitate the P/pi state of initiator tRNA and reorient the G-domain of IF2 to trigger GTP hydrolysis. To reach the elongation-competent 70S complex, the 30S subunit completes back rotation, IF2-GDP dissociates, and the initiator tRNA completes the partial reverse translocation on the 50S subunit to reach the P/P-site state
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human eIF5 competes with eIF1A for binding and has about 100fold higher affinity for eIF5B
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human eIF5 competes with eIF1A for binding and has about 100fold higher affinity for eIF5B
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human eIF5 competes with eIF1A for binding and has about 100fold higher affinity for eIF5B
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in its GTP-bound form, aIF2 specifically binds Met-tRNAi Met and brings it to the initiation complex. The enzyme is active in its GTP-bound form, the GDP-bound form loses affinity for Met-tRNAi Met and eventually dissociates from the initiation complex. With EF1A, productive binding of tRNA is GTP-dependent and related to the ON conformations of two regions of the G domain called switch 1 and switch 2. Structure of the ternary initiation complex aIF2-GDPNP-Met-tRNA, molecular dynamics simulations, overview. Analysis of the nucleotide-binding pocket of Ss-aIF2gamma. QM/MM free energy simulations of the catalytic reaction
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modeling of the closed conformation of eIF2alpha, the model is generated from the structure of human eIF2alpha (PDB ID 1Q8K), based on the intramolecular contact interface mapped using CSPs from the NMR deletion analysis, comparing spectra of full-length eIF2alpha with those of its individual domains, eIF2alpha-NTD and -CTD, docking analysis and comparisons with the structure of Schizosaccharomyces pombe, intramolecular interaction in eIF2alpha. Further structure modeling of eIF2alpha binding in the eIF2Breg regulatory subcomplex pocket, eIF2B complex with eIF2-GTP-Met-tRNAi ternary complex, eIF2B complex with eIF2 in an extended conformation, and eIF2B complex with eIF2 in closed conformation. eIF2alpha-NTD interactions with the eIF2Breg pocket play a role in catalysis, and not just in eIF2B inhibition by phosphorylated eIF2-GDP (eIF2(alpha-P)-GDP). The primary mechanism responsible for the increased affinity of eIF2B for eIF2(alpha-P)-GDP over unphosphorylated eIF2-GDP is the direct effect of phosphorylation on the affinity of the eIF2x02 phosphorylation loop (P-loop) for a corresponding surface on eIF2B. eIF2Balpha and eIF2Bbeta bind to adjacent surfaces on eIF2-N-terminal domain (NTD), and eIF2Balpha, eIF2Bbeta, and eIF2Breg show no significant preference for phosphomimetic over wild-type eIF2alpha-NTD, binding analysis, overview
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structure of the GTP form of elongation factor 4 (EF4) bound to ribosome 50S and 30S subunits with tRNA in the P and E sites, single-particle cryo-electron microscopy and modeling, overview. The superposition of this structure with that of the crystal structure of EF4-GDP bound to the ribosome by aligning on the 23S rRNA clearly shows the different orientations of EF4 in the ribosome. A conformational change of EF4 occurs upon ribosome binding and GTP hydrolysis, the unique domains (domain IV in EF-G and CTD in EF4) are positioned in completely different orientations relative to the shared domains, structure comparison with elongation factor G (EF-G)
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archeal enzyme structure analysis with bound GDP, archaea-specific region of IF5B (helix alpha15) binds and occludes the groove of domain IV, comparison with eukaryotic IF5B enzymes, in which IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A). Archaeal IF5B cannot access IF1A in the same manner as eukaryotic IF5B. Structural comparison of crenarchaeal and euryarchaeal aIF5Bs with crenarchaeal and euryarchaeal, detailed overview
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archeal enzyme structure analysis with bound GDP, archaea-specific region of IF5B (helix alpha15) binds and occludes the groove of domain IV, comparison with eukaryotic IF5B enzymes, in which IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A). Archaeal IF5B cannot access IF1A in the same manner as eukaryotic IF5B. Structural comparison of crenarchaeal and euryarchaeal aIF5Bs with crenarchaeal and euryarchaeal, detailed overview
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in its GTP-bound form, aIF2 specifically binds Met-tRNAi Met and brings it to the initiation complex. The enzyme is active in its GTP-bound form, the GDP-bound form loses affinity for Met-tRNAi Met and eventually dissociates from the initiation complex. With EF1A, productive binding of tRNA is GTP-dependent and related to the ON conformations of two regions of the G domain called switch 1 and switch 2. Structure of the ternary initiation complex aIF2-GDPNP-Met-tRNA, molecular dynamics simulations, overview. Analysis of the nucleotide-binding pocket of Ss-aIF2gamma. QM/MM free energy simulations of the catalytic reaction
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archeal enzyme structure analysis with bound GDP, archaea-specific region of IF5B (helix alpha15) binds and occludes the groove of domain IV, comparison with eukaryotic IF5B enzymes, in which IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A). Archaeal IF5B cannot access IF1A in the same manner as eukaryotic IF5B. Structural comparison of crenarchaeal and euryarchaeal aIF5Bs with crenarchaeal and euryarchaeal, detailed overview
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in its GTP-bound form, aIF2 specifically binds Met-tRNAi Met and brings it to the initiation complex. The enzyme is active in its GTP-bound form, the GDP-bound form loses affinity for Met-tRNAi Met and eventually dissociates from the initiation complex. With EF1A, productive binding of tRNA is GTP-dependent and related to the ON conformations of two regions of the G domain called switch 1 and switch 2. Structure of the ternary initiation complex aIF2-GDPNP-Met-tRNA, molecular dynamics simulations, overview. Analysis of the nucleotide-binding pocket of Ss-aIF2gamma. QM/MM free energy simulations of the catalytic reaction
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histidine 81 is critical for GTPase activity, both the C-terminal domain and the GTPase activity of LepA are critical for its function in vivo
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calorimetric energetic basis describing the recognition of Efl1 to GT(D)P, Sdo1 and their intercommunication in solution, overview. The structure based analysis of the binding signatures indicates that Efl1 has a large structural flexibility
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archeal enzyme structure analysis with bound GDP, archaea-specific region of IF5B (helix alpha15) binds and occludes the groove of domain IV, comparison with eukaryotic IF5B enzymes, in which IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A). Archaeal IF5B cannot access IF1A in the same manner as eukaryotic IF5B. Structural comparison of crenarchaeal and euryarchaeal aIF5Bs with crenarchaeal and euryarchaeal, detailed overview
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in its GTP-bound form, aIF2 specifically binds Met-tRNAi Met and brings it to the initiation complex. The enzyme is active in its GTP-bound form, the GDP-bound form loses affinity for Met-tRNAi Met and eventually dissociates from the initiation complex. With EF1A, productive binding of tRNA is GTP-dependent and related to the ON conformations of two regions of the G domain called switch 1 and switch 2. Structure of the ternary initiation complex aIF2-GDPNP-Met-tRNA, molecular dynamics simulations, overview. Analysis of the nucleotide-binding pocket of Ss-aIF2gamma. QM/MM free energy simulations of the catalytic reaction
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conformational changes of enzyme IF2 upon nucleotide binding control switches I and II in the G domain, modeling, overview
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comparison of crystal structures of prokaryotic initiation factor 2, IF2, from Thermus thermophilus with eukaryotic initiation factor 5B, eIF5B from Methanobacterium thermoautotrophicum, structure homology modeling, overview. The structures are significantly different. Enzyme IF2 is not a classical GTPase and acts more as a conformational switch, although IF2 is not a conformational switch like EF-G and RF3 are proposed to be. Enzyme IF2 functions better with GTP but does not require it, and IF2 does not have an identified nucleotide exchange factor. Comparison of switch II regions of translational GTPases
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in its GTP-bound form, aIF2 specifically binds Met-tRNAi Met and brings it to the initiation complex. The enzyme is active in its GTP-bound form, the GDP-bound form loses affinity for Met-tRNAi Met and eventually dissociates from the initiation complex. With EF1A, productive binding of tRNA is GTP-dependent and related to the ON conformations of two regions of the G domain called switch 1 and switch 2. Structure of the ternary initiation complex aIF2-GDPNP-Met-tRNA, molecular dynamics simulations, overview. Analysis of the nucleotide-binding pocket of Ss-aIF2gamma. QM/MM free energy simulations of the catalytic reaction
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