Guanosine Triphosphate-Binding Proteins
Enrique Pimentel in Handbook of Growth Factors, 2017
Comparison of amino acid sequences has revealed the presence of multiple homologous regions common to all members of the human Ras family and the bacterial translation elongation factors Tu (EF-Tu) and G (EF-G), which also contain in their amino-terminal region a binding site for GTP.114 During protein biosynthesis in bacteria (Escherichia coli), EF-Tu recognizes, transports, and positions the codon-specified aminoacyl-tRNA onto the A site of the ribosome. In this role, EF-Tu interacts with GDP and GTP, which act as allosteric effectors to control the protein conformation required during the elongation cycle.115 High-resolution X-ray diffraction analysis of EF-Tu revealed that four regions of the amino acid sequence that are homologous to human p21ras are located in the vicinity of the GDP-binding site, and most of the invariant amino acids shared by the two proteins interact directly with the GDP ligand.
Translation
Paul Pumpens in Single-Stranded RNA Phages, 2020
The elongation, or translocation, or stepwise addition of each aminoacyl residue to the growing polypeptide chain was the third step after the (i) codon-directed binding of the aminoacyl-tRNA to the 70S initiation complex consisting of 70S ribosome-messenger RNA-fMet-tRNAf and (ii) peptide bond formation. In addition to the ribosome-messenger RNA-aminoacyl-tRNA complex, the elongation step required GTP and three protein factors, designated as elongation factors EF-Tu, EF-Ts, and EF-G. The content and functioning of the complex were reviewed exhaustively at that time by Lucas-Lenard and Lipmann (1971) and by Haselkorn and Rothman-Denes (1973).
Properties of CDC25-Like Proteins
Juan Carlos Lacal, Frank McCormick in The ras Superfamily of GTPases, 2017
The action of the SDC25 C domain is more specific on the GDP than on the GTP complex. In the case of RAS2, the SDC25 C domain is 10 to 15 times more active on the GDP than on the GTP complex, while with p21 the difference between the GDP and GTP complex varies at most from 1.5- to 3-fold.45,46 In addition to the higher specificity of the SDC25 C domain for the GDP complex, the excess in the cell of GTP over GDP (respectively in mM range and around 0.1 mM) further drives the reaction toward the formation of RAS2 · GTP.50,51 This explains why in the yeast cell the action of a GDS with constitutive activity, as in the case of the SDC25 C domain, can induce an activated phenotype similar to that associated with the action of the CDC25 suppressor RAS2G19V. Therefore, the SDC25 C domain can be considered a true GDP to GTP exchange factor with a constitutive activity. In this regard it resembles elongation factor Ts (EF-Ts), of which no regulation is known and whose function is to unlock the tight EF-Tu-GDP conformation allowing EF-Tu to interact with GTP.52,53 EF-Ts acts as a ligand-exchange catalyst in a two-substrate system.54-56 Since the dissociation of EF-Tu-GDP represents the rate-limiting step for the formation of the active EF-Tu-GTP complex, the function of EF-Ts is directed to stabilize the reactive intermediate, the nucleotide-free EF-Tu, as the crucial step in a double displacement mechanism.55 Although in the case of the SDC25 C domain a thorough kinetic study has not yet been provided, our results strongly suggest that the action of the SDC25 C domain in the GDP to GTP exchange of RAS proteins also follows a substitution mechanism, whose events are outlined in Figure 6. This mechanism predicts the formation of a complex between the SDC25 C domain and guanine nucleotide-free ras proteins. We have indeed identified on gel filtration the existence of a nucleotide-free, stable RAS2 • SDC25 C domain complex, as is since long known for EF-Tu and EF-Ts.57,58 Addition of GDP causes the dissociation of this complex.
The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes
Published in Gut Microbes, 2021
Fergus W. J. Collins, Calum J. Walsh, Beatriz Gomez-Sala, Elena Guijarro-García, David Stokes, Klara B. Jakobsdóttir, Kristján Kristjánsson, Finlay Burns, Paul D. Cotter, Mary C. Rea, Colin Hill, R. Paul Ross
Bowtie2 was used to align the paired-end metagenomic reads from the deep-sea dataset against the MEGARes database in order to determine the abundance of known antibiotic resistance genes in the samples.30 Antibiotic resistance genes were found in less than half of all samples analyzed (Table 2). The resistance profile of these samples is dominated by resistance to a class of antibiotics known as elfamycins, which target elongation factor TU (EF-Tu) in bacterial cells.31 Potential resistance to elfamycins was identified in 20 of the metagenomic samples analyzed, in each case due to mutations in the EF-Tu encoding gene tufA. As most bacteria encode two virtually identical copies of the EF-Tu genes, levels of actual resistance due to differences in these genes may be overrepresented.32 As elfamycins are not used therapeutically, the mutations identified here may simply be a result of natural variation in the tufA genes rather than resistance due to the exposure to these antibiotics. EF-Tu has been identified as possibly having an important role in maintaining protein synthesis in response to high-pressure treatment of bacteria, thus potential adaptions of these genes to this environment may confer resistance to these antibiotics.33
Acne vulgaris: new evidence in pathogenesis and future modalities of treatment
Published in Journal of Dermatological Treatment, 2021
NAI: Bacterial elongation factor Tu (EF-Tu) and EF-Ts are interacting proteins involved in polypeptide chain elongation in protein biosynthesis (52). NAI, a semi-synthetic thiopeptide, is a peptide EF-Tu inhibitor, and highly selective against P. acnes, and is currently under evaluation as a 3% gel for acne (2014-001491-62) (36).
Kidney stone proteomics: an update and perspectives
Published in Expert Review of Proteomics, 2021
Paleerath Peerapen, Visith Thongboonkerd
Moreover, the pathogenic roles of common urinary microorganisms in kidney stone formation were also studied using a proteomics approach. Tavichakorntrakool et al. [58] characterized bacteria isolated from catheterized urine samples from the stone formers, as well as cortex and nidus of the stone matrices, to study the mechanisms underlying the association between urinary tract infection (UTI) and kidney stone formation. Thereafter, the differential cellular proteome profiles of the most commonly found bacterium, Escherichia coli, collected from urine and stone nidus of the stone formers were obtained using 2D-PAGE followed by nanoLC-MS/MS [59]. Comparing with the urine-derived bacteria, the nidus-derived bacteria had five proteins with lower levels that were involved in carbohydrate and DNA/protein metabolism, whereas two proteins with greater levels were involved in stress response. Interestingly, the differential cellular proteomes of E. coli were accompanied by some phenotypic differences [59]. Furthermore, E. coli isolated from the stone formers’ urine was compared with that isolated from UTI patients without stone [60]. Gel-based proteomics identified nine differentially expressed proteins. Among them, elongation factor-Tu (EF-Tu) was the most abundant protein with 2-fold greater level in E. coli isolated from the stone formers’ urine [60]. This study also demonstrated the promoting role of bacterial EF-Tu on kidney stone formation. Immunofluorescence staining without cell permeabilization revealed that E. coli isolated from the stone formers’ urine had greater expression level of surface EF-Tu compared with that isolated from the UTI patients without stone. In addition, the promoting activity of bacterial outer membrane vesicles (OMVs) derived from the stone formers’ urine on CaOx crystallization, growth, and aggregation was significantly greater than the bacterial OMVs isolated from the UTI patients without stone. Interestingly, these promoting effects could be ameliorated by neutralization using a specific anti-EF-Tu antibody, strengthening the promoting role of E. coli EF-Tu on CaOx kidney stone formation processes [60].
Related Knowledge Centers
- Elongation Factor
- G Protein
- Protein
- Ribosome
- Transfer Rna
- Amino Acid
- Messenger Rna
- Aminoacyl-Trna
- Translation
- Eef-1