A Conserved Structural Motif at the N Terminus of Bacterial Translation Initiation Factor IF2

Laursen, Brian Søgaard; Mortensen, Karen Vibeke; Sperling‐Petersen, Hans Uffe; Hoffman, David W.

doi:10.1074/jbc.m212960200

Cited by 34 publications

(40 citation statements)

References 39 publications

(45 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These findings indicate that the C1 domain is highly flexible so that it may require additional support to be stabilized. In contrast to C1, the N domain is less flexible, but yet with an orientation differing by ∼40°b etween the two crystal structures (11,12) consistent with some flexibility suggested by an NMR study (13). The more extended conformation of the C1 and C2 domains in solution can be explained by the need by the latter to reach the acceptor end of fMet-tRNA fMet when IF2 is 30S bound (3).…”

Section: Resultsmentioning

confidence: 63%

Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor

Simonetti

Marzi

Billas

et al. 2013

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

View full text Add to dashboard Cite

Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/ L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl (fMet)-tRNA fMet positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process.protein synthesis | integrated structural biology I n bacteria, three translation initiation factors (IF1, IF2, and IF3) participate in the first phase of protein synthesis during which the 30S subunit binds the initiator tRNA to form codonanticodon interactions with the mRNA. The 30S initiation complex (IC) thus formed is converted into a 70S IC by joining of the 50S ribosomal subunit (1, 2). The IFs enhance the rate of ICs formation and ensure translation accuracy. Within this process, IF2 plays a key role by promoting the recruitment and stabilization of the N-formyl-methionyl(fMet)-tRNA fMet on the 30S IC in the peptidyl/initiator (P/I) site of the small ribosomal subunit with the help of initiation factors IF1 and IF3 (3-6). IF2 mediates subunit joining on which its GTPase activity is stimulated, leading to the formation of a 70S IC in a conformation that is productive in the first transpeptidation reaction (7). Snapshots of this process, visualized by cryo electron microscopy (cryo-EM) (3,(8)(9)(10), have localized IF2 on the ribosome and provided structural insights into 30S and 70S IC's.Bacterial IF2 is a multidomain protein (Figs. S1 and S2) for which the overall architecture is unknown. Unlike 70S-interacting elongation GTPases, IF2 contains a specific N-terminal (N) domain that is variable in sequence (in Escherichia coli, two copies of it comprise the bona fide N domain and the G1 domain). Furthermore, it contains a highly conserved C-terminal region with a central core comprising domains G [GTP/GDP (G) binding domain, G2] and G3 (II), and a C-terminal part consisting of domain C1 and of the initiator tRNA-binding domain C2. Recently, the crystal structure of the core part (1-363) of Thermus thermophilus IF2 was determined in different functional states (apo-protein, GTP, and GDP forms) (11). These structures gave important insights into the mechanism of nucleotide binding and GTP hydrolysis and also reveal significant structural differences with a related archaeal and eukaryotic protein a/eIF5B (11). However, because the entire C-terminal region was ...

show abstract

Section: Resultsmentioning

confidence: 63%

Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor

Simonetti

Marzi

Billas

et al. 2013

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

View full text Add to dashboard Cite

show abstract

“…IF2N has homology to the stem contact fold domains of the methionyl-and glutaminyltRNA synthetases and the B5 domain of the phenylalaninetRNA synthetase. However, no specific function has been assigned to the IF2N domain (105). NMR spectroscopy of the full-length E. coli IF2-1 revealed that the IF2N domain is connected to domain IV by a highly flexible linker region (104).…”

Section: Bacillus Subtilis Is the Only Organism That Does Not Belong mentioning

confidence: 99%

“…Domain I contains a small subdomain of approximately 50 residues, found in all bacterial and some plastid IF2s. We solved the structure of the domain by NMR spectroscopy methods (105). The subdomain is now designated IF2N in the protein families database (PFAM).…”

Section: Bacillus Subtilis Is the Only Organism That Does Not Belong mentioning

confidence: 99%

Initiation of Protein Synthesis in Bacteria

Laursen

Sørensen

Mortensen

et al. 2005

Microbiol Mol Biol Rev

Self Cite

522

506

View full text Add to dashboard Cite

Valuable information on translation initiation is available from biochemical data and recently solved structures. We present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. The first section describes the ribosomal features relevant to the initiation process. Subsequent sections describe the structure, function, and interactions of the mRNA, the initiator tRNA, and the initiation factors IF1, IF2, and IF3. Finally, we provide an overview of mechanisms of regulation of the translation initiation event. Translation occurs on ribonucleoprotein complexes called ribosomes. The ribosome is composed of a large subunit and a small subunit that hold the activities of peptidyltransfer and decode the triplet code of the mRNA, respectively. Translation initiation is promoted by IF1, IF2, and IF3, which mediate base pairing of the initiator tRNA anticodon to the mRNA initiation codon located in the ribosomal P-site. The mechanism of translation initiation differs for canonical and leaderless mRNAs, since the latter is dependent on the relative level of the initiation factors. Regulation of translation occurs primarily in the initiation phase. Secondary structures at the mRNA ribosomal binding site (RBS) inhibit translation initiation. The accessibility of the RBS is regulated by temperature and binding of small metabolites, proteins, or antisense RNAs. The future challenge is to obtain atomic-resolution structures of complete initiation complexes in order to understand the mechanism of translation initiation in molecular detail

show abstract

“…More recently, the structure of the first 157 amino acids of the amino-terminal domain of Escherichia coli was characterized by NMR (Laursen et al 2003). Although it is likely that the overall three-dimensional structure of IF2/eIF5B is very similar to that of bacterial IF2, the archaeal protein lacks a large polypeptide segment at its amino terminus (as do a few eubacterial IF2s) and contains two additional ␣-helices at its carboxyl terminus.…”

Section: Introductionmentioning

confidence: 99%

Ribosomal localization of translation initiation factor IF2

Marzi¹,

Knight²,

Brandi³

et al. 2003

RNA

View full text Add to dashboard Cite

Bacterial translation initiation factor IF2 is a GTP-binding protein that catalyzes binding of initiator fMet-tRNA in the ribosomal P site. The topographical localization of IF2 on the ribosomal subunits, a prerequisite for understanding the mechanism of initiation complex formation, has remained elusive. Here, we present a model for the positioning of IF2 in the 70S initiation complex as determined by cleavage of rRNA by the chemical nucleases Cu(II):1,10-orthophenanthroline and Fe(II):EDTA tethered to cysteine residues introduced into IF2. Two specific amino acids in the GII domain of IF2 are in proximity to helices H3, H4, H17, and H18 of 16S rRNA. Furthermore, the junction of the C-1 and C-2 domains is in proximity to H89 and the thiostrepton region of 23S rRNA. The docking is further constrained by the requisite proximity of the C-2 domain with P-site-bound tRNA and by the conserved GI domain of the IF2 with the large subunit's factor-binding center. Comparison of our present findings with previous data further suggests that the IF2 orientation on the 30S subunit changes during the transition from the 30S to 70S initiation complex.

show abstract

A Conserved Structural Motif at the N Terminus of Bacterial Translation Initiation Factor IF2

Cited by 34 publications

References 39 publications

Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor

Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor

Initiation of Protein Synthesis in Bacteria

Ribosomal localization of translation initiation factor IF2

Contact Info

Product

Resources

About