1. Overview

2. Structure

3. tRNA targeting antibiotics

4. References

The P-site (for peptidyl) is the second binding site for tRNA in the ribosome. The other two sites are the A-site (aminoacyl), which is the first binding site in the ribosome, and the E-site (exit), is the third and final binding site in the ribosome.

During protein translation, the P-site holds the tRNA which is linked to the growing polypeptide chain. When a stop codon is reached, the peptidyl-tRNA bond of the tRNA located in the P-site is cleaved releasing the newly synthesized protein.^[1] During the translocation step of the elongation phase, the mRNA is advanced by one codon, coupled to movement of the tRNAs from the ribosomal A to P and P to E sites, catalyzed by elongation factor EF-G.^[2]

Overview

The ribosomal P-site plays a vital role in all phases of translation. Initiation involves recognition of the start codon (AUG) by initiator tRNA in the P-site, elongation phase involves passage of many elongator tRNAs through the P site, termination phase involves hydrolysis of the mature polypeptide from tRNA bound to the P-site, and ribosome recycling involves release of deacylated tRNA. Binding a tRNA to the P-site in the presence of mRNA establishes codon-anticodon interaction and this interaction is important for small subunit ribosome (30S) contacts to the tRNA.^[3]

The classical two-state model ^[4] proposes that ribosome contains two binding sites for tRNA, P-site and A-site. The A-site binds to incoming to aminoacyl-tRNA which has the anti-codon for the corresponding codon in the mRNA presented in the A-site. After peptide formation between the C-terminal carbonyl group of the growing polypeptide chain (attached to a P-site bound tRNA) and the amino group of the aminoacyl-tRNA (A-site bound), the polypeptide chain is then attached to the tRNA in the A-site. The deacylated tRNA remains in the P-site and gets released once the peptidyl-tRNA is transferred to the P-site.

Chemical modification experiments provided evidence of a hybrid model, where tRNAs can sample a hybrid state of binding during elongation phase (pre-translocation step). These hybrid states of binding are in which acceptor and anti-codon ends of tRNA are in different sites (A, P and E). Using Chemical probing methods, a set of phylogenetically conserved bases in ribosomal RNA where the tRNA binds has been examined and suggested to be directly involved in the binding of tRNA to the prokaryotic ribosome.^[5] Correlation of such site specific protected bases in rRNA and occupancy of the A, P and E sites has allowed diagnostic assays of these bases to study the location of tRNA in any given state of the translational cycle. Authors proposed a hybrid model where higher affinity of the deactivated tRNA and peptide tRNA for the E and P sites of the 50S subunit, thermodynamically favour P/P to P/E and A/A to A/P transitions, which were further demonstrated through cryo-EM experiments.^[6] Also, single molecule FRET studies have detected fluctuations in the positions of tRNAs,^[7] leading to the conclusion that the classical (A/A-P/P) and hybrid states (A/P-P/E) of the tRNAs are certainly in dynamic equilibrium.

Prior to peptide bond formation, an aminoacyl-tRNA is bound in the A-site, a peptidyl-tRNA is bound in the P-site, and a deacylated tRNA (ready to exit from the ribosome) is bound to the E-site. Translation moves the tRNA from the A-site through the P- and E-sites, with the exception of the initiator tRNA, which binds directly to the P-site.^[8] Recent experiments have reported that protein translation can also initiate from A-site. Using Toeprinting assay, it has been shown that Protein Synthesis initiates from the A-site of the Ribosome (Eukaryotic) in the cricket paralysis virus (CrPV). IGR-IRES (Intragenic regions-internal ribosome entry sites) can assemble 80S ribosomes from 40S and 60S ribosomal subunits in the absence of eIF2, Met-tRNAi, or GTP hydrolysis and without a coding triplet in the ribosomal P-site. Authors also showed IGR-IRES can direct translation of a protein whose N-terminal residue is not methionine.^[9]

Structure

The complete three dimensional structure of the T. thermophilus 70S ribosome was determined using X-ray crystallography, containing mRNA and tRNAs bound to the P and E sites at 5.5 Å resolution and to the A site at 7 Å resolution. Authors found that all three tRNA binding sites (A, P, and E) of the ribosome contact all three respective tRNAs at universally conserved parts of their structures; this allows the ribosome to bind different tRNA species in precisely the same way. The translocation step of protein synthesis inescapably requires movements of 20 Å or more by the tRNAs, as they move from the A to P to E sites ^[10]

tRNA targeting antibiotics

Oxazolidines (e.g. linezolid) prevent the binding of the initiator tRNA at the P-site.^[11] Oxazolidines have been demonstrated to pleiotropically affect initiator-tRNA binding, EF-P (elongation factor P) stimulated synthesis of peptide bonds, and EF-G-mediated translocation of initiator-tRNA into the P-site.^[12]

Macrolide, Lincosamide and Streptogramin class of antibiotics prevent peptide bond formation and/or the translocation of tRNA from the A-site to the P-site on the ribosome ^[13][14] that eventually leads to interference with the elongation step and thus the inhibition of protein translation.

References

• Bento Gonçalves (city)
• Bento Gonçalves da Silva
• Bentok
• Benton Academy
• Benton Airpark
• Benton & Bowles
• Benton Central
• Benton Central High School
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• Benton Charter
• Benton Charter Township, Berrien County, Michigan
• Benton Community School Corporation
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• Benton Cordell Goodpasture
• Benton County (OR)
• Benton County (Oregon)
• Benton County School District (Mississippi)
• Benton County (Washington)
• Benton, Devon
• Benton (disambiguation)
• Benton Falls (band)
• Benton Field
• Benton Foundation
• Benton Gothic
• Benton Hall