Editing Transfer RNA (section)

==Binding to ribosome==
[[File:Transfer RNA morph AT to PE conformation.ogv|thumb|The range of conformations adopted by tRNA as it transits the A/T through P/E sites on the ribosome. The Protein Data Bank (PDB) codes for the structural models used as end points of the animation are given. Both tRNAs are modeled as phenylalanine-specific tRNA from ''Escherichia coli'', with the A/T tRNA as a homology model of the deposited coordinates. Color coding as shown for [[#Structure|tRNA tertiary structure]]. Adapted from.<ref>{{cite journal | vauthors = Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH | title = Structures of the bacterial ribosome in classical and hybrid states of tRNA binding | journal = Science | volume = 332 | issue = 6032 | pages = 981–984 | date = May 2011 | pmid = 21596992 | pmc = 3176341 | doi = 10.1126/science.1202692 | bibcode = 2011Sci...332..981D }}</ref>]]

The [[ribosome]] has three binding sites for tRNA molecules that span the space between the two [[ribosome#Structure|ribosomal subunits]]: the [[A-site|A (aminoacyl)]],<ref name="pmid14681588">{{cite journal | vauthors = Konevega AL, Soboleva NG, Makhno VI, Semenkov YP, Wintermeyer W, Rodnina MV, Katunin VI | title = Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions | journal = RNA | volume = 10 | issue = 1 | pages = 90–101 | date = January 2004 | pmid = 14681588 | pmc = 1370521 | doi = 10.1261/rna.5142404 }}</ref> [[P-site|P (peptidyl)]], and [[E-site|E (exit) sites]]. In addition, the ribosome has two other sites for tRNA binding that are used during [[mRNA]] decoding or during the initiation of [[translation (biology)|protein synthesis]]. These are the T site (named [[EF-Tu|elongation factor Tu]]) and I site (initiation).<ref name="Agirrezabala">{{cite journal | vauthors = Agirrezabala X, Frank J | title = Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu | journal = Quarterly Reviews of Biophysics | volume = 42 | issue = 3 | pages = 159–200 | date = August 2009 | pmid = 20025795 | pmc = 2832932 | doi = 10.1017/S0033583509990060 }}</ref><ref name="Allen">{{cite journal | vauthors = Allen GS, Zavialov A, Gursky R, Ehrenberg M, Frank J | title = The cryo-EM structure of a translation initiation complex from Escherichia coli | journal = Cell | volume = 121 | issue = 5 | pages = 703–712 | date = June 2005 | pmid = 15935757 | doi = 10.1016/j.cell.2005.03.023 | s2cid = 16146867 | doi-access = free }}</ref> By convention, the tRNA binding sites are denoted with the site on the [[ribosome#Structure|small ribosomal subunit]] listed first and the site on the [[ribosome#Structure|large ribosomal subunit]] listed second. For example, the A site is often written A/A, the P site, P/P, and the E site, E/E.<ref name="Agirrezabala" /> The binding proteins like L27, L2, L14, L15, L16 at the A- and P- sites have been determined by affinity labeling by A. P. Czernilofsky et al. (''Proc. Natl. Acad. Sci, USA'', pp.&nbsp;230–234, 1974).

Once translation initiation is complete, the first aminoacyl tRNA is located in the P/P site, ready for the elongation cycle described below. During translation elongation, tRNA first binds to the ribosome as part of a complex with elongation factor Tu ([[EF-Tu]]) or its eukaryotic ([[eEF-1]]) or archaeal counterpart. This initial tRNA binding site is called the A/T site. In the A/T site, the A-site half resides in the [[ribosome#Structure|small ribosomal subunit]] where the mRNA decoding site is located. The mRNA decoding site is where the [[mRNA]] [[codon]] is read out during translation. The T-site half resides mainly on the [[ribosome#Structure|large ribosomal subunit]] where EF-Tu or eEF-1 interacts with the ribosome. Once mRNA decoding is complete, the aminoacyl-tRNA is bound in the A/A site and is ready for the next [[Bacterial translation#Elongation|peptide bond]]<ref name="PTC">{{cite journal | vauthors = Tirumalai MR, Rivas M, Tran Q, Fox GE | title = The Peptidyl Transferase Center: a Window to the Past | journal = Microbiol Mol Biol Rev | volume = 85 | issue = 4 | pages = e0010421 | date = November 2021 | pmid = 34756086 | pmc = 8579967 | doi = 10.1128/MMBR.00104-21| bibcode = 2021MMBR...85...21T }}</ref> to be formed to its attached amino acid. The peptidyl-tRNA, which transfers the growing polypeptide to the aminoacyl-tRNA bound in the A/A site, is bound in the P/P site. Once the peptide bond is formed, the tRNA in the P/P site is acylated, or has a [[#Structure|free 3' end]], and the tRNA in the A/A site dissociates the growing polypeptide chain. To allow for the next elongation cycle, the tRNAs then move through hybrid A/P and P/E binding sites, before completing the cycle and residing in the P/P and E/E sites. Once the A/A and P/P tRNAs have moved to the P/P and E/E sites, the mRNA has also moved over by one [[codon]] and the A/T site is vacant, ready for the next round of mRNA decoding. The tRNA bound in the E/E site then leaves the ribosome.

The P/I site is actually the first to bind to aminoacyl tRNA, which is delivered by an initiation factor called [[Prokaryotic initiation factor-2|IF2]] in bacteria.<ref name="Allen" /> However, the existence of the P/I site in eukaryotic or archaeal [[ribosome]]s has not yet been confirmed. The P-site protein L27 has been determined by affinity labeling by E. Collatz and A. P. Czernilofsky (''FEBS Lett.'', Vol. 63, pp.&nbsp;283–286, 1976).