T arm

{{Short description|Region on a tRNA molecule}}

Image:Schema ARNt 448 658.svg]]

The T-arm or T-loop is a specialized region on the tRNA molecule which acts as a special recognition site for the ribosome to form a tRNA-ribosome complex during protein biosynthesis or translation (biology).

The T-arm has two components to it; the T-stem and the T-loop.

• The T-stem consists of a series of paired nucleotides, typically 5 pairs, but sometimes as few as 1 or as many as 6.{{cite book |last1=Lang |first1=B. Franz |last2=Lavrov |first2=Dennis |last3=Beck |first3=Natacha |last4=Steinberg |first4=Sergey V. |editor1-last=Bullerwell |editor1-first=Charles E. |title=Organelle Genetics |date=2012 |publisher=Springer |location=Berlin |isbn=9783642223792 |chapter=Mitochondrial tRNA Structure, Identity, and Evolution of the Genetic Code |pages=431–474 |doi=10.1007/978-3-642-22380-8_17}}{{cite book |last1=Dirheimer |first1=G. |last2=Keith |first2=G. |last3=Dumas |first3=P. |last4=Westhof |first4=E. |editor1-last=Söll |editor1-first=Dieter |editor2-last=RajBhandary |editor2-first=Uttam |title=tRNA: Structure, Biosynthesis, and Function |date=1995 |publisher=ASM Press |location=Washington, D.C. |isbn=9781555810733 |chapter=Primary, Secondary, and Tertiary Structures of tRNAs |pages=93–126 |doi=10.1128/9781555818333.ch8 }}
• The T-loop is also often known as the TΨC arm due to the presence of ribothymidine (T/m5U), pseudouridine and cytidine residues. It folds into a unique structural element consisting of stacked bases in a U-turn, now termed the "T-loop motif".{{cite journal |last1=Chan |first1=CW |last2=Chetnani |first2=B |last3=Mondragón |first3=A |title=Structure and function of the T-loop structural motif in noncoding RNAs. |journal=Wiley Interdisciplinary Reviews. RNA |date=September 2013 |volume=4 |issue=5 |pages=507–22 |doi=10.1002/wrna.1175 |pmid=23754657|pmc=3748142 }}
• In archaea, the m5U is replaced with N1-methylpseudouridine (m1Ψ). The m5U/m1Ψ modification at position 54 is thought to increase structural stability.{{cite journal | vauthors = Wurm JP, Griese M, Bahr U, Held M, Heckel A, Karas M, Soppa J, Wöhnert J | display-authors = 6 | title = Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs | journal = RNA | volume = 18 | issue = 3 | pages = 412–420 | date = March 2012 | pmid = 22274954 | pmc = 3285930 | doi = 10.1261/rna.028498.111 | quote = In contrast, in most archaea this position is occupied by another hypermodified nucleotide: the isosteric N1-methylated pseudouridine }}

Organisms with T-loop lacking tRNA exhibit a much lower level of aminoacylation and EF-Tu-binding than in organisms which have the native tRNA.{{Citation needed|date=August 2024}}

The T-loop motif has been identified as a ubiquitous structural element in a number of noncoding RNAs. At least one other instance of the T-loop, found in rRNA, also carries the m5U modification.{{cite journal |last1=Powell |first1=CA |last2=Minczuk |first2=M |title=TRMT2B is responsible for both tRNA and rRNA m(5)U-methylation in human mitochondria. |journal=RNA Biology |date=April 2020 |volume=17 |issue=4 |pages=451–462 |doi=10.1080/15476286.2020.1712544 |pmid=31948311|pmc=7237155 }}