D arm
{{short description|Tertiary structure of tRNA}}
{{Refimprove|date=November 2014}}
Image:Schema ARNt 448 658.svg]]
The D arm is a feature in the tertiary structure of transfer RNA (tRNA). It is composed of the two D stems and the D loop. The D loop contains the base dihydrouridine (D), for which the arm is named.{{cite journal|last1=Hardt|first1=Wolf Dietrich|last2=Schlegl|first2=Judith|last3=Erdmann|first3=Volker A.|last4=Hartmann|first4=Roland K.|title=Role of the D arm and the anticodon arm in tRNA recognition by eubacterial and eukaryotic RNase P enzymes|journal=Biochemistry|date=December 1993|volume=32|issue=48|pages=13046–13053|doi=10.1021/bi00211a014|pmid=7694652 }} The D loop's main function is that of recognition. It is widely believed that it acts as a recognition site for aminoacyl-tRNA synthetase, an enzyme involved in the aminoacylation of the tRNA molecule.{{cite journal|last1=Smith|first1=Drew|last2=Yarus|first2=Michael|title=Transfer RNA structure and coding specificity|journal=Journal of Molecular Biology|date=April 1989|volume=206|issue=3|pages=489–501|doi=10.1016/0022-2836(89)90496-8|pmid=2469803}} The D stem is also believed to have a recognition role although this has yet to be verified.
It is a highly variable region and is notable for its unusual conformation due to the over-crowding on one of the guanosine residues. It appears to play a large role in the stabilization of the tRNA's tertiary structure. The role of the D nucleotide in tRNA structure has been demonstrated in a detailed study comparing the structure of the D arm of the Schizosaccharomyces pombe tRNAiMet with an unmodified uracil (U) to the structure with the modified D nucleotide.{{Cite journal |last=Dyubankova |first=N. |last2=Sochacka |first2=E. |last3=Kraszewska |first3=K. |last4=Nawrot |first4=B. |last5=Herdewijn |first5=P. |last6=Lescrinier |first6=E. |date=2015 |title=Contribution of dihydrouridine in folding of the D-arm in tRNA |url=https://xlink.rsc.org/?DOI=C5OB00164A |journal=Organic & Biomolecular Chemistry |language=en |volume=13 |issue=17 |pages=4960–4966 |doi=10.1039/C5OB00164A |issn=1477-0520}} Despite the importance of the D am in many tRNAs, the D arm is absent from some mitochondrial tRNAs from metazoa.{{Cite journal |last=Jühling |first=Frank |last2=Pütz |first2=Joern |last3=Bernt |first3=Matthias |last4=Donath |first4=Alexander |last5=Middendorf |first5=Martin |last6=Florentz |first6=Catherine |last7=Stadler |first7=Peter F. |date=April 2012 |title=Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements |url=https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkr1131 |journal=Nucleic Acids Research |language=en |volume=40 |issue=7 |pages=2833–2845 |doi=10.1093/nar/gkr1131 |issn=1362-4962 |pmc=3326299 |pmid=22139921}}