D arm

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D arm

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[[Image:Schema ARNt 448 658.svg|thumb|[[Transfer RNA]]]]
[[Image:Schema ARNt 448 658.svg|thumb|[[Transfer RNA]]]]
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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 [[Transfer RNA|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.


== Structure ==
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 |last1=Dyubankova |first1=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 |pmid=25815904 |issn=1477-0520|url-access=subscription }} Despite the importance of the D am in many tRNAs, the D arm is absent from some mitochondrial tRNAs from [[metazoa]].{{Cite journal |last1=Jühling |first1=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 |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}}
The '''D arm''' is a feature in the [[tertiary structure]] of [[transfer RNA]] (tRNA). It is composed of two short D stems around 5bp in length leading up to the D loop.{{Cite journal |last=Krahn |first=Natalie |last2=Fischer |first2=Jonathan T. |last3=Söll |first3=Dieter |date=2020-10-21 |title=Naturally Occurring tRNAs With Non-canonical Structures |url=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.596914/full |journal=Frontiers in Microbiology |language=English |volume=11 |doi=10.3389/fmicb.2020.596914 |issn=1664-302X |pmc=7609411 |pmid=33193279}} 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 }} Dihydrouridine is formed by addition of two hydrogens to a uracil base which remove its planar structure and aromaticity.{{Cite journal |last=Matsuura |first=Jin |last2=Akichika |first2=Shinichiro |last3=Wei |first3=Fan-Yan |last4=Suzuki |first4=Tsutomu |last5=Yamamoto |first5=Takahiro |last6=Watanabe |first6=Yuka |last7=Valášek |first7=Leoš Shivaya |last8=Mukasa |first8=Akitake |last9=Tomizawa |first9=Kazuhito |last10=Chujo |first10=Takeshi |date=2024-10-02 |title=Human DUS1L catalyzes dihydrouridine modification at tRNA positions 16/17, and DUS1L overexpression perturbs translation |url=https://www.nature.com/articles/s42003-024-06942-8 |journal=Communications Biology |language=en |volume=7 |issue=1 |pages=1238 |doi=10.1038/s42003-024-06942-8 |issn=2399-3642 |pmc=11445529 |pmid=39354220}} This D modification provides more flexibility to the D-loop structure of the D-arm. This appears to play a large role in the stabilization of the tRNA's tertiary structure as demonstrated in a detailed study comparing the structure of the D arm of the ''[[Schizosaccharomyces pombe]]'' tRNAiMet with an unmodified [[uracil]] (U) to with the modified D nucleotide.{{Cite journal |last1=Dyubankova |first1=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 |pmid=25815904 |issn=1477-0520|url-access=subscription }} The D-loop is a highly variable region and is notable for its unusual conformation due to the over-crowding on one of the [[guanosine]] residues.

==== Variations in D-arm structure ====
Regions of the tRNA molecule such as the D-loop and D-stem (among others) are broadly conserved among the 20 tRNA types across Bacteria, Archaea, and Eukaryotes.{{Cite journal |last=Tamaki |first=Satoshi |last2=Tomita |first2=Masaru |last3=Suzuki |first3=Haruo |last4=Kanai |first4=Akio |date=2018-01-08 |title=Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data |url=http://journal.frontiersin.org/article/10.3389/fgene.2017.00227/full |journal=Frontiers in Genetics |volume=8 |doi=10.3389/fgene.2017.00227 |issn=1664-8021 |pmc=5766645 |pmid=29358943}} However, there are still some varations such as in bacterial tRNA''Sec'' and tRNA''Ser'' where slight differences in D-stem and D-loop lengths between the two are an important feature in SelA discrimination.{{Cite journal |last=Itoh |first=Yuzuru |last2=Chiba |first2=Shiho |last3=Sekine |first3=Shun-ichi |last4=Yokoyama |first4=Shigeyuki |date=2009-10 |title=Crystal structure of human selenocysteine tRNA |url=https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkp648 |journal=Nucleic Acids Research |language=en |volume=37 |issue=18 |pages=6259–6268 |doi=10.1093/nar/gkp648 |issn=1362-4962 |pmc=2764427 |pmid=19692584}} Continually, there are more D bases found within D-arms of psychrophilic bacteria and less in thermophilic archaea which may reflect their adaptation to decrease or increase tRNA flexibility due to their unique environmental temperatures.

Despite the importance of the D arm in many tRNAs, the D arm is absent from some mitochondrial tRNAs from [[metazoa]].{{Cite journal |last1=Jühling |first1=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 |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}} Furthermore, there are examples of some mt-tRNA's in across a variety of organisms including ''Ascaris suum'', nematodes, and humans that lack a D-arm.

== Function ==
⚫
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 [[Transfer RNA|tRNA]] molecule."hardt1993" />"smith1989">{{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.


==References==
==References==
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