D arm
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Variations in D-arm structure
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.[1] The D-loop contains the base dihydrouridine (D), for which the arm is named.[2] Dihydrouridine is formed by addition of two hydrogens to a uracil (U) base which remove its planar structure and aromaticity.[3] This D modification provides more flexibility to the D-loop structure of the D arm.[3] 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.[4] 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.
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.[5] However, there are still some variations such as in bacterial tRNASec and tRNASer where slight differences in D-stem and D-loop lengths between the two are an important feature in SelA discrimination.[6] 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.[3]
Despite the importance of the D arm in many tRNAs, the it is absent from some mitochondrial tRNAs from metazoa.[7] 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. [1]
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 tRNA molecule.[2][8] The D stem is also believed to have a recognition role although this has yet to be verified.
References
- 1 2 Krahn, Natalie; Fischer, Jonathan T.; Söll, Dieter (2020-10-21). "Naturally Occurring tRNAs With Non-canonical Structures". Frontiers in Microbiology. 11 596914. doi:10.3389/fmicb.2020.596914. ISSN 1664-302X. PMC 7609411. PMID 33193279.
- 1 2 Hardt, Wolf Dietrich; Schlegl, Judith; Erdmann, Volker A.; Hartmann, Roland K. (December 1993). "Role of the D arm and the anticodon arm in tRNA recognition by eubacterial and eukaryotic RNase P enzymes". Biochemistry. 32 (48): 13046–13053. doi:10.1021/bi00211a014. PMID 7694652.
- 1 2 3 Matsuura, Jin; Akichika, Shinichiro; Wei, Fan-Yan; Suzuki, Tsutomu; Yamamoto, Takahiro; Watanabe, Yuka; Valášek, Leoš Shivaya; Mukasa, Akitake; Tomizawa, Kazuhito; Chujo, Takeshi (2024-10-02). "Human DUS1L catalyzes dihydrouridine modification at tRNA positions 16/17, and DUS1L overexpression perturbs translation". Communications Biology. 7 (1): 1238. doi:10.1038/s42003-024-06942-8. ISSN 2399-3642. PMC 11445529. PMID 39354220.
- ↑ Dyubankova, N.; Sochacka, E.; Kraszewska, K.; Nawrot, B.; Herdewijn, P.; Lescrinier, E. (2015). "Contribution of dihydrouridine in folding of the D-arm in tRNA". Organic & Biomolecular Chemistry. 13 (17): 4960–4966. doi:10.1039/C5OB00164A. ISSN 1477-0520. PMID 25815904.
- ↑ Tamaki, Satoshi; Tomita, Masaru; Suzuki, Haruo; Kanai, Akio (2018-01-08). "Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data". Frontiers in Genetics. 8 227. doi:10.3389/fgene.2017.00227. ISSN 1664-8021. PMC 5766645. PMID 29358943.
- ↑ Itoh, Yuzuru; Chiba, Shiho; Sekine, Shun-ichi; Yokoyama, Shigeyuki (9 August 2009). "Crystal structure of human selenocysteine tRNA". Nucleic Acids Research. 37 (18): 6259–6268. doi:10.1093/nar/gkp648. ISSN 1362-4962. PMC 2764427. PMID 19692584.
- ↑ Jühling, Frank; Pütz, Joern; Bernt, Matthias; Donath, Alexander; Middendorf, Martin; Florentz, Catherine; Stadler, Peter F. (April 2012). "Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements". Nucleic Acids Research. 40 (7): 2833–2845. doi:10.1093/nar/gkr1131. ISSN 1362-4962. PMC 3326299. PMID 22139921.
- ↑ Smith, Drew; Yarus, Michael (April 1989). "Transfer RNA structure and coding specificity". Journal of Molecular Biology. 206 (3): 489–501. doi:10.1016/0022-2836(89)90496-8. PMID 2469803.
