About Secmarker web server
The Secmarker web server was created by Didac Santesmasses, with support of Marco Mariotti. It provides online access to Secmarker, a selenocysteine tRNA (tRNA-Sec) identification tool. Secmarker was developed at Roderic Guigó lab at the CRG.
Selenocysteine tRNA (tRNA-Sec)
Selenocysteine (Sec) is the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. Selenoproteins are present in the three domain of life: Eukarya, Bacteria and Archaea. Selenocysteine cognate tRNA (tRNA-Sec) is central to the selenoprotein synthesis process, playing a key role in both Sec biosynthesis and insertion. Sec is formed in a multistep process in which tRNA-Sec serves as a scaffold, so that Sec is synthesized already loaded on the tRNA. In selenoprotein synthesis, tRNA-Sec drives the re-coding of highly specific UGA codons from stop signals to Sec. Not all organisms use Sec. In selenoprotein-devoid organisms, tRNA-Sec is absent. Identification of tRNA-Sec in a genome can be used as marker for the Sec utilization trait.
The anticodon in tRNA-Sec is the UCA, (complementary to UGA). Like all tRNAs, its secondary structure comprises (Fig 1) an aminoacyl acceptor arm (A-stem), a dihydrouridine arm (D-stem and D-loop), an anticodon arm (C-stem and C-loop), a variable arm (V-stem and V-loop) and a TψC arm (T-stem and T-loop). It is the longest tRNA, with 90-100 nucleotides, rather than the conventional ~75 nucleotides in canonical tRNAs . It has an unusual structure, different from the canonical 7/5 in other tRNAs (where 7 and 5 are the number of base pairs (bp) in the A and T stems, respectively). The tRNA-Sec adopts a 9/4 fold in eukaryotes and archaea, and a 8/5 fold in bacteria . The acceptor and T arms have 13 bp in total, compared to 12 bp in the usual 7/5 structure in other tRNAs. It has an exceptionally long variable arm, even longer than those of type-2 tRNAs (e.g. tRNA-Ser) . The D arm of tRNA-Sec has a long D-stem, with 6 bp in eukaryotes and bacteria, and 7 bp in archaea , and a 4 bp D-loop, in contrast to the 3-4 bp D-stem and 7-12 nt D-loop in the canonical tRNAs . The unique structure of tRNA-Sec allows it to be recognized by SerRS, like tRNA-Ser, while conversely acting as the exclusive target of PSTK, SecS (or SelA), and EF-Sec (or SelB): SerRS recognizes the variable arm of tRNA-Sec, similar to the long variable arm in tRNA-Ser, while the Sec synthesis factors must strictly discriminate the tRNA-Sec. In contrast, PSTK phosphorylates tRNA-Sec but not tRNA-Ser by recognizing the tRNA-Sec D arm , and SecS contacts the characteristic 13 bp AT-stem .
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