C-terminal domain of archaeal O -phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA Sec

Sherrer, R. Lynn; Araiso, Yuhei; Aldag, Caroline; Ishitani, Ryuichiro; Ho, Joanne M. L.; Söll, Dieter; Nureki, Osamu

doi:10.1093/nar/gkq845

Cited by 22 publications

(27 citation statements)

References 24 publications

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“…Similar base stacking of the nucleotide at position 9 is also observed in the eukaryal/archaeal tRNA Sec s (Figure 4F–I) (10,11,14). U9 of human tRNA Sec is only stacked on the A48 base of the G45:A48 pair, while A9 of the archaeal tRNA Sec s is stacked on the interbase hydrogen-bonding region of the base pair G45:C48.…”

Section: Resultssupporting

confidence: 72%

“…The asymmetric unit contains two tRNA Sec molecules (chains C and D) and one PSTK dimer, and the A9s in chains C and D adopt different ribose puckering modes, C3′-endo and C2′-endo, respectively (G and H). The C2′-endo puckering is assumed by the U9s of the A. aeolicus (E) and human (F) tRNA Sec s. On the other hand, the asymmetric unit of the M. jannaschii tRNA Sec •PSTK co-crystal contains one tRNA Sec molecule and one-half of a PSTK dimer [PDB ID: 3AM1 (14)], and the A9 ribose puckering is C2′-endo (I). C8 and U8 of the M. kandleri and M. jannaschii tRNA Sec s, respectively, are further stacked on A9.…”

Section: Resultsmentioning

confidence: 99%

“…A9 in chain D has the same C2′-endo ribose puckering and base orientation as those of the U9s in the A. aeolicus and human tRNA Sec s, while the A9 in chain C has the C3′-endo puckering and a different base orientation. On the other hand, both A9s exhibit the C2′-endo puckering in the two molecules of tRNA Sec from another archaeon, Methanocaldococcus jannaschii in complex with the PSTK dimer [PDB ID: 3AM1 (14)] (Figure 4I). The corresponding base stacking is also observed in tRNA Ser .…”

Section: Resultsmentioning

confidence: 99%

“…We previously reported the crystal structures of human tRNA Sec and the archaeal tRNA Sec •PSTK complex (10,11), and those of the human tRNA Sec •SepSecS complex (12), mouse tRNA Sec (13) and another archaeal tRNA Sec •PSTK complex have also been solved (14). These studies confirmed the ‘9 + 4’ secondary structure, and revealed the characteristic features of their tertiary cores.…”

Section: Introductionmentioning

confidence: 99%

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Tertiary structure of bacterial selenocysteine tRNA

Itoh

Sekine

Suetsugu

et al. 2013

Nucleic Acids Research

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Selenocysteine (Sec) is translationally incorporated into proteins in response to the UGA codon. The tRNA specific to Sec (tRNASec) is first ligated with serine by seryl-tRNA synthetase (SerRS). In the present study, we determined the 3.1 Å crystal structure of the tRNASec from the bacterium Aquifex aeolicus, in complex with the heterologous SerRS from the archaeon Methanopyrus kandleri. The bacterial tRNASec assumes the L-shaped structure, from which the long extra arm protrudes. Although the D-arm conformation and the extra-arm orientation are similar to those of eukaryal/archaeal tRNASecs, A. aeolicus tRNASec has unique base triples, G14:C21:U8 and C15:G20a:G48, which occupy the positions corresponding to the U8:A14 and R15:Y48 tertiary base pairs of canonical tRNAs. Methanopyrus kandleri SerRS exhibited serine ligation activity toward A. aeolicus tRNASec in vitro. The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNASec. Similar interactions exist in the reported tRNASer and SerRS complex structure from the bacterium Thermus thermophilus. Although the catalytic C-terminal domain of M. kandleri SerRS lacks interactions with A. aeolicus tRNASec in the present complex structure, the conformational flexibility of SerRS is likely to allow the CCA terminal region of tRNASec to enter the SerRS catalytic site.

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Section: Resultssupporting

confidence: 72%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Tertiary structure of bacterial selenocysteine tRNA

Itoh

Sekine

Suetsugu

et al. 2013

Nucleic Acids Research

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“…A mutated human tRNA Sec with a fourbase-pair D-loop showed decreased PSTK phosphorylation when compared with the wild type with a six-base-pair Dloop [22], and recent data demonstrated that identification of tRNA Sec in archaea is dependent on the D-loop structure [23]. Moreover, the Kinetoplastidae tRNA Sec has a 7/5 structure in the acceptor-T C stem, with seven nucleotides in the acceptor stem and five nucleotides in the T C stem, while the human [24] and the archaea [25] tRNA Sec have a 9/4 structure. These structural differences in the tRNA Sec of Kinetoplastidae suggest an equivalent adaptive modification in the enzymes that interact with and recognize such tRNAs, including the ribosome A site.…”

Section: Specific Characteristics Of Kinetoplas-tid Selenocysteine Bimentioning

confidence: 96%

Biological Implications of Selenium and its Role in Trypanosomiasis Treatment

Silva¹,

Silva²,

Thiemann³

2014

CMC

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Selenium (Se) is an essential trace element for several organisms and is present in proteins as selenocysteine (Sec or U), an amino acid that is chemically distinct from serine and cysteine by a single atom (Se instead of O or S, respectively). Sec is incorporated into selenoproteins at an in-frame UGA codon specified by an mRNA stem-loop structure called the selenocysteine incorporating sequence (SECIS) presented in selenoprotein mRNA and specific selenocysteine synthesis and incorporation machinery. Selenoproteins are presented in all domains but are not found in all organisms. Although several functions have been attributed to this class, the majority of the proteins are involved in oxidative stress defense. Here, we discuss the kinetoplastid selenocysteine pathway and how selenium supplementation is able to alter the infection course of trypanosomatids in detail. These organisms possess the canonical elements required for selenoprotein production such as phosphoseryl tRNA kinase (PSTK), selenocysteine synthase (SepSecS), selenophosphase synthase (SelD or SPS), and elongation factor EFSec (SelB), whereas other important factors presented in mammal cells, such as SECIS binding protein 2 (SBP) and SecP 43, are absent. The selenoproteome of trypanosomatids is small, as is the selenoproteome of others parasites, which is in contrast to the large number of selenoproteins found in bacteria, aquatic organisms and higher eukaryotes. Trypanosoma and Leishmania are sensitive to auranofin, a potent selenoprotein inhibitor; however, the probable drug mechanism is not related to selenoproteins in kinetoplastids. Selenium supplementation decreases the parasitemia of various Trypanosome infections and reduces important parameters associated with diseases such as anemia and parasite-induced organ damage. New experiments are necessary to determine how selenium acts, but evidence suggests that immune response modulation and increased host defense against oxidative stress contribute to control of the parasite infection.

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The Chemistry of Selenocysteine

Metanis¹,

Beld²,

Hilvert³

2011

Patai's Chemistry of Functional Groups

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Selenocysteine is a redox active amino acid. It is inserted co‐translationally into a number of natural proteins, providing them with a range of interesting enzymatic activities; it can also be incorporated into artificial peptides and proteins as a structural and mechanistic probe. In this chapter, the chemistry and biochemistry of this novel amino acid is reviewed. In addition to the (bio)synthesis of selenocysteine, selenopeptides and selenoproteins, the roles selenium plays in enzyme catalysis and its utility for diverse biotechnological applications are discussed.

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C-terminal domain of archaeal O -phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA Sec

Cited by 22 publications

References 24 publications

Tertiary structure of bacterial selenocysteine tRNA

Tertiary structure of bacterial selenocysteine tRNA

Biological Implications of Selenium and its Role in Trypanosomiasis Treatment

The Chemistry of Selenocysteine

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