Evidence map›Paper›PMID 20870747›Full record

ArticleNucleic acids research2011

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

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

Open access · goldAbstract read
In one paragraph

Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
0.4field-weighted citation impact, top 37% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed, 23 citations in OpenAlex.

  1. Article
  2. Unconventional genetic code systems in archaea.Frontiers in microbiology · 2022
    Review
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Biophysical analysis ofThe Journal of biological chemistry · 2017
    Article
  9. Article
  10. RNA folding pathways in stop motion.Nucleic acids research · 2016
    Article
  11. Review
  12. Article
  13. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 1 institution in 2 countries.

R Lynn SherrerDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA.
Yuhei Araiso
Caroline Aldag
Ryuichiro Ishitani
Joanne M L Ho
Dieter Söll
Osamu Nureki
Tokyo Institute of Technology · JP

Funding

TRANSFER RNAR01GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER · 1985 to 2016
$21.3M
TRANSFER RNAR37GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER G · 1991 to 2000
$786k
NIGMS NIH HHS GM22854
6 · The paper itself

Abstract

O-Phosphoseryl-tRNA kinase (PSTK) is the key enzyme in recruiting selenocysteine (Sec) to the genetic code of archaea and eukaryotes. The enzyme phosphorylates Ser-tRNA(Sec) to produce O-phosphoseryl-tRNA(Sec) (Sep-tRNA(Sec)) that is then converted to Sec-tRNA(Sec) by Sep-tRNA:Sec-tRNA synthase. Earlier we reported the structure of the Methanocaldococcus jannaschii PSTK (MjPSTK) complexed with AMPPNP. This study presents the crystal structure (at 2.4-Å resolution) of MjPSTK complexed with an anticodon-stem/loop truncated tRNA(Sec) (Mj*tRNA(Sec)), a good enzyme substrate. Mj*tRNA(Sec) is bound between the enzyme's C-terminal domain (CTD) and N-terminal kinase domain (NTD) that are connected by a flexible 11 amino acid linker. Upon Mj*tRNA(Sec) recognition the CTD undergoes a 62-Å movement to allow proper binding of the 7-bp D-stem. This large reorganization of the PSTK quaternary structure likely provides a means by which the unique tRNA(Sec) species can be accurately recognized with high affinity by the translation machinery. However, while the NTD recognizes the tRNA acceptor helix, shortened versions of MjPSTK (representing only 60% of the original size, in which the entire CTD, linker loop and an adjacent NTD helix are missing) are still active in vivo and in vitro, albeit with reduced activity compared to the full-length enzyme.

Indexed as

AnticodonArchaeal ProteinsBase SequenceBinding SitesCrystallographyMethanococcalesModels, MolecularMolecular Sequence DataMotionMutationPhosphotransferasesProtein BindingProtein Structure, TertiaryRNA, ArchaealRNA, Transfer, Amino Acid-SpecificAnticodonArchaeal ProteinsPhosphotransferasesRNA, ArchaealRNA, Transfer, Amino Acid-SpecifictRNA, selenocysteine-

Identifiers

PMID20870747
PMCPMC3035459
OpenAlexW2050289674

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.