Evidence map›Paper›PMID 28427904›Full record

ArticleBiochimie2017

Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts.

Ximena Barros-Álvarez, Keshia M Kerchner, Cho Yeow Koh, Stewart Turley, Els Pardon, Jan Steyaert, Ranae M Ranade, J Robert Gillespie, Zhongsheng Zhang, Christophe L M J Verlinde and 3 more

Open access · bronzeAbstract readComparative Study
In one paragraph

Article in Biochimie, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
0.6field-weighted citation impact, top 34% 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

7 citing papers in PubMed, 16 citations in OpenAlex.

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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

13 authors at 2 institutions in 3 countries.

Ximena Barros-ÁlvarezDepartment of Biochemistry, University of Washington, Seattle, WA, USA; Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela.
Keshia M KerchnerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Cho Yeow KohDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Stewart TurleyDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Els PardonStructural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.
Jan SteyaertStructural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.
Ranae M RanadeDivision of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA.
J Robert GillespieDivision of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA.
Zhongsheng ZhangDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Christophe L M J VerlindeDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Erkang FanDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Frederick S BucknerDivision of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA.
Wim G J HolDepartment of Biochemistry, University of Washington, Seattle, WA, USA. Electronic address: wghol@u.washington.edu.
University of Washington · USVrije Universiteit Brussel · BE

Funding

X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
Structure-based Optimization of T. brucei methionyl tRNA Synthetase InhibitorsR01AI097177 · NIAID · UNIVERSITY OF WASHINGTON · PI BUCKNER, FREDERICK SIMMONS, FAN, ERKANG · 2012 to 2019
$5.3M
Selective inhibition of tRNA synthetases from pathogenic protozoaR01AI084004 · NIAID · UNIVERSITY OF WASHINGTON · PI HOL, WILHELMUS G. J. · 2010 to 2014
$3.3M
NIAID NIH HHS R01 AI084004NIAID NIH HHS R01 AI097177NIGMS NIH HHS P41 GM103393
6 · The paper itself

Abstract

The crystal structure of Leishmania donovani tyrosyl-tRNA synthetase (LdTyrRS) in complex with a nanobody and the tyrosyl adenylate analog TyrSA was determined at 2.75 Å resolution. Nanobodies are the variable domains of camelid heavy chain-only antibodies. The nanobody makes numerous crystal contacts and in addition reduces the flexibility of a loop of LdTyrRS. TyrSA is engaged in many interactions with active site residues occupying the tyrosine and adenine binding pockets. The LdTyrRS polypeptide chain consists of two pseudo-monomers, each consisting of two domains. Comparing the two independent chains in the asymmetric unit reveals that the two pseudo-monomers of LdTyrRS can bend with respect to each other essentially as rigid bodies. This flexibility might be useful in the positioning of tRNA for catalysis since both pseudo-monomers in the LdTyrRS chain are needed for charging tRNA

Indexed as

Catalytic DomainModels, MolecularAdenosine MonophosphateAmino Acid SequenceBinding SitesHumansLeishmania donovaniProtein Structure, TertiarySequence AlignmentSingle-Chain AntibodiesTyrosineTyrosine-tRNA LigaseAdenosine MonophosphateSingle-Chain AntibodiesTyrosineTyrosine-tRNA LigaseAminoacyl-tRNA synthetaseLeishmaniaNanobodyNeglected tropical diseasesTrypanosomatidsTyrosyl adenylate analog

Identifiers

PMID28427904
PMCPMC5484532
OpenAlexW2606808179

What OpenQuestion holds

Textmetadata
LicenceTDM
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.