Evidence map›Paper›PMID 31832688›Full record

ArticleNucleic acids research2020

Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.

Yuichiro Nomura, Eric J Montemayor, Johanna M Virta, Samuel M Hayes, Samuel E Butcher

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact, top 88% 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

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

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

5 authors at 1 institution in 1 country.

Yuichiro NomuraDepartment of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Eric J MontemayorDepartment of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Johanna M VirtaDepartment of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Samuel M HayesDepartment of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
Samuel E ButcherDepartment of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
University of Wisconsin–Madison · US

Funding

Overall EvaluationP41GM103403 · NIGMS · CORNELL UNIVERSITY · PI EALICK, STEVEN E · 2012 to 2017
$14.3M
Biophysical investigations of RNA complexes essential for gene expressionR35GM118131 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI Samuel E Butcher · 2016 to 2026
$5.1M
Pixel Array Detector for X-ray CrystallographyS10RR029205 · NCRR · CORNELL UNIVERSITY · PI EALICK, STEVEN E · 2010 to 2010
$1.8M
NCRR NIH HHS S10 RR029205NIGMS NIH HHS P41 GM103403NIGMS NIH HHS R35 GM118131
6 · The paper itself

Abstract

U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n - 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.

Indexed as

Evolution, MolecularBinding SitesCatalytic DomainHumansKluyveromycesMitochondrial ProteinsModels, MolecularNucleic Acid ConformationNucleotidesPhosphatesPhosphoric Diester HydrolasesRNA, Small NuclearRNA SplicingSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSpliceosomesMitochondrial ProteinsNucleotidesPhosphatesPhosphoric Diester HydrolasesRNA, Small NuclearSaccharomyces cerevisiae ProteinsU6 small nuclear RNAUSB1 protein, humanUsb1 protein, S cerevisiae

Identifiers

PMID31832688
PMCPMC7026655
OpenAlexW2994860319

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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.