Evidence map›Paper›PMID 24607692›Full record

ArticleJournal of molecular biology2014

The histone H4 tail regulates the conformation of the ATP-binding pocket in the SNF2h chromatin remodeling enzyme.

Lisa R Racki, Nariman Naber, Ed Pate, John D Leonard, Roger Cooke, Geeta J Narlikar

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
1.6field-weighted citation impact, top 17% 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

20 citing papers in PubMed, 33 citations in OpenAlex.

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  14. Remodelers tap into nucleosome plasticity.Nature structural & molecular biology · 2017
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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

6 authors at 2 institutions in 1 country.

Lisa R RackiDepartment of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA.
Nariman NaberDepartment of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA.
Ed PateVoiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA.
John D LeonardDepartment of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA.
Roger CookeDepartment of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA.
Geeta J NarlikarDepartment of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA. Electronic address: geeta.narlikar@ucsf.edu.
University of California, San Francisco · USWashington State University · US

Funding

Mechanistic Analysis of Chromatin RemodelingR01GM073767 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI NARLIKAR, GEETA J · 2005 to 2018
$4.7M
Mechanisms Controlling the Super-Relaxed StateR01AR062279 · NIAMS · WASHINGTON STATE UNIVERSITY · PI KOSTYUKOVA, ALLA S. · 2012 to 2016
$2.4M
Molecular dynamics studies of muscle proteinsR01AR053720 · NIAMS · WASHINGTON STATE UNIVERSITY · PI PATE, EDWARD F · 2007 to 2010
$1.1M
NIAMS NIH HHS AR053720NIAMS NIH HHS R01 AR053720NIAMS NIH HHS R01 AR062279NIGMS NIH HHS GM073767NIGMS NIH HHS R01 GM073767
6 · The paper itself

Abstract

The chromatin remodeling complex ACF helps establish the appropriate nucleosome spacing for generating repressed chromatin states. ACF activity is stimulated by two defining features of the nucleosomal substrate: a basic patch on the histone H4 N-terminal tail and the specific length of flanking DNA. However, the mechanisms by which these two substrate cues function in the ACF remodeling reaction is not well understood. Using electron paramagnetic resonance spectroscopy with spin-labeled ATP analogs to probe the structure of the ATP active site under physiological solution conditions, we identify a closed state of the ATP-binding pocket that correlates with ATPase activity. We find that the H4 tail promotes pocket closure. We further show that ATPase stimulation by the H4 tail does not require a specific structure connecting the H4 tail and the globular domain. In the case of many DNA helicases, closure of the ATP-binding pocket is regulated by specific DNA substrates. Pocket closure by the H4 tail may analogously provide a mechanism to directly couple substrate recognition to activity. Surprisingly, the flanking DNA, which also stimulates ATP hydrolysis, does not promote pocket closure, suggesting that the H4 tail and flanking DNA may be recognized in different reaction steps.

Indexed as

Chromatin Assembly and DisassemblyAdenosine TriphosphatasesAdenosine TriphosphateAmino Acid SequenceAnimalsBinding SitesChromosomal Proteins, Non-HistoneHistonesHumansMolecular Sequence DataProtein BindingProtein ConformationProtein Structure, TertiarySf9 CellsSpodopteraAdenosine TriphosphatasesAdenosine TriphosphateChromosomal Proteins, Non-HistoneHistonesSMARCA5 protein, humanbasic patchEPR spectroscopyhuman hACFnucleosomespin-labeled nucleotide

Identifiers

PMID24607692
PMCPMC4059342
OpenAlexW2085566464

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.