Evidence map›Paper›PMID 27650958›Full record

ArticleJournal of structural biology2016

A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme.

Shreya Dharadhar, Marcello Clerici, Willem J van Dijk, Alexander Fish, Titia K Sixma

Open access · hybridAbstract read
In one paragraph

Article in Journal of structural biology, 2016. 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
1.9field-weighted citation impact, top 14% 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, 37 citations in OpenAlex.

  1. Review
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  6. Article
  7. Review
  8. Article
  9. Structural basis of FANCD2 deubiquitination by USP1-UAF1.Nature structural & molecular biology · 2021
    Article
  10. Review
  11. Molecular Mechanisms of DUBs Regulation in Signaling and Disease.International journal of molecular sciences · 2021
    Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
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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

5 authors at 2 institutions in 2 countries.

Shreya DharadharDivision of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Marcello ClericiDivision of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
Willem J van DijkDivision of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Alexander FishDivision of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Titia K SixmaDivision of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. Electronic address: t.sixma@nki.nl.
The Netherlands Cancer Institute · NLCancer Genomics Centre · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Regulation of deubiquitinating enzyme (DUB) activity is an essential step for proper function of cellular ubiquitin signals. UAF1 is a WD40 repeat protein, which binds and activates three important DUBs, USP1, USP12 and USP46. Here, we report the crystal structure of the USP12-Ub/UAF1 complex at a resolution of 2.8Å and of UAF1 at 2.3Å. In the complex we find two potential sites for UAF1 binding, analogous to what was seen in a USP46/UAF1 complex. In line with these observed dual binding states, we show here that USP12/UAF1 complex has 1:2 stoichiometry in solution, with a two-step binding at 4nM and 325nM respectively. Mutagenesis studies show that the fingers sub-domain of USP12 interacts with UAF1 to form the high affinity interface. Our activation studies confirm that the high affinity binding is important for activation while the second UAF1 binding does not affect activation. Nevertheless, we show that this two step binding is conserved in the well-studied USP12 paralog, USP1. Our results highlight the interfaces essential for regulation of USP12 activity and show a conserved second binding of UAF1 which could be important for regulatory functions independent of USP12 activity.

Indexed as

Binding SitesCatalysisCrystallography, X-RayDeubiquitinating EnzymesHumansNuclear ProteinsProtein BindingScattering, Small AngleSurface Plasmon ResonanceUbiquitinUbiquitin ThiolesteraseX-RaysDeubiquitinating EnzymesNuclear ProteinsUbiquitinUbiquitin ThiolesteraseUSP12 protein, humanWDR48 protein, humanAllosteric regulationDeubiquitinating enzymeEnzyme catalysisProtein structureSmall angle X-ray scattering (SAXS)Surface Plasmon Resonance (SPR)

Identifiers

PMID27650958
PMCPMC5131612
OpenAlexW2522240652

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.