Evidence map›Paper›PMID 39052481›Full record

ArticleCell reports2024

Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity.

Martin A Michel, Simon Scutts, David Komander

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
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

2 citing papers in PubMed.

  1. Article
  2. Review
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

3 authors.

Martin A MichelDivision of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK.
Simon ScuttsThe Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia.
David KomanderDivision of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK; The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia. Electronic address: dk@wehi.edu.au.

Funding

Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically UnderservedR13CA192732 · NCI · AMERICAN ASSOCIATION FOR CANCER RESEARCH · PI FOTI, MARGARET · 2014 to 2014
$74k
European Research CouncilNCI NIH HHS R13 CA192732
6 · The paper itself

Abstract

Small ubiquitin-binding domains (UBDs) recognize small surface patches on ubiquitin with weak affinity, and it remains a conundrum how specific cellular responses may be achieved. Npl4-type zinc-finger (NZF) domains are ∼30 amino acid, compact UBDs that can provide two ubiquitin-binding interfaces, imposing linkage specificity to explain signaling outcomes. We here comprehensively characterize the linkage preference of human NZF domains. TAB2 prefers Lys6 and Lys63 linkages phosphorylated on Ser65, explaining why TAB2 recognizes depolarized mitochondria. Surprisingly, most NZF domains do not display chain linkage preference, despite conserved, secondary interaction surfaces. This suggests that some NZF domains may specifically bind ubiquitinated substrates by simultaneously recognizing substrate and an attached ubiquitin. We show biochemically and structurally that the NZF1 domain of the E3 ligase HOIPbinds preferentially to site-specifically ubiquitinated forms of NEMO and optineurin. Thus, despite their small size, UBDs may impose signaling specificity via multivalent interactions with ubiquitinated substrates.

Indexed as

Adaptor Proteins, Signal TransducingProtein BindingUbiquitinCell Cycle ProteinsHEK293 CellsHumansI-kappa B KinaseMembrane Transport ProteinsPhosphorylationProtein DomainsSubstrate SpecificityUbiquitinationUbiquitin-Protein LigasesZinc FingersAdaptor Proteins, Signal TransducingCell Cycle ProteinsI-kappa B KinaseIKBKG protein, humanMembrane Transport ProteinsOPTN protein, humanTAB2 protein, humanUbiquitinUbiquitin-Protein LigasesautophagyCP: Molecular biologyIKKmono-ubiquitinationoptineurinubiquitin binding domainubiquitin chain linkageubiquitin code

Identifiers

PMID39052481
PMCPMC11372445

What OpenQuestion holds

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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.