Evidence map›Paper›PMID 40404649›Full record

ArticleNature communications2025

Structural basis for the human SENP5's SUMO isoform discrimination.

Lucía Sánchez-Alba, Li Ying, Matthew D Maletic, Anna De Bolòs, Helena Borràs-Gas, Bing Liu, Nathalia Varejão, Virginia Amador, Monique P C Mulder, David Reverter

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. 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

10 authors.

Lucía Sánchez-Alba *Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.ORCID http://orcid.org/0000-0001-7353-1097
Li Ying *Institut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.ORCID http://orcid.org/0000-0002-5377-6262
Matthew D MaleticDepartment of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.ORCID http://orcid.org/0009-0005-8238-4048
Anna De BolòsInstitut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona, Spain.
Helena Borràs-GasInstitut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.ORCID http://orcid.org/0000-0002-3633-9132
Bing LiuInstitut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.ORCID http://orcid.org/0000-0002-6018-998X
Nathalia VarejãoInstitut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Virginia AmadorInstitut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona, Spain.ORCID http://orcid.org/0000-0002-3016-2874
Monique P C MulderDepartment of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands.ORCID http://orcid.org/0000-0001-5386-7132
David ReverterInstitut de Biotecnologia i de Biomedicina (IBB) and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain. david.reverter@uab.cat.ORCID http://orcid.org/0000-0002-5347-0992

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Post-translational SUMO modification is a widespread mechanism for regulating protein function within cells. In humans, SUMO-conjugated proteins are partially regulated by the deconjugating activity of six SENP family members. The proteolytic activity of these enzymes resides within a conserved catalytic domain that exhibits specificity for the two primary SUMO isoforms: SUMO1 and SUMO2/3. SENP5, along with SENP3, are nucleolar proteins involved in ribosome biogenesis and preferentially target SUMO2/3 isoforms. Here, we present the crystal structures of human SENP5 in complex with both SUMO1 and SUMO2 isoforms. These structures reveal a minimal complex interface and elucidate the molecular basis for SENP5's preference for the SUMO2 isoform. This preference can be attributed to a basic patch surrounding SENP5 Arg624 at the interface. Swapping mutagenesis and structural analysis demonstrate that Arg624 is favorably oriented to interact with Asp63 in SUMO2/3, while its interaction with the equivalent Glu67 in SUMO1 is less favorable. These results suggest that subtle structural differences within SUMO isoforms can significantly influence their deconjugation by SENP enzymes, opening new avenues for exploring the regulation of SUMOylation in various cellular processes and for developing therapeutic agents targeting SUMOylation pathways.

Indexed as

Cysteine EndopeptidasesSmall Ubiquitin-Related Modifier ProteinsSUMO-1 ProteinCatalytic DomainCrystallography, X-RayHumansModels, MolecularProtein BindingProtein IsoformsSumoylationUbiquitinsCysteine EndopeptidasesProtein IsoformsSENP3 protein, humanSmall Ubiquitin-Related Modifier ProteinsSUMO-1 ProteinSUMO1 protein, humanSUMO2 protein, humanSUMO3 protein, humanUbiquitins

Identifiers

PMID40404649
PMCPMC12098989

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Registered trials

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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.