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We are analyzing https://www.nature.com/articles/s41594-025-01561-1.

Title:
TRIP12 structures reveal HECT E3 formation of K29 linkages and branched ubiquitin chains | Nature Structural & Molecular Biology
Description:
Regulation by ubiquitin depends on E3 ligases forging chains of specific topologies, yet the mechanisms underlying the generation of atypical linkages remain largely elusive. Here we utilize biochemistry, chemistry, and cryo-EM to define the catalytic architecture producing K29 linkages and K29/K48 branches for the human HECT E3 TRIP12. TRIP12 resembles a pincer. One pincer side comprises tandem ubiquitin-binding domains, engaging the proximal ubiquitin to direct its K29 towards the ubiquitylation active site, and selectively capturing a distal ubiquitin from a K48-linked chain. The opposite pincer side—the HECT domain—precisely juxtaposes the ubiquitins to be joined, further ensuring K29 linkage specificity. Comparison to the prior structure visualizing K48-linked chain formation by UBR5 reveals a similar mechanism shared by two human HECT enzymes: parallel features of the E3s, donor and acceptor ubiquitins configure the active site around the targeted lysine, with E3-specific domains buttressing the acceptor for linkage-specific polyubiquitylation. Using biochemistry, chemical biology, and cryo-EM, Maiwald et al. elucidate how TRIP12 forms K29 linkages and K29/K48-linked branched ubiquitin chains, revealing a mechanism for polyubiquitylation shared by some HECT E3s.
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Keywords {🔍}

trip, acceptor, chain, pubmed, data, klinked, fig, article, chains, google, scholar, hect, ubiquitin, cas, donor, formation, branched, extended, ubs, domain, diub, central, site, chromatography, ubr, structure, clobe, nature, structural, tripδn, monoub, nat, assays, biol, catalytic, cryoem, cell, nacl, reactions, mol, linkages, proximal, ligase, trips, kklinked, protein, purified, source, map, linkage,

Topics {✒️}

nature portfolio semi-synthetic k48-linked di-ubs privacy policy ube2k–ub/e3/polyub reveals mechanisms mutant k48-linked di-ubs branched k29/k48-linked chain k29/k48-linked branched chain k29-linked di-ubiquitin chain ubiquitylating k48-linked di-ubs form k29/k48-branched polyubiquitination k29/k48-linked branched chains ubr1-mediated n-degron polyubiquitination advertising european research council k29/k48-branched ubiquitin chains k48/k63-branched ubiquitin chains k48-linked di-ub chain 5 mm isopropyl β-d-thiogalactopyranoside k48-linked di-ub substrate febs open bio testing k48-linked di-ubs e6-ap ubiquitin-protein ligase ub1–75–intein–chitin binding domain k48-linked di-ub target intrinsically-disordered n-terminal region social media model-building tools k48-linked chain formation k48-linked di-ub acceptors k29-linked chain formation cryo-em volume post-processing research design horizon 2020 research heterotypic nature generate k48-linked chains k63-ubiquitin chain formation moderate-resolution cryo-em maps k29-linked ubiquitin chain reprints k48-linked ubiquitin chains k48-linked di-ubs cryo-electron microscopy cullin-ring ligase crl2vhl tandem ub-binding regions k29-linked chain produced k29/k48-linked chains hect-type ubiquitin ligases k48-linked di-ub k63-linked ubiquitin chains forms k29-linked branches

Schema {🗺️}

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      headline:TRIP12 structures reveal HECT E3 formation of K29 linkages and branched ubiquitin chains
      description:Regulation by ubiquitin depends on E3 ligases forging chains of specific topologies, yet the mechanisms underlying the generation of atypical linkages remain largely elusive. Here we utilize biochemistry, chemistry, and cryo-EM to define the catalytic architecture producing K29 linkages and K29/K48 branches for the human HECT E3 TRIP12. TRIP12 resembles a pincer. One pincer side comprises tandem ubiquitin-binding domains, engaging the proximal ubiquitin to direct its K29 towards the ubiquitylation active site, and selectively capturing a distal ubiquitin from a K48-linked chain. The opposite pincer side—the HECT domain—precisely juxtaposes the ubiquitins to be joined, further ensuring K29 linkage specificity. Comparison to the prior structure visualizing K48-linked chain formation by UBR5 reveals a similar mechanism shared by two human HECT enzymes: parallel features of the E3s, donor and acceptor ubiquitins configure the active site around the targeted lysine, with E3-specific domains buttressing the acceptor for linkage-specific polyubiquitylation. Using biochemistry, chemical biology, and cryo-EM, Maiwald et al. elucidate how TRIP12 forms K29 linkages and K29/K48-linked branched ubiquitin chains, revealing a mechanism for polyubiquitylation shared by some HECT E3s.
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      dateModified:2025-05-26T00:00:00Z
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         Life Sciences
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         Protein Structure
         Membrane Biology
         Biological Microscopy
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            type:Organization
            name:Max Planck Institute of Biochemistry
            address:
               name:Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany
      name:Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
      name:Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
      name:ISREC, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
      name:Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
      name:Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
      name:Lyterian Therapeutics, South San Francisco, USA
      name:Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
      name:Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
      name:MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
      name:Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
      name:Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany
      name:Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany

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