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Cited by 4Ubiquitin and proteasome pathwaysProtein Degradation and InhibitorsEnzyme Structure and Function

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Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin

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Yang, Woo Seok, Kim, Seu Ha, Kim, Minsang, Shin, Hejeong, Lee, Juyeon, Sandmann, Alexander, Park, Ohkmae K., Dissmeyer, Nico, Song, Hyun Kyu·2025·Nature Communications
DOI 10.1038/s41467-025-63282-9PMC PMC12370974

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Abstract

Abstract PROTEOLYSIS1 (PRT1), an N-recognin of Arabidopsis thaliana, has a specificity for recognizing the N-terminal aromatic hydrophobic residue (Tyr/Phe/Trp) of its substrates, subsequently degrading them through ubiquitylation. Here, we report the complex structures of the ZZ domain of A. thaliana PRT1 (PRT1ZZ) with bulky hydrophobic N-degron peptides. Unlike other ZZ domains, the binding site of PRT1ZZ has a novel structure organized into two hydrophobic regions. The N-terminal aromatic residues of N-degron interact hydrophobically with Ile333 and Phe352 in the flexible loops, which undergo dramatic conformational change. Notably, we also identified a third N-degron residue that participates in the hydrophobic network with N-recognin. Moreover, the ubiquitylation assay of PRT1 using the N-terminal tyrosine-exposed substrate BIG BROTHER showed that the tandem RING organization in PRT1 is critical for its robust activity. Therefore, the current study expands our knowledge of the structural repertoire in the N-degron pathway and provides insights into the regulation of E3 ubiquitin ligases containing tandem RING domains.

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Metadata

Authors
Yang, W. S., Kim, S. H., Kim, M., Shin, H., Lee, J., Sandmann, A., Park, O. K., Dissmeyer, N., & Song, H. K.
Affiliations
  • Korea University (KR)
  • Osnabrück University (DE)
Corresponding author
Song, Hyun Kyu
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-08-21
Volume
16
Issue
1
Pages
7817-7817
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-63282-9
PMC
PMC12370974
OpenAlex
W4413383725
Cited by
4
References
2
Citations by year
2025: 3
FWCI
0.90
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • Research Square (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
National Research Foundation of Korea (RS-2020-NR049540, RS-2021-NR056525, RS-2021-NR056577, RS-2022-NR067411, RS-2025-00521009)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
N-recognin, N-degron, ubiquitination, Arabidopsis thaliana, ZZ domain, protein structure, aromatic amino acids, RING E3 ligases, Big Brother, ubiquitin-proteasome system, protein degradation
MeSH terms
Protein Domains, Degrons, Binding Sites, Models, Molecular, Protein Binding, Substrate Specificity, Arabidopsis, Crystallography, X-Ray, Arabidopsis Proteins, Ubiquitin-Protein Ligases, Ubiquitination, Hydrophobic and Hydrophilic Interactions, Proteolysis

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