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PMID: 25752577 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Assembly and specific recognition of k29- and k33-linked polyubiquitin.

Molecular cell ·Vol. 58 ·No. 1 ·2015-04-02 ·Pages 95-109

Michel MA, Elliott PR, Swatek KN, Simicek M, Pruneda JN, Wagstaff JL, Freund SM, Komander D

Abstract

Protein ubiquitination regulates many cellular processes via attachment of structurally and functionally distinct ubiquitin (Ub) chains. Several atypical chain types have remained poorly characterized because the enzymes mediating their assembly and receptors with specific binding properties have been elusive. We found that the human HECT E3 ligases UBE3C and AREL1 assemble K48/K29- and K11/K33-linked Ub chains, respectively, and can be used in combination with DUBs to generate K29- and K33-linked chains for biochemical and structural analyses. Solution studies indicate that both chains adopt open and dynamic conformations. We further show that the N-terminal Npl4-like zinc finger (NZF1) domain of the K29/K33-specific deubiquitinase TRABID specifically binds K29/K33-linked diUb, and a crystal structure of this complex explains TRABID specificity and suggests a model for chain binding by TRABID. Our work uncovers linkage-specific components in the Ub system for atypical K29- and K33-linked Ub chains, providing tools to further understand these unstudied posttranslational modifications.

MeSH Terms
Amino Acid Sequence Crystallography, X-Ray Endopeptidases/chemistry,genetics,metabolism Escherichia coli/genetics,metabolism HEK293 Cells Humans Hydrophobic and Hydrophilic Interactions Lysine/chemistry,metabolism Models, Molecular Molecular Sequence Data Proteasome Endopeptidase Complex/metabolism Protein Binding Protein Conformation Protein Processing, Post-Translational Protein Structure, Tertiary Proteolysis Recombinant Fusion Proteins/chemistry,genetics,metabolism Signal Transduction Ubiquitin/chemistry,genetics,metabolism Ubiquitin-Protein Ligases/chemistry,genetics,metabolism Ubiquitination
Chemicals
Recombinant Fusion Proteins Ubiquitin UBE3C protein, human Ubiquitin-Protein Ligases Endopeptidases ZRANB1 protein, human Proteasome Endopeptidase Complex Lysine
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Michel Martin A
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Elliott Paul R
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Swatek Kirby N
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Simicek Michal
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Pruneda Jonathan N
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Wagstaff Jane L
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Freund Stefan M V
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
Komander David
Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: dk@mrc-lmb.cam.ac.uk.
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Article Info
Journal
Molecular cell
Abbr.
Mol Cell
ISSN
1097-4164
DOI
10.1016/j.molcel.2015.01.042
Email
dk@mrc-lmb.cam.ac.uk
Published
2015-04-02
Epub
2015-00-05
Pages
95-109
Language
English
Region
United States
NLM ID
9802571
PMCID
PMC4386031
Subset
IM
Grants
European Research Council · 309756 · International
Medical Research Council · MC_U105192732 · United Kingdom
Medical Research Council · U105192732 · United Kingdom
Databases
PDB
5AF4, 5AF5, 5AF6
Corrections
CommentIn
PMID: 25839429
External Links
PubMed source DOI: 10.1016/j.molcel.2015.01.042 PMC Full Text View journal details
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