Structure and recognition of polyubiquitin chains of different lengths and linkage

The polyubiquitin signal is post-translationally attached to a large number of proteins, often directing formation of macromolecular complexes resulting in the translocation, assembly or degradation of the attached protein. Recent structural and functional studies reveal general mechanisms by which different architectures and length of the signal are distinguished.

• Publication year

  2011

• Venue

  F1000 Biology Reports

• Publication date

  2011-12-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.3410/B3-26PMID 22162729PMCID 3229271
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Cdc48/p97 mediates UV-dependent turnover of RNA Pol II.

  2011cited by this paper
• Controlled enzymatic synthesis of natural-linkage, defined-length polyubiquitin chains using lysines with removable protecting groups.

  2011cited by this paper
• Polyubiquitin Linkage Profiles in Three Models of Proteolytic Stress Suggest the Etiology of Alzheimer Disease*

  2011cited by this paper
• Diverse polyubiquitin chains accumulate following 26S proteasomal dysfunction in mammalian neurones.

  2011cited by this paper
• Segmental isotopic labeling of ubiquitin chains to unravel monomer-specific molecular behavior.

  2011cited by this paper
• Structure of the HECT:ubiquitin complex and its role in ubiquitin chain elongation

  2011cited by this paper
• Interferon-Stimulated Gene 15 and the Protein ISGylation System

  2011cited by this paper
• Nonenzymatic assembly of natural polyubiquitin chains of any linkage composition and isotopic labeling scheme.

  2011cited by this paper
• Emerging roles for Lys11-linked polyubiquitin in cellular regulation.

  2011cited by this paper
• Ubiquitination of PCNA and Its Essential Role in Eukaryotic Translesion Synthesis

  2011cited by this paper
• SHARPIN is a component of the NF-κB-activating linear ubiquitin chain assembly complex

  2011cited by this paper
• Hierarchical binding of cofactors to the AAA ATPase p97.

  2011cited by this paper
• Linear ubiquitination in NF-κB signaling and inflammation: What we do understand and what we do not.

  2011cited by this paper
• SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis

  2011cited by this paper
• Lights and shadows of proteomic technologies for the study of protein species including isoforms, splicing variants and protein post‐translational modifications

  2011cited by this paper
• Constructing and decoding unconventional ubiquitin chains

  2011cited by this paper
• Total chemical synthesis of a 304 amino acid K48-linked tetraubiquitin protein.

  2011cited by this paper
• Traceless and Site-Specific Ubiquitination of Recombinant Proteins

  2011cited by this paper
• Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase.

  2010cited by this paper
• Recent advances in polyubiquitin chain recognition

  2010influential reference
• Ubiquitin-like protein conjugation and the ubiquitin–proteasome system as drug targets

  2010cited by this paper
• The Rad23 ubiquitin receptor, the proteasome and functional specificity in transcriptional control

  2010cited by this paper
• Mechanisms, regulation and consequences of protein SUMOylation.

  2010cited by this paper
• K11-linked polyubiquitination in cell cycle control revealed by a K11 linkage-specific antibody.

  2010cited by this paper
• Chemical Synthesis of Ubiquitin, Ubiquitin-Based Probes, and Diubiquitin**

  2010cited by this paper
• Structure of Rpn10 and Its Interactions with Polyubiquitin Chains and the Proteasome Subunit Rpn12

  2010cited by this paper
• The ESCRT complexes

  2010influential reference
• c‐IAP1 and UbcH5 promote K11‐linked polyubiquitination of RIP1 in TNF signalling

  2010cited by this paper
• K33-linked polyubiquitination of T cell receptor-zeta regulates proteolysis-independent T cell signaling.

  2010cited by this paper
• Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity.

  2010cited by this paper
• Anchors Away for Ubiquitin Chains

  2010cited by this paper
• Distinct consequences of posttranslational modification by linear versus K63-linked polyubiquitin chains

  2010cited by this paper
• Properties of natural and artificial proteins displaying multiple ubiquitin-binding domains.

  2010influential reference
• The diversity of ubiquitin recognition: hot spots and varied specificity.

  2010cited by this paper
• Structure of proteasome ubiquitin receptor hRpn13 and its activation by the scaffolding protein hRpn2.

  2010cited by this paper
• Mechanism for recognition of polyubiquitin chains: balancing affinity through interplay between multivalent binding and dynamics.

  2010cited by this paper
• Total chemical synthesis of di-ubiquitin chains.

  2010cited by this paper
• Exploring the linkage dependence of polyubiquitin conformations using molecular modeling.

  2010cited by this paper
• Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne

  2010cited by this paper
• Synthesis of K48-linked diubiquitin using dual native chemical ligation at lysine.

  2010cited by this paper
• Avid interactions underlie the K63-linked polyubiquitin binding specificities observed for UBA domains

  2009cited by this paper
• The structure and conformation of Lys63-linked tetraubiquitin.

  2009cited by this paper
• UBE2S elongates ubiquitin chains on APC/C substrates to promote mitotic exit

  2009cited by this paper
• Identification of a physiological E2 module for the human anaphase-promoting complex

  2009cited by this paper
• Ubiquitin-binding domains and their role in the DNA damage response.

  2009cited by this paper
• Linkage-specific avidity defines the lysine 63-linked polyubiquitin-binding preference of rap80.

  2009cited by this paper
• Structural basis for specific recognition of Lys 63‐linked polyubiquitin chains by tandem UIMs of RAP80

  2009cited by this paper
• Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates.

  2009cited by this paper
• Defining the human deubiquitinating enzyme interaction landscape.

  2009cited by this paper
• Together, Rpn10 and Dsk2 can serve as a polyubiquitin chain-length sensor.

  2009cited by this paper
• The role of ubiquitin linkages on α‐synuclein induced‐toxicity in a Drosophila model of Parkinson’s disease

  2009cited by this paper
• Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation.

  2009cited by this paper
• Evidence for bidentate substrate binding as the basis for the K48 linkage specificity of otubain 1.

  2009cited by this paper
• Building ubiquitin chains: E2 enzymes at work

  2009cited by this paper
• Direct Activation of Protein Kinases by Unanchored Polyubiquitin Chains

  2009cited by this paper
• Origin and function of ubiquitin-like proteins

  2009cited by this paper
• An additional role for SUMO in ubiquitin-mediated proteolysis

  2009cited by this paper
• Ubiquitin-binding domains — from structures to functions

  2009cited by this paper
• Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.

  2009cited by this paper
• The structure of the CYLD USP domain explains its specificity for Lys63-linked polyubiquitin and reveals a B box module.

  2008cited by this paper
• UBX domain proteins: major regulators of the AAA ATPase Cdc48/p97

  2008cited by this paper
• The Atg8 and Atg12 ubiquitin‐like conjugation systems in macroautophagy

  2008cited by this paper
• Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.

  2008cited by this paper
• Structural Basis for Ubiquitin Recognition by the Otu1 Ovarian Tumor Domain Protein*

  2008cited by this paper
• Polyubiquitin chains: functions, structures, and mechanisms

  2008cited by this paper
• Recognition of Polyubiquitin Isoforms by the Multiple Ubiquitin Binding Modules of Isopeptidase T*

  2008cited by this paper
• Protein partners of deubiquitinating enzymes.

  2008cited by this paper
• Certain Pairs of Ubiquitin-conjugating Enzymes (E2s) and Ubiquitin-Protein Ligases (E3s) Synthesize Nondegradable Forked Ubiquitin Chains Containing All Possible Isopeptide Linkages*

  2007cited by this paper
• Crystal structure and solution NMR studies of Lys48-linked tetraubiquitin at neutral pH.

  2007cited by this paper
• E2–BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages

  2007cited by this paper
• A model of interdomain mobility in a multidomain protein.

  2007cited by this paper
• A ubiquitin ligase complex assembles linear polyubiquitin chains

  2006cited by this paper
• Ubiquitin-binding domains.

  2006cited by this paper
• Interdomain mobility in di‐ubiquitin revealed by NMR

  2006cited by this paper
• Structural determinants for selective recognition of a Lys48-linked polyubiquitin chain by a UBA domain.

  2005cited by this paper
• Ubiquitin-binding domains

  2005cited by this paper
• Controlled synthesis of polyubiquitin chains.

  2005cited by this paper
• Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition.

  2005cited by this paper
• Binding of polyubiquitin chains to ubiquitin-associated (UBA) domains of HHR23A.

  2004cited by this paper
• Solution Conformation of Lys63-linked Di-ubiquitin Chain Provides Clues to Functional Diversity of Polyubiquitin Signaling*

  2004cited by this paper
• Polyubiquitin chains: polymeric protein signals.

  2004cited by this paper
• The Ubiquitin System: From Basic Mechanisms to the Patient Bed

  2004cited by this paper
• A proteomics approach to understanding protein ubiquitination

  2003cited by this paper
• Structural properties of polyubiquitin chains in solution.

  2002cited by this paper
• Recognition of the polyubiquitin proteolytic signal

  2000cited by this paper
• The hydrophobic effect contributes to polyubiquitin chain recognition.

  1998cited by this paper
• Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting.

  1996cited by this paper
• Structure of a diubiquitin conjugate and a model for interaction with ubiquitin conjugating enzyme (E2).

  1993cited by this paper
• Electronic Reprint Biological Crystallography Structure of a New Crystal Form of Tetraubiquitin Biological Crystallography Structure of a New Crystal Form of Tetraubiquitin

  year unknowncited by this paper

• Amide 1H and 15N NMR signal assignments of all naturally-occurring di-ubiquitins

  2026cites this paper
• Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation

  2023cites this paper
• NMR

  2021cites this paper
• JMJD6 negatively regulates cytosolic RNA induced antiviral signaling by recruiting RNF5 to promote activated IRF3 K48 ubiquitination

  2021cites this paper
• Conformational space sampled by domain reorientation of linear diubiquitin reflected in its binding mode for target proteins.

  2021cites this paper
• The dynamics of linear polyubiquitin

  2020cites this paper
• Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1.

  2020cites this paper
• Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments

  2020cites this paper
• Die Länge spezifischer Ubiquitin-ketten beeinflusst ihre Erkennung

  2020cites this paper
• N-cadherin-regulated FGFR ubiquitination and degradation control mammalian neocortical projection neuron migration

  2019cites this paper
• Ubiquitin Chains Bearing Genetically Encoded Photo-Cross-Linkers Enable Efficient Covalent Capture of (Poly)ubiquitin-Binding Domains.

  2019cites this paper
• Addition of flexible linkers to GPU-accelerated coarse-grained simulations of protein-protein docking

  2019cites this paper
• Impact of different ionization states of phosphorylated Serine-65 on ubiquitin structure and interactions

  2018influential citation
• Role of p53 circuitry in tumorigenesis: A brief review.

  2018cites this paper
• Identification of Proteins Interacting with Ubiquitin Chains.

  2017cites this paper
• Cullin neddylation may allosterically tune polyubiquitin chain length and topology.

  2017cites this paper
• Identifizierung von Interaktoren von Ubiquitinketten

  2017cites this paper
• ESI-IM-MS and Collision-Induced Unfolding That Provide Insight into the Linkage-Dependent Interfacial Interactions of Covalently Linked Diubiquitin.

  2017cites this paper
• Hydrophobic Patch of Ubiquitin is Important for its Optimal Activation by Ubiquitin Activating Enzyme E1.

  2017cites this paper
• Identification of primary and secondary UBA footprints on the surface of ubiquitin in cell‐mimicking crowded solution

  2017cites this paper
• Polyubiquitin-Photoactivatable Crosslinking Reagents for Mapping Ubiquitin Interactome Identify Rpn1 as a Proteasome Ubiquitin-Associating Subunit.

  2017cites this paper
• Ubiquitin Ligases and Posttranslational Regulation of Energy in the Heart: The Hand that Feeds.

  2017cites this paper
• Differential Contributions of Ubiquitin-Modified APOBEC3G Lysine Residues to HIV-1 Vif-Induced Degradation.

  2016cites this paper
• Steady-state kinetic studies reveal that the anti-cancer target Ubiquitin-Specific Protease 17 (USP17) is a highly efficient deubiquitinating enzyme.

  2016cites this paper
• Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease

  2016cites this paper
• Chapter Two - Heterotrimeric G Protein Ubiquitination as a Regulator of G Protein Signaling.

  2016cites this paper
• Molecular mechanisms regulating formation, trafficking and processing of annular gap junctions

  2016influential citation
• How to tackle protein structural data from solution and solid state: An integrated approach.

  2016cites this paper
• Linkage-specific conformational ensembles of non-canonical polyubiquitin chains.

  2016cites this paper
• Regulation and localization of vascular endothelial growth factor within the mammary glands during the transition from late gestation to lactation.

  2016cites this paper
• New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.

  2016cites this paper
• Defining Noncovalent Ubiquitin Homodimer Interfacial Interactions through Comparisons with Covalently Linked Diubiquitin.

  2016cites this paper
• Autophagy Degrades Endocytosed Gap Junctions

  2015cites this paper
• DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin.

  2015cites this paper
• Dynamics of an Active-Site Flap Contributes to Catalysis in a JAMM Family Metallo Deubiquitinase.

  2015cites this paper
• Catalytic Function and Substrate Specificity of the Papain-Like Protease Domain of nsp3 from the Middle East Respiratory Syndrome Coronavirus

  2014cites this paper
• Disassembly of Lys11 and Mixed Linkage Polyubiquitin Conjugates Provides Insights into Function of Proteasomal Deubiquitinases Rpn11 and Ubp6*

  2014cites this paper
• Using Chemistry to Investigate the Molecular Consequences of Protein Ubiquitylation

  2014cites this paper
• Ubiquibodies: Engineered Ubiquitin Ligases With Unnatural Substrate Specificity For Targeted Protein Silencing

  2014cites this paper
• PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

  2014cites this paper
• Alanine scan of core positions in ubiquitin reveals links between dynamics, stability, and function.

  2014cites this paper
• Analyses of All Possible Point Mutations within a Protein Reveals Relationships between Function and Experimental Fitness: A Dissertation

  2014cites this paper
• Catalytic Function and Substrate Specificity of the PLpro Domain of nsp 3 from 1 the Middle East Respiratory Syndrome Coronavirus ( MERS-CoV ) 2 3

  2014cites this paper
• Characterisation of DISC1 ubiquitination and its potential as a therapeutic intervention for psychiatric disorders

  2014cites this paper
• Disassembly of Lys 11-and mixed-linkage polyubiquitin conjugates provide insights into function of proteasomal deubiquitinases Rpn 11 and Ubp

  2014cites this paper
• deubiquitinases Rpn11 and Ubp6 into function of proteasomal polyubiquitin conjugates provide insights Disassembly of Lys11- and mixed-linkage Protein Synthesis and Degradation:

  2014cites this paper
• V-type nerve agents phosphonylate ubiquitin at biologically relevant lysine residues and induce intramolecular cyclization by an isopeptide bond

  2014cites this paper
• Regulation of proteolysis by human deubiquitinating enzymes.

  2014cites this paper
• Nonenzymatic rubylation and ubiquitination of proteins for structural and functional studies.

  2014cites this paper
• UBE3B and ZRANB1 polymorphisms and transcript abundance are associated with water holding capacity of porcine M. longissimus dorsi.

  2013cites this paper
• The UBE2E proteins as conjugating dispersers: extending function with extended extensions.

  2013cites this paper
• Nonenzymatic assembly of branched polyubiquitin chains for structural and biochemical studies.

  2013cites this paper
• Mixed-linkage ubiquitin chains send mixed messages.

  2013cites this paper
• Unique structural, dynamical, and functional properties of k11-linked polyubiquitin chains.

  2013cites this paper
• Deubiquitylases from genes to organism.

  2013cites this paper
• Analyses of the effects of all ubiquitin point mutants on yeast growth rate.

  2013cites this paper
• Proteasome activation by the 19S regulatory particle: structural dynamics of 26S assembly and substrate recognition

  2013cites this paper
• Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

  2013cites this paper
• Assembly, Internalization, and Degradation Proteins and Mechanisms Regulating Gap-junction

  2013cites this paper
• Structural insights into proteasome activation by the 19S regulatory particle.

  2013cites this paper
• Proteins and mechanisms regulating gap-junction assembly, internalization, and degradation.

  2013cites this paper
• Stabilization of an unusual salt bridge in ubiquitin by the extra C-terminal domain of the proteasome-associated deubiquitinase UCH37 as a mechanism of its exo specificity.

  2013cites this paper
• Ubiquitination-Induced Fluorescence Complementation (UiFC) for Detection of K48 Ubiquitin Chains In Vitro and in Live Cells

  2013cites this paper
• Design principles of a universal protein degradation machine.

  2013cites this paper
• Structural and biochemical studies of the open state of Lys48-linked diubiquitin.

  2012cites this paper
• Cyclisation of Lys48‐linked diubiquitin in vitro and in vivo

  2012cites this paper
• Degradation of Endocytosed Gap Junctions by Autophagosomal and Endo-/lysosomal Pathways: A Perspective

  2012cites this paper
• This is to certify that the thesis/dissertation prepared

  2010cites this paper