Ubiquitin-binding domains: Mechanisms of ubiquitin recognition and use as tools to investigate ubiquitin-modified proteomes

PROTEOMICS ◽  
2014 ◽  
Vol 15 (5-6) ◽  
pp. 844-861 ◽  
Author(s):  
Daniel Scott ◽  
Neil J. Oldham ◽  
Jo Strachan ◽  
Mark S. Searle ◽  
Robert Layfield
Keyword(s):  
Binding Domains ◽  
Ubiquitin Binding

Probing Affinity and Ubiquitin Linkage Selectivity of Ubiquitin-Binding Domains Using Mass Spectrometry

2012 ◽  
Vol 134 (14) ◽  
pp. 6416-6424 ◽  
Author(s):  
Kleitos Sokratous ◽  
Lucy V. Roach ◽  
Debora Channing ◽  
Joanna Strachan ◽  
Jed Long ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Domains ◽  
Ubiquitin Binding

scholarly journals A novel polyubiquitin chain linkage formed by viral Ubiquitin prevents cleavage by deubiquitinating enzymes

2019 ◽  
Author(s):  
Hitendra Negi ◽  
Pothula Puroshotham Reddy ◽  
Chhaya Patole ◽  
Ranabir Das
Keyword(s):  
Biochemical Properties ◽  
Autographa Californica ◽  
Polyubiquitin Chain ◽  
Deubiquitinating Enzymes ◽  
Polyubiquitin Chains ◽  
Antiviral Responses ◽  
Binding Domains ◽  
Central Helix ◽  
Ubiquitin Binding ◽  
The Stability

ABSTRACTThe Baculoviridae family of viruses encode a viral Ubiquitin gene. Although the viral Ubiquitin is homologous to eukaryotic Ubiquitin (Ub), preservation of this gene in the viral genome indicates a unique function that is absent in the host eukaryotic Ub. We report the structural, biophysical, and biochemical properties of the viral Ubiquitin from Autographa Californica Multiple Nucleo-Polyhedrosis Virus (AcMNPV). The structure of viral Ubiquitin (vUb) differs from Ub in the packing of the central helix α1 to the beta-sheet of the β-grasp fold. Consequently, the stability of the fold is lower in vUb compared to Ub. However, the surface properties, ubiquitination activity, and the interaction with Ubiquitin binding domains are similar between vUb and Ub. Interestingly, vUb forms atypical polyubiquitin chain linked by lysine at the 54th position (K54). The K54-linked polyubiquitin chains are neither effectively cleaved by deubiquitinating enzymes, nor are they targeted by proteasomal degradation. We propose that modification of proteins with the viral Ubiquitin is a mechanism to counter the host antiviral responses.

scholarly journals Poly‐ubiquitin chains paradox: development of novel and selective poly‐ubiquitin binding domains (LB184)

2014 ◽  
Vol 28 (S1) ◽  
Author(s):  
Valerie Brubaker ◽  
Christian Loch ◽  
Kathryn Longenecker ◽  
James Strickler
Keyword(s):  
Binding Domains ◽  
Ubiquitin Binding

scholarly journals Ubiquitin Chains Bearing Genetically Encoded Photo-Cross-Linkers Enable Efficient Covalent Capture of (Poly)ubiquitin-Binding Domains

Biochemistry ◽  
2019 ◽  
Vol 58 (7) ◽  
pp. 883-886 ◽  
Author(s):  
Courtney N. Braxton ◽  
Evan Quartner ◽  
Westley Pawloski ◽  
David Fushman ◽  
T. Ashton Cropp
Keyword(s):  
Binding Domains ◽  
Ubiquitin Binding

scholarly journals CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1

Biomolecules ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 284 ◽  
Author(s):  
Ridvan Nepravishta ◽  
Federica Ferrentino ◽  
Walter Mandaliti ◽  
Anna Mattioni ◽  
Janine Weber ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Structural Model ◽  
Functional Characterization ◽  
Binding Domain ◽  
15N Nmr ◽  
Protein Sequence Analysis ◽  
Hydrophobic Patch ◽  
Binding Domains ◽  
Ubiquitin Binding ◽  
Ubiquitin Binding Domain

Ubiquitin binding domains (UBDs) are modular elements that bind non-covalently to ubiquitin and act as downstream effectors and amplifiers of the ubiquitination signal. With few exceptions, UBDs recognize the hydrophobic path centered on Ile44, including residues Leu8, Ile44, His68, and Val70. A variety of different orientations, which can be attributed to specific contacts between each UBD and surface residues surrounding the hydrophobic patch, specify how each class of UBD specifically contacts ubiquitin. Here, we describe the structural model of a novel ubiquitin-binding domain that we identified in NEDD4 binding protein 1 (N4BP1). By performing protein sequence analysis, mutagenesis, and nuclear magnetic resonance (NMR) spectroscopy of the 15N isotopically labeled protein, we demonstrate that a Phe-Pro motif in N4BP1 recognizes the canonical hydrophobic patch of ubiquitin. This recognition mode resembles the molecular mechanism evolved in the coupling of ubiquitin conjugation to endoplasmic-reticulum (ER) degradation (CUE) domain family, where an invariant proline, usually following a phenylalanine, is required for ubiquitin binding. Interestingly, this novel UBD, which is not evolutionary related to CUE domains, shares a 40% identity and 47% similarity with cullin binding domain associating with NEDD8 (CUBAN), a protein module that also recognizes the ubiquitin-like NEDD8. Based on these features, we dubbed the region spanning the C-terminal 50 residues of N4BP1 the CoCUN domain, for Cousin of CUBAN. By performing circular dichroism and 15N NMR chemical shift perturbation of N4BP1 in complex with ubiquitin, we demonstrate that the CoCUN domain lacks the NEDD8 binding properties observed in CUBAN. We also show that, in addition to mediating the interaction with ubiquitin and ubiquitinated substrates, both CUBAN and CoCUN are poly-ubiquitinated in cells. The structural and the functional characterization of this novel UBD can contribute to a deeper understanding of the molecular mechanisms governing N4BP1 function, providing at the same time a valuable tool for clarifying how the discrimination between ubiquitin and the highly related NEDD8 is achieved.

scholarly journals Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs)

2016 ◽  
Vol 15 (4) ◽  
pp. 1381-1396 ◽  
Author(s):  
Yuan Gao ◽  
Yanchang Li ◽  
Chengpu Zhang ◽  
Mingzhi Zhao ◽  
Chen Deng ◽  
...  
Keyword(s):  
Ubiquitinated Proteins ◽  
Binding Domains ◽  
Ubiquitin Binding

Epsins and Vps27p/Hrs contain ubiquitin-binding domains that function in receptor endocytosis

2002 ◽  
Vol 4 (5) ◽  
pp. 389-393 ◽  
Author(s):  
Susan C. Shih ◽  
David J. Katzmann ◽  
Joshua D. Schnell ◽  
Myra Sutanto ◽  
Scott D. Emr ◽  
...  
Keyword(s):  
Receptor Endocytosis ◽  
Binding Domains ◽  
Ubiquitin Binding

scholarly journals Ubiquitin-binding domains

2006 ◽  
Vol 399 (3) ◽  
pp. 361-372 ◽  
Author(s):  
James H. Hurley ◽  
Sangho Lee ◽  
Gali Prag
Keyword(s):  
Weak Interactions ◽  
Cell Cycle Control ◽  
Binding Activity ◽  
Covalent Modification ◽  
Binding Domains ◽  
Protein Ubiquitination ◽  
Wide Range ◽  
Ubiquitin Binding ◽  
Growth Factor Signalling ◽  
Ubiquitin Conjugating Enzyme

The covalent modification of proteins by ubiquitination is a major regulatory mechanism of protein degradation and quality control, endocytosis, vesicular trafficking, cell-cycle control, stress response, DNA repair, growth-factor signalling, transcription, gene silencing and other areas of biology. A class of specific ubiquitin-binding domains mediates most of the effects of protein ubiquitination. The known membership of this group has expanded rapidly and now includes at least sixteen domains: UBA, UIM, MIU, DUIM, CUE, GAT, NZF, A20 ZnF, UBP ZnF, UBZ, Ubc, UEV, UBM, GLUE, Jab1/MPN and PFU. The structures of many of the complexes with mono-ubiquitin have been determined, revealing interactions with multiple surfaces on ubiquitin. Inroads into understanding polyubiquitin specificity have been made for two UBA domains, whose structures have been characterized in complex with Lys48-linked di-ubiquitin. Several ubiquitin-binding domains, including the UIM, CUE and A20 ZnF (zinc finger) domains, promote auto-ubiquitination, which regulates the activity of proteins that contain them. At least one of these domains, the A20 ZnF, acts as a ubiquitin ligase by recruiting a ubiquitin–ubiquitin-conjugating enzyme thiolester adduct in a process that depends on the ubiquitin-binding activity of the A20 ZnF. The affinities of the mono-ubiquitin-binding interactions of these domains span a wide range, but are most commonly weak, with Kd>100 μM. The weak interactions between individual domains and mono-ubiquitin are leveraged into physiologically relevant high-affinity interactions via several mechanisms: ubiquitin polymerization, modification multiplicity, oligomerization of ubiquitinated proteins and binding domain proteins, tandem-binding domains, binding domains with multiple ubiquitin-binding sites and co-operativity between ubiquitin binding and binding through other domains to phospholipids and small G-proteins.

scholarly journals Two NEMO-like Ubiquitin-Binding Domains in CEP55 Differently Regulate Cytokinesis

iScience ◽  
2019 ◽  
Vol 20 ◽  
pp. 292-309 ◽  
Author(s):  
Keïs Nabhane Said Halidi ◽  
Elisabeth Fontan ◽  
Alix Boucharlat ◽  
Laurianne Davignon ◽  
Marine Charpentier ◽  
...  
Keyword(s):  
Binding Domains ◽  
Ubiquitin Binding
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