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

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

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
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