scholarly journals The ASCC2 CUE domain contacts adjacent ubiquitins to recognize K63-linked polyubiquitin

2021 ◽  
Author(s):  
Patrick M Lombardi ◽  
Sara Haile ◽  
Timur Rusanov ◽  
Rebecca Rodell ◽  
Rita Anoh ◽  
...  
Keyword(s):  
Terminal Portion ◽  
Binding Interaction ◽  
Polyubiquitin Chains ◽  
Alkylation Damage ◽  
Dna And Rna ◽  
Ubiquitin Binding ◽  
Damage Response ◽  
Ubiquitin Binding Domain ◽  
A Subunit ◽  
Cue Domain

Alkylation of DNA and RNA is a potentially toxic lesion that can result in mutations and cell death. In response to alkylation damage, K63-linked polyubiquitin chains are assembled that localize the ALKBH3-ASCC repair complex to damage sites in the nucleus. The protein ASCC2, a subunit of the ASCC complex, selectively binds K63-linked polyubiquitin chains using its CUE domain, a type of ubiquitin-binding domain that typically binds monoubiquitin and does not discriminate among different polyubiquitin linkage types. We report here that the ASCC2 CUE domain selectively binds K63-linked diubiquitin by contacting both the distal and proximal ubiquitin. Whereas the ASCC2 CUE domain binds the distal ubiquitin in a manner similar to that reported for other CUE domains bound to a single ubiquitin, the contacts with the proximal ubiquitin are unique to ASCC2. The N-terminal portion of the ASCC2 α1 helix, including residues E467 and S470, contributes to the binding interaction with the proximal ubiquitin of K63-linked diubiquitin. Mutation of residues within the N-terminal portion of the ASCC2 α1 helix decreases ASCC2 recruitment in response to DNA alkylation, supporting the functional significance of these interactions during the alkylation damage response.

scholarly journals Regulation of the Fanconi anemia pathway by a CUE ubiquitin-binding domain in the FANCD2 protein

Blood ◽  
2012 ◽  
Vol 120 (10) ◽  
pp. 2109-2117 ◽  
Author(s):  
Meghan A. Rego ◽  
Frederick W. Kolling ◽  
Elizabeth A. Vuono ◽  
Maurizio Mauro ◽  
Niall G. Howlett
Keyword(s):  
Fanconi Anemia ◽  
Noncovalent Interaction ◽  
Binding Domain ◽  
Covalent Attachment ◽  
Pathway Activation ◽  
Ubiquitin Binding ◽  
Ubiquitin Binding Domain ◽  
Ubiquitin Conjugation ◽  
Cue Domain

Abstract The Fanconi anemia (FA)–BRCA pathway is critical for the repair of DNA interstrand crosslinks (ICLs) and the maintenance of chromosome stability. A key step in FA-BRCA pathway activation is the covalent attachment of monoubiquitin to FANCD2 and FANCI. Monoubiquitinated FANCD2 and FANCI localize in chromatin-associated nuclear foci where they interact with several well-characterized DNA repair proteins. Importantly, very little is known about the structure, function, and regulation of FANCD2. Herein, we describe the identification and characterization of a CUE (coupling of ubiquitin conjugation to endoplasmic reticulum degradation) ubiquitin-binding domain (UBD) in FANCD2, and demonstrate that the CUE domain mediates noncovalent binding to ubiquitin in vitro. We show that although mutation of the CUE domain destabilizes FANCD2, the protein remains competent for DNA damage-inducible monoubiquitination and phosphorylation. Importantly, we demonstrate that the CUE domain is required for interaction with FANCI, retention of monoubiquitinated FANCD2, and FANCI in chromatin, and for efficient ICL repair. Our results suggest a model by which heterodimerization of monoubiquitinated FANCD2 and FANCI in chromatin is mediated in part through a noncovalent interaction between the FANCD2 CUE domain and monoubiquitin covalently attached to FANCI, and that this interaction shields monoubiquitinated FANCD2 from polyubiquitination and proteasomal degradation.

scholarly journals A Ubiquitin-Binding Domain that Does Not Bind Ubiquitin

2018 ◽  
Author(s):  
Michael Lim ◽  
Joseph A. Newman ◽  
Hannah L. Williams ◽  
Hazel Aitkenhead ◽  
Opher Gileadi ◽  
...  
Keyword(s):  
Structural Model ◽  
Coiled Coil ◽  
Biological Processes ◽  
Hydrophobic Residues ◽  
X Ray ◽  
X Ray Crystallography ◽  
Binding Domains ◽  
Ubiquitin Binding ◽  
Ubiquitin Binding Domain ◽  
Cue Domain

Ubiquitylation, the post-translational linkage of ubiquitin moieties to lysines in target proteins, helps regulate a myriad of biological processes. Ubiquitin, and sometimes ubiquitin-homology domains, are recognized by ubiquitin-binding domains, including CUE domains. CUE domains are thus generally thought to function exclusively by mediating interactions with ubiquitylated proteins. The chromatin remodeler, SMARCAD1, interacts with KAP1, a transcriptional corepressor. We show that the SMARCAD1-KAP1 interaction is direct and involves the first SMARCAD1 CUE domain (CUE1) and the RBCC domain of KAP1. A structural model of the minimal KAP1 RBCC-SMARCAD1 CUE1 complex based on X-ray crystallography analysis is presented. Remarkably, the CUE1 domain, which resembles a canonical CUE domain, recognizes 2 clusters of exposed hydrophobic residues on KAP1, but these are presented in the context of a coiled-coil domain, not in a structure resembling ubiquitin. Together, these data challenge the well-established dogma that CUE domains exclusively recognize the ubiquitin-fold.

scholarly journals Discovery of small molecule antagonists of the USP5 zinc finger ubiquitin-binding domain

2019 ◽  
Author(s):  
Mandeep K. Mann ◽  
Ivan Franzoni ◽  
Renato Ferreira de Freitas ◽  
Wolfram Tempel ◽  
Scott Houliston ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Allosteric Modulation ◽  
Binding Domain ◽  
Signalling Pathways ◽  
Chemical Library ◽  
Polyubiquitin Chains ◽  
Structure Activity ◽  
Ubiquitin Binding ◽  
Ubiquitin Binding Domain ◽  
Health And Disease

AbstractUSP5 disassembles unanchored polyubiquitin chains to recycle free mono-ubiquitin, and is one of twelve ubiquitin-specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signalling pathways in health and disease.

A ubiquitin-binding CUE domain in presenilin-1 enables interaction with K63-linked polyubiquitin chains

FEBS Letters ◽  
2015 ◽  
Vol 589 (9) ◽  
pp. 1001-1008 ◽  
Author(s):  
Stephen P. Duggan ◽  
Run Yan ◽  
Justin V. McCarthy
Keyword(s):  
Presenilin 1 ◽  
Polyubiquitin Chains ◽  
Ubiquitin Binding ◽  
Cue Domain

scholarly journals Slx4 Regulates DNA Damage Checkpoint-dependent Phosphorylation of the BRCT Domain Protein Rtt107/Esc4

2006 ◽  
Vol 17 (1) ◽  
pp. 539-548 ◽  
Author(s):  
Tania M. Roberts ◽  
Michael S. Kobor ◽  
Suzanne A. Bastin-Shanower ◽  
Miki Ii ◽  
Sonja A. Horte ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Dna Damage Checkpoint ◽  
Checkpoint Activation ◽  
Alkylation Damage ◽  
Binding Partner ◽  
Replication Restart ◽  
Damage Response ◽  
Domain Protein

RTT107 (ESC4, YHR154W) encodes a BRCA1 C-terminal-domain protein that is important for recovery from DNA damage during S phase. Rtt107 is a substrate of the checkpoint protein kinase Mec1, although the mechanism by which Rtt107 is targeted by Mec1 after checkpoint activation is currently unclear. Slx4, a component of the Slx1-Slx4 structure-specific nuclease, formed a complex with Rtt107. Deletion of SLX4 conferred many of the same DNA-repair defects observed in rtt107Δ, including DNA damage sensitivity, prolonged DNA damage checkpoint activation, and increased spontaneous DNA damage. These phenotypes were not shared by the Slx4 binding partner Slx1, suggesting that the functions of the Slx4 and Slx1 proteins in the DNA damage response were not identical. Of particular interest, Slx4, but not Slx1, was required for phosphorylation of Rtt107 by Mec1 in vivo, indicating that Slx4 was a mediator of DNA damage-dependent phosphorylation of the checkpoint effector Rtt107. We propose that Slx4 has roles in the DNA damage response that are distinct from the function of Slx1-Slx4 in maintaining rDNA structure and that Slx4-dependent phosphorylation of Rtt107 by Mec1 is critical for replication restart after alkylation damage.

Alkylation damage in DNA and RNA—repair mechanisms and medical significance

DNA Repair ◽  
2004 ◽  
Vol 3 (11) ◽  
pp. 1389-1407 ◽  
Author(s):  
Finn Drabløs ◽  
Emadoldin Feyzi ◽  
Per Arne Aas ◽  
Cathrine B. Vaagbø ◽  
Bodil Kavli ◽  
...  
Keyword(s):  
Rna Repair ◽  
Alkylation Damage ◽  
Dna And Rna ◽  
Repair Mechanisms

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 Cks1 Activates Transcription by Binding to the Ubiquitylated Proteasome

2010 ◽  
Vol 30 (15) ◽  
pp. 3894-3901 ◽  
Author(s):  
Roman Holic ◽  
Alexander Kukalev ◽  
Sophie Lane ◽  
Edward J. Andress ◽  
Ivy Lau ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcriptional Activation ◽  
Protein Complexes ◽  
Cyclin Dependent Kinase ◽  
Transcription Activator ◽  
Large Protein ◽  
Ubiquitin Binding ◽  
Ubiquitin Binding Domain ◽  
Proteasome Subunits

ABSTRACT Cyclin-dependent kinase-associated protein 1 (Cks1) is involved in the control of the transcription of a subset of genes in addition to its role in controlling the cell cycle in the budding yeast Saccharomyces cerevisiae. By directly ligating Cks1 onto a GAL1 promoter-driven reporter, we demonstrated that Cks1 acts as a transcription activator. Using this method, we dissected the downstream events from Cks1 recruitment at the promoter. We showed that subsequent to promoter binding, Cdc28 binding is required to modulate the level of gene expression. The ubiquitin-binding domain of Cks1 is essential for implementing downstream transcription events, which appears to recruit the proteasome via ubiquitylated proteasome subunits. We propose that the selective ability of Cks1 to bind ubiquitin allows this small molecule the flexibility to bind large protein complexes with specificity and that this may represent a novel mechanism of regulating transcriptional activation.

scholarly journals Function of the p97–Ufd1–Npl4 complex in retrotranslocation from the ER to the cytosol

2003 ◽  
Vol 162 (1) ◽  
pp. 71-84 ◽  
Author(s):  
Yihong Ye ◽  
Hemmo H. Meyer ◽  
Tom A. Rapoport
Keyword(s):  
Atp Hydrolysis ◽  
Bound State ◽  
Polyubiquitin Chain ◽  
Polyubiquitin Chains ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Complex Functions ◽  
Ubiquitin Binding ◽  
Subsequent Degradation ◽  
Er Membrane

Amember of the family of ATPases associated with diverse cellular activities, called p97 in mammals and Cdc48 in yeast, associates with the cofactor Ufd1–Npl4 to move polyubiquitinated polypeptides from the endoplasmic reticulum (ER) membrane into the cytosol for their subsequent degradation by the proteasome. Here, we have studied the mechanism by which the p97–Ufd1–Npl4 complex functions in this retrotranslocation pathway. Substrate binding occurs when the first ATPase domain of p97 (D1 domain) is in its nucleotide-bound state, an interaction that also requires an association of p97 with the membrane through its NH2-terminal domain. The two ATPase domains (D1 and D2) of p97 appear to alternate in ATP hydrolysis, which is essential for the movement of polypeptides from the ER membrane into the cytosol. The ATPase itself can interact with nonmodified polypeptide substrates as they emerge from the ER membrane. Polyubiquitin chains linked by lysine 48 are recognized in a synergistic manner by both p97 and an evolutionarily conserved ubiquitin-binding site at the NH2 terminus of Ufd1. We propose a dual recognition model in which the ATPase complex binds both a nonmodified segment of the substrate and the attached polyubiquitin chain; polyubiquitin binding may activate the ATPase p97 to pull the polypeptide substrate out of the membrane.

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