Search results for DDB1

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Pathway (7 results from a total of 7)

Identifier: R-HSA-8866654
Species: Homo sapiens
E3 ubiquitin ligases catalyze the transfer of an ubiquitin from an E2-ubiquitin conjugate to a target protein. Generally, ubiquitin is transferred via formation of an amide bond to a particular lysine residue of the target protein, but ubiquitylation of cysteine, serine and threonine residues in a few targeted proteins has also been demonstrated (reviewed in McDowell and Philpott 2013, Berndsen and Wolberger 2014). Based on protein homologies, families of E3 ubiquitin ligases have been identified that include RING-type ligases (reviewed in Deshaies et al. 2009, Metzger et al. 2012, Metzger et al. 2014), HECT-type ligases (reviewed in Rotin et al. 2009, Metzger et al. 2012), and RBR-type ligases (reviewed in Dove et al. 2016). A subset of the RING-type ligases participate in CULLIN-RING ligase complexes (CRLs which include SCF complexes, reviewed in Lee and Zhou 2007, Genschik et al. 2013, Skaar et al. 2013, Lee et al. 2014).
Some E3-E2 combinations catalyze mono-ubiquitination of the target protein (reviewed in Nakagawa and Nakayama 2015). Other E3-E2 combinations catalyze conjugation of further ubiquitin monomers to the initial ubiquitin, forming polyubiquitin chains. (It may also be possible for some E3-E2 combinations to preassemble polyubiquitin and transfer it as a unit to the target protein.) Ubiquitin contains several lysine (K) residues and a free alpha amino group to which further ubiquitin can be conjugated. Thus different types of polyubiquitin are possible: K11 linked polyubiquitin is observed in endoplasmic reticulum-associated degradation (ERAD), K29 linked polyubiquitin is observed in lysosomal degradation, K48 linked polyubiquitin directs target proteins to the proteasome for degradation, whereas K63 linked polyubiquitin generally acts as a scaffold to recruit other proteins in several cellular processes, notably DNA repair (reviewed in Komander et al. 2009).
Identifier: R-HSA-8852135
Species: Homo sapiens
Ubiquitin is a small, 76 amino acid residue protein that is conjugated by E3 ubiquitin ligases to other proteins in order to regulate their function or degradation (enzymatic cascade reviewed in Neutzner and Neutzner 2012, Kleiger and Mayor 2014, structures and mechanisms of conjugating enzymes reviewed in Lorenz et al. 2013). Ubiquitination of target proteins usually occurs between the C-terminal glycine residue of ubiquitin and a lysine residue of the target, although linkages with cysteine, serine, and threonine residues are also observed (reviewed in Wang et al. 2012, McDowell and Philpott 2013).
Ubiquitin must first be processed from larger precursors and then activated by formation of a thiol ester bond between ubiquitin and an E1 activating enzyme (UBA1 or UBA6) and transfer to an E2 conjugating enzyme before being transferred by an E3 ligase to a target protein. Precursor proteins containing multiple ubiquitin monomers (polyubiquitins) are produced from the UBB and UBC genes; precursors containing a single ubiquitin monomer and a ribosomal protein are produced from the UBA52 and RPS27A genes. Many proteases (deubiquitinases) may potentially process these precursors yielding monomeric ubiquitin. The proteases OTULIN and USP5 are particularly active in cleaving the polyubiquitin precursors, whereas the proteases UCHL3, USP7, and USP9X cleave the ubiquitin-ribosomal protein precursors yielding ubiquitin monomers (Grou et al. 2015). A resultant ubiquitin monomer is activated by adenylation of the C-terminal glycine followed by conjugation of the C-terminus to a cysteine residue of the E1 enzymes UBA1 or UBA6 via a thiol ester bond. The ubiquitin is then transferred from the E1 enzyme to a cysteine residue of one of several E2 enzymes (reviewed in van Wijk and Timmers 2010, Stewart et al. 2016). Through a less well characterized mechanism, E3 ubiquitin ligases then bring a target protein and the E2-ubiquitin conjugate into proximity so that the ubiquitin is transferred via formation of an amide bond to a particular lysine residue (or, in rarer cases, a thiol ester bond to a cysteine residue or an ester bond to a serine or threonine residue) of the target protein (reviewed in Berndsen and Wolberger 2014). Based on protein homologies, families of E3 ubiquitin ligases have been identified that include RING-type ligases (reviewed in Deshaies et al. 2009, Metzger et al. 2012, Metzger et al. 2014), HECT-type ligases (reviewed in Rotin et al. 2009, Metzger et al. 2012), and RBR-type ligases (reviewed in Dove et al. 2016). A subset of the RING-type ligases participate in CULLIN-RING ligase complexes (CRLs which include SCF complexes, reviewed in Lee and Zhou 2007, Genschik et al. 2013, Skaar et al. 2013, Lee et al. 2014).
Some E3-E2 combinations catalyze mono-ubiquitination of the target protein (reviewed in Nakagawa and Nakayama 2015). Other E3-E2 combinations catalyze conjugation of further ubiquitin monomers to the initial ubiquitin, forming polyubiquitin chains. (It may also be possible for some E3-E2 combinations to preassemble polyubiquitin and transfer it as a unit to the target protein.) Ubiquitin contains several lysine (K) residues and a free alpha amino group to which further ubiquitin can be conjugated. Thus different types of polyubiquitin are possible: K11 linked polyubiquitin is observed in endoplasmic reticulum-associated degradation (ERAD), K29 linked polyubiquitin is observed in lysosomal degradation, K48 linked polyubiquitin directs target proteins to the proteasome for degradation, whereas K63 linked polyubiquitin generally acts as a scaffold to recruit other proteins in several cellular processes, notably DNA repair (reviewed in Komander et al. 2009). Ubiquitination is highly regulated (reviewed in Vittal et al. 2015) and affects all cellular processes including DNA damage response (reviewed in Brown and Jackson 2015), immune signaling (reviewed in Park et al. 2014, Lutz-Nicoladoni et al. 2015), and regulation of normal and cancerous cell growth (reviewed in Skaar and Pagano 2009, Yerlikaya and Yontem 2013, Strikoudis et al. 2014).
Identifier: R-HSA-5696394
Species: Homo sapiens
Compartment: nucleoplasm
In global genome nucleotide excision repair (GG-NER), the DNA damage is recognized by two protein complexes. The first complex consists of XPC, RAD23A or RAD23B, and CETN2. This complex probes the DNA helix and recognizes damage that disrupts normal Watson-Crick base pairing, which results in binding of the XPC:RAD23:CETN2 complex to the undamaged DNA strand. The second complex is a ubiquitin ligase UV-DDB that consists of DDB2, DDB1, CUL4A or CUL4B and RBX1. The UV-DDB complex is necessary for the recognition of UV-induced DNA damage and may contribute to the retention of the XPC:RAD23:CETN2 complex at the DNA damage site. The UV-DDB complex binds the damaged DNA strand (Fitch et al. 2003, Wang et al. 2004, Moser et al. 2005, Camenisch et al. 2009, Oh et al. 2011).
Identifier: R-HSA-5696399
Species: Homo sapiens
Compartment: nucleoplasm
The DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex, is an ubiquitin ligase composed of DDB1, CUL4A or CUL4B, RBX1 and a GG-NER specific protein DDB2. In vitro, the UV-DDB complex is onlynecessary for GG-NER mediated repair of UV-induced pyrimidine dimers. In vivo, however, where DNA repair occurs in the chromatin context, the UV-DDB complex likely facilitates GG-NER mediated repair irrespective of the DNA damage type.
After DNA damage recognition, the TFIIH complex, together with XPA, verifies the DNA damage and unwinds the DNA helix around the damage, creating an open bubble. Two DNA endonucleases, ERCC5 (XPG) and the complex of ERCC1 and ERCC4 (XPF), excise the oligonucleotide that contains damaged base(s) from the affected DNA strand. DNA polymerases delta, epsilon and/or kappa perform DNA repair synthesis, followed by DNA ligation, thus completing GG-NER.
For a recent review, please refer to Marteijn et al. 2014.
Identifier: R-HSA-6781823
Species: Homo sapiens
Compartment: nucleoplasm
Formation of TC-NER pre-incision complex is initiated when the RNA polymerase II (RNA Pol II) complex stalls at a DNA damage site. The stalling is caused by misincorporation of a ribonucleotide opposite to a damaged base (Brueckner et al. 2007). Cockayne syndrome protein B (ERCC6, CSB) binds stalled RNA Pol II and recruits Cockayne syndrome protein A (ERCC8, CSA). ERCC8 is part of an ubiquitin ligase complex that also contains DDB1, CUL4A or CUL4B and RBX1. This complex is implicated in the regulation of TC-NER progression probably by ubiquitinating one or more factors involved in this pathway, which may include RNA Pol II and ERCC6 at the later stages of repair (Bregman et al. 1996, Fousteri et al. 2006, Groisman et al. 2006). XPA is recruited to the TC-NER site through its interaction with the TFIIH complex (Furuta et al. 2002, Ziani et al. 2014). The XAB2 complex, which probably regulates the accessibility of the DNA damage site through its RNA-DNA helicase activity, binds the TC-NER site via the interaction of its XAB2 subunit with RNA Pol II, ERCC6, ERCC8 and XPA (Nakatsu et al. 2000, Sollier et al. 2014). TCEA1 (TFIIS) is a transcription elongation factor that may facilitate backtracking of the stalled RNA Pol II, enabling access of repair proteins to the DNA damage site and promotes partial digestion of the 3' protruding end of the nascent mRNA transcript by the backtracked RNA Pol II, allowing resumption of RNA synthesis after damage removal (Donahue et al. 1994). Access to DNA damage sites in TC-NER was suggested to be facilitated by a chromatin remodeler HMGN1 (Birger et al. 2003), but another sudy found that HMGN1 was not needed for human TC-NER (Apelt et al. 2020). UVSSA protein interacts with ubiquitinated ERCC6 and RNA Pol II, recruiting ubiquitin protease USP7 to the TC-NER site and promoting ERCC6 stabilization (Nakazawa et al. 2012, Schwertman et al. 2012, Zhang et al. 2012, Fei and Chen 2012).
Identifier: R-HSA-5696398
Species: Homo sapiens
Compartment: nucleoplasm
Nucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recovery of DNA synthesis and cell survival. Deficient NER processes have been identified from the cells of cancer-prone patients with different variants of xeroderma pigmentosum (XP), trichothiodystrophy (TTD), and Cockayne's syndrome. The XP cells exhibit an ultraviolet radiation hypersensitivity that leads to a hypermutability response to UV, offering a direct connection between deficient NER, increased mutation rate, and cancer. While the NER pathway in prokaryotes is unique, the pathway utilized in yeast and higher eukaryotes is highly conserved.
NER is involved in the repair of bulky adducts in DNA, such as UV-induced photo lesions (both 6-4 photoproducts (6-4 PPDs) and cyclobutane pyrimidine dimers (CPDs)), as well as chemical adducts formed from exposure to aflatoxin, benzopyrene and other genotoxic agents. Specific proteins have been identified that participate in base damage recognition, cleavage of the damaged strand on both sides of the lesion, and excision of the oligonucleotide bearing the lesion. Reparative DNA synthesis and ligation restore the strand to its original state.
NER consists of two related pathways called global genome nucleotide excision repair (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER). The pathways differ in the way in which DNA damage is initially recognized, but the majority of the participating molecules are shared between these two branches of NER. GG-NER is transcription-independent, removing lesions from non-coding DNA strands, as well as coding DNA strands that are not being actively transcribed. TC-NER repairs damage in transcribed strands of active genes.
Several of the proteins involved in NER are key components of the basal transcription complex TFIIH. An ubiquitin ligase complex composed of DDB1, CUL4A or CUL4B and RBX1 participates in both GG-NER and TC-NER, implying an important role of ubiquitination in NER regulation. The establishment of mutant mouse models for NER genes and other DNA repair-related genes has been useful in demonstrating the associations between NER defects and cancer.
For past and recent reviews of nucleotide excision repair, please refer to Lindahl and Wood 1998, Friedberg et al. 2002, Christmann et al. 2003, Hanawalt and Spivak 2008, Marteijn et al. 2014).
Identifier: R-HSA-6781827
Species: Homo sapiens
Compartment: nucleoplasm
DNA damage in transcribed strands of active genes is repaired through a specialized nucleotide excision repair (NER) pathway known as transcription-coupled nucleotide excision repair (TC-NER). TC-NER impairment is the underlying cause of a severe hereditary disorder Cockayne syndrome, an autosomal recessive disease characterized by hypersensitivity to UV light.
TC-NER is triggered by helix distorting lesions that block the progression of elongating RNA polymerase II (RNA Pol II). Stalled RNA Pol II complex triggers the recruitment of ERCC6. ERCC6, commonly known as CSB (Cockayne syndrome protein B) recruits ERCC8, commonly known as CSA (Cockayne syndrome protein A). ERCC8 has 7 WD repeat motifs and is part of the ubiquitin ligase complex that also includes DDB1, CUL4A or CUL4B and RBX1. The ERCC8 ubiquitin ligase complex is one of the key regulators of TC-NER that probably exerts its role by ubiquitinating one or more factors involved in this repair process, including the RNA Pol II complex and ERCC6.
In addition to RNA Pol II, ERCC6 and the ERCC8 complex, the transcription elongation factor TFIIH, which is also involved in global genome nucleotide excision repair (GG-NER), is recruited to sites of TC-NER. The TC-NER pre-incision complex also includes XPA, XAB2 complex, TCEA1 (TFIIS), HMGN1, UVSSA in complex with USP7, and EP300 (p300). XPA probably contributes to the assembly and stability of the pre-incision complex, similar to its role in GG-NER. The XAB2 complex is involved in pre-mRNA splicing and may modulate the structure of the nascent mRNA hybrid with template DNA through its RNA-DNA helicase activity, allowing proper processing of DNA damage. TCEA1 may be involved in RNA Pol II backtracking, which allows repair proteins to gain access to the damage site. It also facilitates trimming of the 3' end of protruding nascent mRNA from the stalled RNA Pol II, enabling recovery of RNA synthesis after repair.

Deubiquitinating activity of the UVSSA:USP7 complex is needed for ERCC6 stability at repair sites. Non-histone nucleosomal binding protein HMGN1 and histone acetyltransferase p300 (EP300) remodel the chromatin around the damaged site, thus facilitating repair.

Dual incision of the lesion-containing oligonucleotide from the affected DNA strand is performed by two DNA endonucleases, the ERCC1:ERCC4 (ERCC1:XPF) complex and ERCC5 (XPG), which also participate in GG-NER. DNA polymerases delta, epsilon or kappa fill in the single stranded gap after dual incision and the remaining single strand nick is sealed by DNA ligases LIG1 or LIG3 (the latter in complex with XRCC1), similar to GG-NER. After the repair of DNA damage is complete, RNA Pol II resumes RNA synthesis.
For past and recent reviews, see Mellon et al. 1987, Svejstrup 2002, Hanawalt and Spivak 2008, Vermeulen and Fousteri 2013 and Marteijn et al. 2014.

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