Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniPathway vocabulary mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Gene Ontology annotation based on curation of immunofluorescence data
Manual transfer of experimentally-verified manual GO annotation data to homologous complexes by curator judgment of sequence, composition and function similarity
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo.
DDB accumulates at DNA damage sites immediately after UV irradiation and directly stimulates nucleotide excision repair.
The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage.
In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimers by the DDB2 gene product.
Human DDB2 splicing variants are dominant negative inhibitors of UV-damaged DNA repair.
The DDB1-CUL4ADDB2 ubiquitin ligase is deficient in xeroderma pigmentosum group E and targets histone H2A at UV-damaged DNA sites.
A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1.
CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation.
HIV-1 Vpr function is mediated by interaction with the damage-specific DNA-binding protein DDB1.
The cullin 4B-based UV-damaged DNA-binding protein ligase binds to UV-damaged chromatin and ubiquitinates histone H2A.
Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex.
A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery.
Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics.
Regulation of nucleotide excision repair by UV-DDB: prioritization of damage recognition to internucleosomal DNA.
The molecular basis of CRL4DDB2/CSA ubiquitin ligase architecture, targeting, and activation.
Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair.
Monoubiquitinated histone H2A destabilizes photolesion-containing nucleosomes with concomitant release of UV-damaged DNA-binding protein E3 ligase.
A human interactome in three quantitative dimensions organized by stoichiometries and abundances.
Architecture of the human interactome defines protein communities and disease networks.
Inflammation-dependent overexpression of c-Myc enhances CRL4(DCAF4) E3 ligase activity and promotes ubiquitination of ST7 in colitis-associated cancer.
The deacetylase SIRT6 promotes the repair of UV-induced DNA damage by targeting DDB2.
Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
USP44 Stabilizes DDB2 to Facilitate Nucleotide Excision Repair and Prevent Tumors.
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DDB2 directly binds CPDs, undergoes ubiquitination/proteasomal degradation, and must remain on damaged chromatin to recruit and hand off lesions to XPC; USP44 deubiquitinates DDB2 to prevent premature degradation.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
OpenCell: Endogenous tagging for the cartography of human cellular organization.
Multimodal cell maps as a foundation for structural and functional genomics.
Characterization of a human DNA damage binding protein implicated in xeroderma pigmentosum E.
Mutations specific to the xeroderma pigmentosum group E Ddb- phenotype.
DDB, a putative DNA repair protein, can function as a transcriptional partner of E2F1.
Falcon deep research report for human DDB2
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DDB2 has an N-terminal helix-loop-helix that associates with DDB1 and a seven-bladed WD40 beta-propeller that mediates DNA binding.
"Structural work defines an N-terminal **helix–loop–helix (HLH)** used for DDB1 association and a **7-bladed WD40 β-propeller** that mediates DNA binding, matching the WD-repeat family/domain expectations given in the prompt."
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The DDB2 propeller contacts ~7 bp around the lesion and bends the DNA by ~40 degrees with local strand separation; the DDB1-DDB2 interface is large (~3900 square angstroms).
"DDB2 contacts ~7 bp around the lesion and induces an approximately **40° DNA kink** with local strand separation. The DDB1–DDB2 interface is large (reported ~**3900 Ų**), consistent with stable heterodimerization."
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Polyubiquitination abrogates DDB2 damaged-DNA binding and promotes proteasomal degradation after UV, whereas unmodified DDB2 binds UV-damaged DNA.
"while unmodified DDB2 binds UV-damaged DNA, **poly-ubiquitinated DDB2** is recovered predominantly unbound and **poly-ubiquitination abrogates damaged-DNA binding**, promoting proteasomal degradation after UV exposure."
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XPC competitively suppresses DDB2 ubiquitination (enhanced by centrin-2), stabilizing DDB2 so it can initiate multiple rounds of repair.
"XPC competitively suppresses DDB2 ubiquitination in vitro, and this protection is enhanced by **centrin-2**, supporting a model in which XPC enables DDB2 to initiate multiple rounds of repair by limiting DDB2 degradation."
Formation of the pre-incision complex in GG-NER
Recruitment of XPA and release of CAK
DNA polymerases delta, epsilon or kappa bind the GG-NER site
3'-incision of DNA by ERCC5 (XPG) in GG-NER
5'- incision of DNA by ERCC1:ERCC4 in GG-NER
Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in GG-NER
ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA
TFIIH binds GG-NER site to form a verification complex
XPC:RAD23:CETN2 and UV-DDB bind distorted dsDNA site
PARP1 or PARP2 PARylates DDB2 and autoPARylates
PARP1 or PARP2 binds DDB2 at GG-NER site
CHD1L is recruited to GG-NER site
USP24 deubiquitinates DDB2
RNF111 ubiquitinates SUMOylated XPC
TP53 stimulates DDB2 expression
AcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex
NEDD8:AcM-UBE2M binds CRL4 E3 ubiquitin ligase complex
CAND1 binds CRL4 E3 ubiquitin ligase in the nucleus
COMMDs displace CAND1 from CRL4 E3 ubiquitin ligase complex
COP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex