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    DDB1A damaged DNA binding protein 1A [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 825890, updated on 18-Sep-2024

    Summary

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    Official Symbol
    DDB1A
    Official Full Name
    damaged DNA binding protein 1A
    Primary source
    TAIR:AT4G05420
    Locus tag
    AT4G05420
    See related
    Araport:AT4G05420
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    C6L9.100; C6L9_100; damaged DNA binding protein 1A
    Summary
    Structurally similar to damaged DNA binding proteins. DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis. DDB1a is shown to be RUB-modified.
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    Genomic context

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    See DDB1A in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    19
    Sequence:
    Chromosome: 4; NC_003075.7 (2746114..2753014)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene copper ion binding protein Neighboring gene ncRNA Neighboring gene Transducin/WD40 repeat-like superfamily protein Neighboring gene Carbohydrate-binding X8 domain superfamily protein Neighboring gene temperature sensing protein-like protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. RNAi silencing of the Arabidopsis thaliana ULCS1 gene results in pleiotropic phenotypes during plant growth and development. Beris D, et al. Int J Dev Biol, 2022. PMID 34549791
    2. Arabidopsis DDB1a and DDB1b are critical for embryo development. Bernhardt A, et al. Planta, 2010 Aug. PMID 20499085
    3. RNAi-mediated silencing of the Arabidopsis thaliana ULCS1 gene, encoding a WDR protein, results in cell wall modification impairment and plant infertility. Beris D, et al. Plant Sci, 2016 Apr. PMID 26940493
    4. The Arabidopsis DDB1 interacting protein WDR55 is required for vegetative development. Bjerkan KN, et al. Plant Signal Behav, 2013 Sep. PMID 23803743, Free PMC Article
    5. DWD HYPERSENSITIVE TO UV-B 1 is negatively involved in UV-B mediated cellular responses in Arabidopsis. Kim SH, et al. Plant Mol Biol, 2014 Dec. PMID 25193399

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ABD1 interacts with DDB1 in vitro and in vivo, indicating that it likely functions as a CUL4 E3 ligase substrate receptor.
      Title: ABD1 is an Arabidopsis DCAF substrate receptor for CUL4-DDB1-based E3 ligases that acts as a negative regulator of abscisic acid signaling.
    2. that a DDB1(WDR55) complex could regulate embryo and endosperm development.
      Title: The Arabidopsis DDB1 interacting protein WDR55 is required for vegetative development.
    3. UVH6, DDB1A, and DDB2 all contribute to UV tolerance, heat tolerance and floral patterning.
      Title: Interactions between Arabidopsis DNA repair genes UVH6, DDB1A, and DDB2 during abiotic stress tolerance and floral development.
    4. DDB1A and DDB1B contribute to DET1 regulation of adult plant growth.
      Title: Genetic interactions of Arabidopsis thaliana damaged DNA binding protein 1B (DDB1B) with DDB1A, DET1, and COP1.
    5. DDB1a is an novel RUB-modified protein.
      Title: Recovery of DDB1a (damaged DNA binding protein1a) in a screen to identify novel RUB-modified proteins in Arabidopsis thaliana.
    6. WDR55-DDB1 complex is involved in the establishment of bilateral symmetry in the Arabidopsis embryo.
      Title: Arabidopsis WD repeat domain55 Interacts with DNA damaged binding protein1 and is required for apical patterning in the embryo.
    7. CUL4-DDB1 complex interacts with MSI1 and is required to maintain MEDEA parental imprinting.
      Title: The Arabidopsis CUL4-DDB1 complex interacts with MSI1 and is required to maintain MEDEA parental imprinting.
    8. data suggest that the plant CUL4-DDB1A(CSAat1A and B) complex represents a unique mechanism to promote ubiquitination of substrates in response to DNA damage
      Title: Arabidopsis cockayne syndrome A-like proteins 1A and 1B form a complex with CULLIN4 and damage DNA binding protein 1A and regulate the response to UV irradiation.
    9. demonstrated that DDB1a, like DDB1b, is critical for embryo development, and that both proteins have distinct functions in whole plant development
      Title: Arabidopsis DDB1a and DDB1b are critical for embryo development.
    10. CUL4-DDB1 and COP1-SPA complexes act together to regulate photomorphogenesis.
      Title: Arabidopsis CULLIN4-damaged DNA binding protein 1 interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA complexes to regulate photomorphogenesis and flowering time.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_001125468.1
    NM_116781.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of photomorphogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Cul4-RING E3 ubiquitin ligase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol HDA PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    damaged DNA binding protein 1A
    NP_001118940.1
    • damaged DNA binding protein 1A (DDB1A); FUNCTIONS IN: protein binding, DNA binding; INVOLVED IN: negative regulation of transcription, negative regulation of photomorphogenesis; LOCATED IN: nucleus, CUL4 RING ubiquitin ligase complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), Cleavage/polyadenylation specificity factor, A subunit, C-terminal (InterPro:IPR004871); BEST Arabidopsis thaliana protein match is: damaged DNA binding protein 1B (TAIR:AT4G21100.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
    NP_192451.1
    • damaged DNA binding protein 1A (DDB1A); FUNCTIONS IN: protein binding, DNA binding; INVOLVED IN: negative regulation of transcription, negative regulation of photomorphogenesis; LOCATED IN: nucleus, CUL4 RING ubiquitin ligase complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), Cleavage/polyadenylation specificity factor, A subunit, C-terminal (InterPro:IPR004871); BEST Arabidopsis thaliana protein match is: damaged DNA binding protein 1B (TAIR:AT4G21100.1); Has 1490 Blast hits to 1182 proteins in 227 species: Archae - 0; Bacteria - 0; Metazoa - 604; Fungi - 374; Plants - 231; Viruses - 0; Other Eukaryotes - 281 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003075.7 Reference assembly

      Range
      2746114..2753014
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_116781.3 → NP_192451.1  damaged DNA binding protein 1A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_192451.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WL42, Q8VY31, Q9M0V3
      UniProtKB/TrEMBL
      A0A178UYD4, A0A5S9XPQ1, A0A5S9XUD6, A0A654FRB3
      Conserved Domains (2) summary
      pfam03178
      Location:744 → 1057
      CPSF_A; CPSF A subunit region
      pfam10433
      Location:76 → 537
      MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term

    2. NM_001125468.1 → NP_001118940.1  damaged DNA binding protein 1A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001118940.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9XUD6, A0A654FRB3, B3H6I9
      Conserved Domains (2) summary
      pfam03178
      Location:723 → 1036
      CPSF_A; CPSF A subunit region
      pfam10433
      Location:76 → 516
      MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9M0V3.1

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