DDB2 damaged DNA binding 2 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: DDB2
Official Full Name: damaged DNA binding 2
Primary source: TAIR:AT5G58760
Locus tag: AT5G58760
See related: Araport:AT5G58760
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: damaged DNA binding 2; MZN1.20; MZN1_20
Summary: Encodes a DDB1a interacting protein DDB2 required for UV-B tolerance and genomic integrity.
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Genomic context

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See DDB2 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 11

Sequence:: Chromosome: 5; NC_003076.8 (23730450..23733707, complement)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DDB2 forms a complex with ROS1 and AGO4 and that they act at the ROS1 locus to modulate levels of DNA methylation and therefore ROS1 expression. DDB2 acts as a critical regulator of ROS1-mediated active DNA demethylation.
Title: Dual control of ROS1-mediated active DNA demethylation by DNA damage-binding protein 2 (DDB2).
DDB2 role in the repair of UV-induced DNA lesions
Title: Small RNA-mediated repair of UV-induced DNA lesions by the DNA DAMAGE-BINDING PROTEIN 2 and ARGONAUTE 1.
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.
Altogether, these data suggest that DET1, CUL4 and DDB2 cooperate during the excision repair process.
Title: The conserved factor DE-ETIOLATED 1 cooperates with CUL4-DDB1DDB2 to maintain genome integrity upon UV stress.
DDB2 but not ATCSA-1 expression is upregulated upon UV treatment.
Title: The DDB1a interacting proteins ATCSA-1 and DDB2 are critical factors for UV-B tolerance and genomic integrity in Arabidopsis thaliana.
Results show that DDB1A is required for UV regulation of DDB1B and DDB2 mRNA levels while DDB1A is sufficient to increase Arabidopsis UV tolerance.
Title: Overexpression of Arabidopsis damaged DNA binding protein 1A (DDB1A) enhances UV tolerance.
CUL4-DDB1A-DDB2 complex is involved in global genome repair of UV-induced DNA lesions.
Title: Regulation and role of Arabidopsis CUL4-DDB1A-DDB2 in maintaining genome integrity upon UV stress.
DDB1A-dependent phenotypes indicate a competition between DDB2- and DET1-containing complexes for available DDB1A, while, for DDB1A-independent phenotypes, DDB1B is able to fulfill this role.
Title: DDB2, DDB1A and DET1 exhibit complex interactions during Arabidopsis development.
AtUV-DDB2 functions in DNA repair and has a direct or indirect influence on cell proliferation in the plant meristem. [UV-DDB2]
Title: Characterization of T-DNA insertion mutants and RNAi silenced plants of Arabidopsis thaliana UV-damaged DNA binding protein 2 (AtUV-DDB2).

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

At-8.5BJ-343 (e-PCR)
- UniSTS:229381

Homology

Orthologs from OrthoDB

NM_001345321.1

Supported by ESTs:

NM_125263.5

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables damaged DNA 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 DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to UV-B	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to UV-B	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Cul4-RING E3 ubiquitin ligase complex	IEA Inferred from Electronic Annotation more info
part_of Cul4-RING E3 ubiquitin ligase complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: damaged DNA binding 2

NP_200684.2

damaged DNA binding 2 (DDB2); FUNCTIONS IN: nucleotide binding, zinc ion binding, nucleic acid binding; INVOLVED IN: DNA repair, response to UV-B; LOCATED IN: nucleus, CUL4 RING ubiquitin ligase complex; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: WD40 repeat 2 (InterPro:IPR019782), WD40 repeat, conserved site (InterPro:IPR019775), WD40 repeat (InterPro:IPR001680), WD40 repeat-like-containing domain (InterPro:IPR011046), WD40-repeat-containing domain (InterPro:IPR017986), WD40/YVTN repeat-like-containing domain (InterPro:IPR015943), Zinc finger, CCHC-type (InterPro:IPR001878), WD40 repeat, subgroup (InterPro:IPR019781); BEST Arabidopsis thaliana protein match is: DROUGHT SENSITIVE 1 (TAIR:AT1G80710.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (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

NC_003076.8 Reference assembly

Range

23730450..23733707 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_125263.5 → NP_200684.2 damaged DNA binding 2 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_200684.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q6NQ88, Q9LUY5

UniProtKB/TrEMBL

A0A5S9YHN1, A0A654GCT9

Conserved Domains (3) summary

COG2319
Location:165 → 508

WD40; WD40 repeat [General function prediction only]

COG5082
Location:75 → 120

AIR1; Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

sd00039
Location:174 → 213

7WD40; WD40 repeat [structural motif]
NM_001345321.1 → NP_001332069.1 damaged DNA binding 2 [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A178UF88, A0A1P8BFU8, A0A654GCT9