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Reviewed, UniProtKB/Swiss-Prot Q92466 (DDB2_HUMAN)

Last modified November 25, 2008. Version 88. Feed History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Alternative products · Sequence annotation (Features) · Sequences · References · Web resources · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    DNA damage-binding protein 2
Alternative name(s):
    Damage-specific DNA-binding protein 2
    DDB p48 subunit
      Short name=DDBb
    UV-damaged DNA-binding protein 2
      Short name=UV-DDB 2
Gene names
Name: DDB2
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length427 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.

Pathway

Protein modification; protein ubiquitination.

Subunit structure

Component of the UV-DDB complex which includes DDB1 and DDB2. The UV-DDB complex interacts with monoubiquitinated histone H2A and binds to XPC via the DDB2 subunit. Component of the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1), which includes CUL4A or CUL4B, DDB1, DDB2 and RBX1. DDB2 may function as the substrate recognition module within this complex. The DDB1-CUL4-ROC1 complex may associate with the COP9 signalosome, and this inhibits the E3 ubiquitin-protein ligase activity of the complex. A large number of other DCX complexes may also exist in which an alternate substrate targeting subunit replaces DDB2. These targeting subunits are generally known as DCAF (DDB1- and CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat) proteins. Isoform D1 and isoform D2 do not interact with DDB1.

Subcellular location

Nucleus. Note= Accumulates at sites of DNA damage following UV irradiation.

Tissue specificity

Ubiquitously expressed; with highest levels in corneal endothelium and lowest levels in brain. Isoform D1 is highly expressed in brain and heart. Isoform D2, isoform D3 and isoform D4 are weakly expressed.

Induction

Expression is induced in response to treatment with IR or UV and this requires p53 activity.

Domain

The DWD box is required for interaction with DDB1.

Post-translational modification

Ubiquitinated by CUL4A in response to UV irradiation. Ubiquitination appears to both impair DNA-binding and promotes ubiquitin-dependent proteolysis. Degradation of DDB2 at sites of DNA damage may be a prerequisite for their recognition by XPC and subsequent repair. CUL4A-mediated degradation appears to be promoted by ABL1/c-ABL.

Involvement in disease

Defects in DDB2 are a cause of xeroderma pigmentosum complementation group E (XP-E) [MIM:278740]; also known as xeroderma pigmentosum V (XP5). XP-E is a rare human autosomal recessive disease characterized by solar sensitivity, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities.

Sequence similarities

Belongs to the WD repeat DDB2/WDR76 family.

Contains 5 WD repeats.

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Binary interactions

With

Entry

#Exp.

IntAct

Notes

CUL4AQ136191EBI-1176171,EBI-456106
DDB1Q165312EBI-1176171,EBI-350322
E2F1Q010942EBI-1176171,EBI-448924

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Alternative products

This entry describes 5 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q92466-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform D1 (identifier: Q92466-2)

The sequence of this isoform differs from the canonical sequence as follows:
     153-341: Missing.
Isoform D2 (identifier: Q92466-3)

The sequence of this isoform differs from the canonical sequence as follows:
     153-156: IGAG → HLVL
     157-427: Missing.
Isoform D3 (identifier: Q92466-4)

The sequence of this isoform differs from the canonical sequence as follows:
     89-152: Missing.
Isoform D4 (identifier: Q92466-5)

The sequence of this isoform differs from the canonical sequence as follows:
     236-244: WNLRMHKKK → VSVPMEPGS
     245-427: Missing.

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 427427DNA damage-binding protein 2
PRO_0000050953

Regions

Repeat109 – 14941WD 1
Repeat154 – 19542WD 2
Repeat240 – 28041WD 3
Repeat286 – 32540WD 4
Repeat389 – 42638WD 5
Region68 – 7912Required for interaction with DDB1
Region87 – 9812Required for interaction with DDB1
Motif256 – 27419DWD box

Amino acid modifications

Modified residue241Phosphoserine
Modified residue261Phosphoserine

Natural variations

Alternative sequence89 – 15264Missing in isoform D3.
VSP_014674
Alternative sequence153 – 341189Missing in isoform D1.
VSP_014675
Alternative sequence153 – 1564IGAG → HLVL in isoform D2.
VSP_014676
Alternative sequence157 – 427271Missing in isoform D2.
VSP_014677
Alternative sequence236 – 2449WNLRMHKKK → VSVPMEPGS in isoform D4.
VSP_014678
Alternative sequence245 – 427183Missing in isoform D4.
VSP_014679
Natural variant2151M → T: dbSNP rs4647750.
VAR_016337
Natural variant2441K → E in XP-E; impairs DNA-binding of the UV-DDB complex.
VAR_010141
Natural variant2731R → H in XP-E; impairs interaction with DDB1 and CUL4A.
VAR_010142
Natural variant2931A → T: dbSNP rs4647751.
VAR_016338

Experimental info

Mutagenesis2581L → A: Impairs interaction with DDB1
Mutagenesis2621S → A: Impairs interaction with DDB1
Mutagenesis2641D → A: Impairs interaction with DDB1
Mutagenesis2691I → A: Impairs interaction with DDB1
Mutagenesis2701W → A: Impairs interaction with DDB1
Mutagenesis2721L → A: Impairs interaction with DDB1
Mutagenesis2731R → A: Impairs interaction with DDB1
Mutagenesis3501L → P: Impairs interaction with DDB1

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Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 1, 1997. Version 1.
Checksum: E881F21242CA44D2

FASTA42747,864
        10         20         30         40         50         60 
MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP 

        70         80         90        100        110        120 
QILPPCRSIV RTLHQHKLGR ASWPSVQQGL QQSFLHTLDS YRILQKAAPF DRRATSLAWH 

       130        140        150        160        170        180 
PTHPSTVAVG SKGGDIMLWN FGIKDKPTFI KGIGAGGSIT GLKFNPLNTN QFYASSMEGT 

       190        200        210        220        230        240 
TRLQDFKGNI LRVFASSDTI NIWFCSLDVS ASSRMVVTGD NVGNVILLNM DGKELWNLRM 

       250        260        270        280        290        300 
HKKKVTHVAL NPCCDWFLAT ASVDQTVKIW DLRQVRGKAS FLYSLPHRHP VNAACFSPDG 

       310        320        330        340        350        360 
ARLLTTDQKS EIRVYSASQW DCPLGLIPHP HRHFQHLTPI KAAWHPRYNL IVVGRYPDPN 

       370        380        390        400        410        420 
FKSCTPYELR TIDVFDGNSG KMMCQLYDPE SSGISSLNEF NPMGDTLASA MGYHILIWSQ 


EEARTRK

« Hide

Isoform D1 [UniParc].

Checksum: F40BD646C1C26FDA
Show »

23826,744
Isoform D2 [UniParc].

Checksum: FBC8A060B4DC7A4D
Show »

15617,434
Isoform D3 [UniParc].

Checksum: 2A90D5BD9E322889
Show »

36340,772
Isoform D4 [UniParc].

Checksum: 367D99AA1DD984F9
Show »

24426,758

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References

« Hide 'large scale' references
[1]"Chromosomal localization and cDNA cloning of the genes (DDB1 and DDB2) for the p127 and p48 subunits of a human damage-specific DNA binding protein."
Dualan R., Brody T., Keeney S., Nichols A.F., Admon A., Linn S.
Genomics 29:62-69(1995) [PubMed: 8530102] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Epidermis.
[2]"Human DDB2 splicing variants are dominant negative inhibitors of UV-damaged DNA repair."
Inoki T., Yamagami S., Inoki Y., Tsuru T., Hamamoto T., Kagawa Y., Mori T., Endo H.
Biochem. Biophys. Res. Commun. 314:1036-1043(2004) [PubMed: 14751237] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS D1; D2; D3 AND D4), FUNCTION, INTERACTION WITH DDB1, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
Tissue: Epithelium.
[3]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[4]"NIEHS-SNPs, environmental genome project, NIEHS ES15478, Department of Genome Sciences, Seattle, WA (URL: http://egp.gs.washington.edu)."
Rieder M.J., Livingston R.J., Daniels M.R., Montoya M.A., Chung M.-W., Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D., Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.
Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS THR-215 AND THR-293.
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Brain.
[6]"p48 Activates a UV-damaged-DNA binding factor and is defective in xeroderma pigmentosum group E cells that lack binding activity."
Hwang B.J., Toering S., Francke U., Chu G.
Mol. Cell. Biol. 18:4391-4399(1998) [PubMed: 9632823] [Abstract]
Cited for: INTERACTION WITH DDB1, DNA-BINDING, CHARACTERIZATION OF VARIANTS GLU-244 AND HIS-273.
[7]"Expression of the p48 xeroderma pigmentosum gene is p53-dependent and is involved in global genomic repair."
Hwang B.J., Ford J.M., Hanawalt P.C., Chu G.
Proc. Natl. Acad. Sci. U.S.A. 96:424-428(1999) [PubMed: 9892649] [Abstract]
Cited for: FUNCTION, DNA-BINDING.
[8]"Human damage-specific DNA-binding protein p48. Characterization of XPE mutations and regulation following UV irradiation."
Nichols A.F., Itoh T., Graham J.A., Liu W., Yamaizumi M., Linn S.
J. Biol. Chem. 275:21422-21428(2000) [PubMed: 10777490] [Abstract]
Cited for: DNA-BINDING, SUBCELLULAR LOCATION, INDUCTION, CHARACTERIZATION OF VARIANTS GLU-244 AND HIS-273.
[9]"Nuclear transport of human DDB protein induced by ultraviolet light."
Liu W., Nichols A.F., Graham J.A., Dualan R., Abbas A., Linn S.
J. Biol. Chem. 275:21429-21434(2000) [PubMed: 10777491] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[10]"Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis."
Tang J.Y., Hwang B.J., Ford J.M., Hanawalt P.C., Chu G.
Mol. Cell 5:737-744(2000) [PubMed: 10882109] [Abstract]
Cited for: FUNCTION.
[11]"Damaged DNA-binding protein DDB stimulates the excision of cyclobutane pyrimidine dimers in vitro in concert with XPA and replication protein A."
Wakasugi M., Shimizu M., Morioka H., Linn S., Nikaido O., Matsunaga T.
J. Biol. Chem. 276:15434-15440(2001) [PubMed: 11278856] [Abstract]
Cited for: FUNCTION, DNA-BINDING.
[12]"UV-damaged DNA-binding proteins are targets of CUL-4A-mediated ubiquitination and degradation."
Chen X., Zhang Y., Douglas L., Zhou P.
J. Biol. Chem. 276:48175-48182(2001) [PubMed: 11673459] [Abstract]
Cited for: INTERACTION WITH CUL4A, UBIQUITINATION, CHARACTERIZATION OF VARIANT HIS-273.
[13]"DDB accumulates at DNA damage sites immediately after UV irradiation and directly stimulates nucleotide excision repair."
Wakasugi M., Kawashima A., Morioka H., Linn S., Sancar A., Mori T., Nikaido O., Matsunaga T.
J. Biol. Chem. 277:1637-1640(2002) [PubMed: 11705987] [Abstract]
Cited for: FUNCTION, DNA-BINDING, SUBCELLULAR LOCATION.
[14]"The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage."
Groisman R., Polanowska J., Kuraoka I., Sawada J., Saijo M., Drapkin R., Kisselev A.F., Tanaka K., Nakatani Y.
Cell 113:357-367(2003) [PubMed: 12732143] [Abstract]
Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN A COMPLEX WITH CUL4A; DDB1 AND RBX1 AND THE COP9 SIGNALOSOME, DNA-BINDING.
[15]"In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimers by the DDB2 gene product."
Fitch M.E., Nakajima S., Yasui A., Ford J.M.
J. Biol. Chem. 278:46906-46910(2003) [PubMed: 12944386] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[16]"UV-induced ubiquitylation of XPC protein mediated by UV-DDB-ubiquitin ligase complex."
Sugasawa K., Okuda Y., Saijo M., Nishi R., Matsuda N., Chu G., Mori T., Iwai S., Tanaka K., Tanaka K., Hanaoka F.
Cell 121:387-400(2005) [PubMed: 15882621] [Abstract]
Cited for: FUNCTION, INTERACTION WITH CUL4A; DDB1; RBX1 AND XPC, DNA-BINDING, UBIQUITINATION.
[17]"DDB1-DDB2 (xeroderma pigmentosum group E) protein complex recognizes a cyclobutane pyrimidine dimer, mismatches, apurinic/apyrimidinic sites, and compound lesions in DNA."
Wittschieben B.O., Iwai S., Wood R.D.
J. Biol. Chem. 280:39982-39989(2005) [PubMed: 16223728] [Abstract]
Cited for: INTERACTION WITH DDB1, DNA-BINDING, CHARACTERIZATION OF VARIANTS GLU-244 AND HIS-273.
[18]"Xeroderma pigmentosum complementation group E protein (XPE/DDB2): purification of various complexes of XPE and analyses of their damaged DNA binding and putative DNA repair properties."
Kulaksiz G., Reardon J.T., Sancar A.
Mol. Cell. Biol. 25:9784-9792(2005) [PubMed: 16260596] [Abstract]
Cited for: FUNCTION, INTERACTION WITH CUL4A; DDB1; RBX1 AND THE COP9 SIGNALOSOME, DNA-BINDING.
[19]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed: 17081983] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-24 AND SER-26, MASS SPECTROMETRY.
Tissue: Epithelium.
[20]"DDB1 functions as a linker to recruit receptor WD40 proteins to CUL4-ROC1 ubiquitin ligases."
He Y.J., McCall C.M., Hu J., Zeng Y., Xiong Y.
Genes Dev. 20:2949-2954(2006) [PubMed: 17079684] [Abstract]
Cited for: INTERACTION WITH CUL4A AND DDB1, DWD BOX MOTIF, MUTAGENESIS OF LEU-258; SER-262; ASP-264; ILE-269; TRP-270; LEU-272 AND ARG-273.
[21]"Cullin 4A-mediated proteolysis of DDB2 protein at DNA damage sites regulates in vivo lesion recognition by XPC."
El-Mahdy M.A., Zhu Q., Wang Q.-E., Wani G., Praetorius-Ibba M., Wani A.A.
J. Biol. Chem. 281:13404-13411(2006) [PubMed: 16527807] [Abstract]
Cited for: INTERACTION WITH CUL4A AND DDB1, UBIQUITINATION.
[22]"Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage."
Wang H., Zhai L., Xu J., Joo H.-Y., Jackson S., Erdjument-Bromage H., Tempst P., Xiong Y., Zhang Y.
Mol. Cell 22:383-394(2006) [PubMed: 16678110] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN A COMPLEX WITH DDB1; CUL4A; CUL4B AND RBX1, FUNCTION.
[23]"A kinase-independent function of c-Abl in promoting proteolytic destruction of damaged DNA binding proteins."
Chen X., Zhang J., Lee J., Lin P.S., Ford J.M., Zheng N., Zhou P.
Mol. Cell 22:489-499(2006) [PubMed: 16713579] [Abstract]
Cited for: SUBCELLULAR LOCATION, UBIQUITINATION.
[24]"A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which is required for S phase destruction of the replication factor Cdt1."
Jin J., Arias E.E., Chen J., Harper J.W., Walter J.C.
Mol. Cell 23:709-721(2006) [PubMed: 16949367] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH DDB1, MUTAGENESIS OF LEU-350, CHARACTERIZATION OF VARIANT HIS-273.
[25]"Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery."
Angers S., Li T., Yi X., MacCoss M.J., Moon R.T., Zheng N.
Nature 443:590-593(2006) [PubMed: 16964240] [Abstract]
Cited for: INTERACTION WITH DDB1, CHARACTERIZATION OF VARIANT HIS-273.
[26]"CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation."
Higa L.A., Wu M., Ye T., Kobayashi R., Sun H., Zhang H.
Nat. Cell Biol. 8:1277-1283(2006) [PubMed: 17041588] [Abstract]
Cited for: INTERACTION WITH CUL4A AND CUL4B.
[27]"The DDB1-CUL4ADDB2 ubiquitin ligase is deficient in xeroderma pigmentosum group E and targets histone H2A at UV-damaged DNA sites."
Kapetanaki M.G., Guerrero-Santoro J., Bisi D.C., Hsieh C.L., Rapic-Otrin V., Levine A.S.
Proc. Natl. Acad. Sci. U.S.A. 103:2588-2593(2006) [PubMed: 16473935] [Abstract]
Cited for: FUNCTION, INTERACTION WITH CUL4A; DDB1; HISTONE H2A AND RBX1, DNA-BINDING, SUBCELLULAR LOCATION.
[28]"Dynamic in vivo interaction of DDB2 E3 ubiquitin ligase with UV-damaged DNA is independent of damage-recognition protein XPC."
Luijsterburg M.S., Goedhart J., Moser J., Kool H., Geverts B., Houtsmuller A.B., Mullenders L.H.F., Vermeulen W., van Driel R.
J. Cell Sci. 120:2706-2716(2007) [PubMed: 17635991] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[29]"Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column."
Imami K., Sugiyama N., Kyono Y., Tomita M., Ishihama Y.
Anal. Sci. 24:161-166(2008) [PubMed: 18187866] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-26, MASS SPECTROMETRY.
[30]"The cullin 4B-based UV-damaged DNA-binding protein ligase binds to UV-damaged chromatin and ubiquitinates histone H2A."
Guerrero-Santoro J., Kapetanaki M.G., Hsieh C.L., Gorbachinsky I., Levine A.S., Rapic-Otrin V.
Cancer Res. 68:5014-5022(2008) [PubMed: 18593899] [Abstract]
Cited for: FUNCTION, INTERACTION WITH CUL4A; CUL4B AND DDB1, SUBCELLULAR LOCATION.
[31]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-24 AND SER-26, MASS SPECTROMETRY.
[32]"Mutations specific to the xeroderma pigmentosum group E Ddb-phenotype."
Nichols A.F., Ong P., Linn S.
J. Biol. Chem. 271:24317-24320(1996) [PubMed: 8798680] [Abstract]
Cited for: VARIANTS XP-E GLU-244 AND HIS-273.
+Additional computationally mapped references.

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Cross-references