Gene

KWMTBOMO15423  Validated by peptides from experiments

Pre Gene Modal

BGIBMGA004740

Annotation

DNA_damage-binding_protein_1_[Papilio_xuthus]

Location

Bomo_Chr25(+):12849370-12851682      View in EpiBrowser

Full name

DNA damage-binding protein 1      

Alternative Name

DDB p127 subunit
DNA damage-binding protein a
Damage-specific DNA-binding protein 1
HBV X-associated protein 1
UV-damaged DNA-binding factor
UV-damaged DNA-binding protein 1
XPE-binding factor
Xeroderma pigmentosum group E-complementing protein

Location in the cell

Cytoplasmic   Reliability : 2.341

CDS

ATGGAAGTGTCGGTGGGGGGAGGGTTGGGGGGCGAGGTCGGTAACGGCTTGTGGGTCCACAGCGCGGCCACCACGGACGAGGACCGGCAGCAGATGGGCTACGCGGGGCAGTTCCACCTCGGCGACATGGTCAACGTCATGCGCGCCGGCTCCCTCGTGGCGCCGCACCACCACGCCGACTCCGCCGCGCCCACGCACCGCCCCGTGCTGCTCGCCACCGTGCACGGCGCCATCTTTTTAGTGGCTCAGATATCCCAGGAGCTGTTCGAGTTCCTGCAGCAGGTGGAGGAGCGGCTGTCGCACTGCATCAAGTCCGTGGGCCGCATCCCGCACGCCTTCTGGCGCTCCTTCAACACCGACATCAAGACCGAGCCCGCCGAGGGGTTCGTCGACGGGGACCTCATCGAGACCTTCCTCGACCTCAACAGGGACGTGCAGCACGACATCGTCAAGGGACTACAGATCGACGAGGGCAGCGGCATGATGAGGGACGCCAAAATAGACGACTTAATCAAAATAGTGGAAGACCTAACGAGGATACATTGA

Protein

MEVSVGGGLGGEVGNGLWVHSAATTDEDRQQMGYAGQFHLGDMVNVMRAGSLVAPHHHADSAAPTHRPVLLATVHGAIFLVAQISQELFEFLQQVEERLSHCIKSVGRIPHAFWRSFNTDIKTEPAEGFVDGDLIETFLDLNRDVQHDIVKGLQIDEGSGMMRDAKIDDLIKIVEDLTRIH

Description

Required for DNA repair. Binds to DDB2 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 a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) 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. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2. The DDB1-CUL4A-DTL E3 ligase complex regulates the circadian clock function by mediating the ubiquitination and degradation of CRY1 (PubMed:26431207). DDB1-mediated CRY1 degradation promotes FOXO1 protein stability and FOXO1-mediated gluconeogenesis in the liver (By similarity).

Subunit

Component of the UV-DDB complex which includes DDB1 and DDB2; the heterodimer dimerizes to give rise to a heterotetramer when bound to damaged DNA (PubMed:22822215). The UV-DDB complex interacts with monoubiquitinated histone H2A and binds to XPC via the DDB2 subunit. Component of numerous DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which consist of a core of DDB1, CUL4A or CUL4B and RBX1. DDB1 may recruit specific substrate targeting subunits to the DCX complex. These substrate targeting subunits are generally known as DCAF (DDB1- and CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat) proteins. Interacts with AMBRA1, ATG16L1, BTRC, CRBN, DCAF1, DCAF4, DCAF5, DCAF6, DCAF7, DCAF8, DCAF9, DCAF10, DCAF11, DCAF12, DCAF15, DCAF16, DCAF17, DDA1, DET1, DTL, ERCC8, FBXW5, FBXW8, GRWD1, KATNB1, NLE1, NUP43, PAFAH1B1, PHIP, PWP1, RBBP4, RBBP5, RBBP7, COP1, SNRNP40, DCAF1, WDR5, WDR5B, WDR12, WDR26, WDR39, WDR42, WDR53, WDR59, WDR61, WSB1, WSB2, LRWD1 and WDTC1. DCX complexes may associate with the COP9 signalosome, and this inhibits the E3 ubiquitin-protein ligase activity of the complex. Interacts with NF2, TSC1 and TSC2. Interaction with SV5 protein V may prevent the recruitment of DCAF proteins to DCX complexes. Interacts with AGO1 and AGO2. Associates with the E3 ligase complex containing DYRK2, EDD/UBR5, DDB1 and DCAF1 proteins (EDVP complex). Interacts directly with DYRK2. DCX(DTL) complex interacts with FBXO11; does not ubiquitinate and degradate FBXO11. Interacts with TRPC4AP (PubMed:19966799). Interacts with CRY1 and CRY2 (By similarity). The DDB1-CUL4A complex interacts with CRY1 (PubMed:26431207).
(Microbial infection) Interacts with Simian virus 5 protein V.
(Microbial infection) Interacts with hepatitis B virus protein HBX; the viral protein contains a short helical motif that competes for the same binding site as the N-terminal helical motif found in endogenous DCAF proteins.

Similarity

Belongs to the DDB1 family.

Keywords

3D-structure   Acetylation   Alternative splicing   Biological rhythms   Complete proteome   Cytoplasm   DNA damage   DNA repair   DNA-binding   Host-virus interaction   Isopeptide bond   Nucleus   Phosphoprotein   Polymorphism   Reference proteome   Repeat   Ubl conjugation   Ubl conjugation pathway  

Feature

chain  DNA damage-binding protein 1
splice variant  In isoform 2.
sequence variant  In dbSNP:rs28720299.

Uniprot

H9J5F0   A0A2H1WKE8   S4NWY3   A0A194PP99   A0A194RJH7   A0A212FBZ7   + More
A0A2A4JZ82   A0A3S2LJK0   A0A2J7R6I6   A0A2Z5TRE2   A0A2J7R6I4   A0A067QWW9   A0A1B6IJV9   A0A1B6I554   A0A1B6ETQ7   A0A2P8YXD9   L7LV98   L7M756   A0A1B6DCC1   A0A131XUS2   A0A210PZE9   V9IJQ1   K1RKZ5   A0A232F584   A0A224YX42   K7IUN5   A0A131YKZ0   A0A131XG70   A0A1E1XLY5   A0A0C9RQP9   U5EVD6   A0A2D4KBE6   A0A0P5HHR3   A0A0P5RE31   A0A1E1XAG8   A0A0P6HGV3   A0A0P6EYQ9   E0VJ24   A0A0P5RR17   A0A0P6FCL2   A0A0P5RXC9   A0A0P6FRV4   A0A0P5R5T6   A0A0P5LWX0   A0A164LX96   E9FU30   R7UIH1   A0A151JS91   A0A195EXY0   A0A158NJ58   A0A293MTW8   A0A0P6GZA2   A0A0P5LCR1   A0A1Z5LES1   A0A195C340   A0A151X0H4   F4W766   A0A195BL46   E2BJY1   A0A0P6C9R4   A0A0P5IFL8   A0A0P5AAI7   A0A2R5L5Y4   A0A154PI86   A0A0P5KLL0   B7PIF3   A0A0N0BDG5   A0A2A3EQ74   A0A087ZZR8   A0A026WBL0   A0A1S3IIX8   A0A1S3IIM7   E2A411   A0A0J7L6L1   A0A2R7W2L8   C3ZMJ6   A8E561   U6DWG1   A0A1W4X581   A0A087SY87   V9K9R8   Q16531-2   A0A0P6GFZ4   K7G405   F7FU40   A0A0L7R1I9   C0PUD7   A0A151NYZ5   A0A0B7AQY1   A0A0F7Z6E4   A0A0B8RR16   A0A098LZ59   A0A0F7ZE80   D6WR91   A0A3Q0GSF5   A0A1W7RHX9   A0A146LUG5   T1DLK0   Q3ULS8   H9GPM9  

Pubmed

19121390    23622113    26354079    22118469    26760975    24845553    + More
29403074    25576852    28812685    22992520    28648823    28797301    20075255    26830274    28049606    29209593    28503490    20566863    21292972    23254933    21347285    28528879    21719571    20798317    24508170    30249741    18563158    12477932    24402279    8530102    7815490    8538642    14702039    16554811    15489334    9632823    10777491    11673459    11531405    12732143    12743284    15448697    14739464    15882621    16223728    16227264    16260596    16482215    17079684    16407242    16407252    16527807    16678110    16949367    16940174    17041588    16473935    17932509    18593899    18381890    18606781    18332868    19413330    19287380    19608861    21269460    22935713    23478445    24275569    26431207    28790135    28112733    16413485    16964240    19109893    19966799    22118460    21468892    22822215    25043012    25108355    17381049    18464734    22293439    25476704    18362917    19820115    26358130    26823975    23758969    25727380    10349636    11042159    11076861    11217851    12466851    16141073    21881562   

EMBL

BABH01028209    BABH01028210    BABH01028211    BABH01028212    ODYU01009154    SOQ53382.1    + More
GAIX01012372    JAA80188.1    KQ459596    KPI95266.1    KQ460118    KPJ17707.1    AGBW02009250    OWR51255.1    NWSH01000383    PCG76813.1    RSAL01000001    RVE55275.1    NEVH01006756    PNF36444.1    FX985782    BBA93669.1    PNF36443.1    KK853153    KDR10581.1    GECU01020496    JAS87210.1    GECU01025672    JAS82034.1    GECZ01028511    JAS41258.1    PYGN01000302    PSN48913.1    GACK01009507    JAA55527.1    GACK01005342    JAA59692.1    GEDC01013957    JAS23341.1    GEFM01005389    JAP70407.1    NEDP02005356    OWF41789.1    JR049167    AEY60882.1    JH817518    EKC34976.1    NNAY01000904    OXU25996.1    GFPF01007246    MAA18392.1    AAZX01002644    GEDV01009976    JAP78581.1    GEFH01003870    JAP64711.1    GFAA01003094    JAU00341.1    GBYB01010825    JAG80592.1    GANO01001076    JAB58795.1    IACL01047310    LAB06002.1    GDIQ01227878    JAK23847.1    GDIQ01102720    JAL49006.1    GFAC01003127    JAT96061.1    GDIQ01019023    JAN75714.1    GDIQ01056143    JAN38594.1    DS235219    EEB13380.1    GDIQ01106321    JAL45405.1    GDIQ01058842    JAN35895.1    GDIQ01095023    JAL56703.1    GDIQ01145109    GDIQ01061387    GDIQ01034995    JAN33350.1    GDIQ01112270    JAL39456.1    GDIQ01174390    JAK77335.1    LRGB01003123    KZS04522.1    GL732524    EFX89472.1    AMQN01008593    AMQN01008594    KB303505    ELU03057.1    KQ978579    KYN30011.1    KQ981920    KYN33006.1    ADTU01017499    GFWV01019585    MAA44313.1    GDIQ01038902    JAN55835.1    GDIQ01171396    JAK80329.1    GFJQ02001064    JAW05906.1    KQ978317    KYM95279.1    KQ982612    KYQ53861.1    GL887813    EGI69950.1    KQ976453    KYM85435.1    GL448708    EFN83990.1    GDIP01003641    JAN00075.1    GDIQ01214033    JAK37692.1    GDIP01202767    GDIP01030642    JAJ20635.1    GGLE01000766    MBY04892.1    KQ434905    KZC11204.1    GDIQ01182249    JAK69476.1    ABJB010287562    ABJB010324138    ABJB010534196    ABJB010642340    ABJB010687854    ABJB010731674    ABJB010884463    ABJB010898466    ABJB010908998    ABJB011009818    DS718559    EEC06375.1    KQ435863    KOX70388.1    KZ288194    PBC33915.1    KK107293    QOIP01000005    EZA53445.1    RLU22890.1    GL436519    EFN71863.1    LBMM01000453    KMQ98301.1    KK854164    PTY12415.1    GG666646    EEN46206.1    BC153473    AAI53474.1    HAAF01014436    CCP86258.1    KK112505    KFM57826.1    JW862087    AFO94604.1    U18299    L40326    U32986    AJ002955    AK294341    AK312436    AY960579    AP003037    AP003108    CH471076    BC011686    BC050530    BC051764    GDIQ01044145    JAN50592.1    AGCU01001011    AGCU01001012    AGCU01001013    KQ414667    KOC64712.1    BT072289    ACN58665.1    AKHW03001628    KYO41665.1    HACG01036107    CEK82972.1    GBEW01000291    JAI10074.1    GBSH01000871    JAG68154.1    GBSI01000729    JAC95767.1    GBEX01000981    JAI13579.1    KQ971354    EFA07036.1    GDAY02000691    JAV50736.1    GDHC01007884    JAQ10745.1    GAAZ01000708    GBKC01001015    GBKD01000636    JAA97235.1    JAG45055.1    JAG46982.1    AK145328    BAE26370.1    AAWZ02021149   

Proteomes

UP000005204    UP000053268    UP000053240    UP000007151    UP000218220    UP000283053    + More
UP000235965    UP000027135    UP000245037    UP000242188    UP000005408    UP000215335    UP000002358    UP000009046    UP000076858    UP000000305    UP000014760    UP000078492    UP000078541    UP000005205    UP000078542    UP000075809    UP000007755    UP000078540    UP000008237    UP000076502    UP000001555    UP000053105    UP000242457    UP000005203    UP000053097    UP000279307    UP000085678    UP000000311    UP000036403    UP000001554    UP000192223    UP000054359    UP000005640    UP000007267    UP000002279    UP000053825    UP000050525    UP000007266    UP000189705    UP000001646   

PRIDE

H9J5F0    B7PIF3    Q16531    Q3ULS8   

Pfam

PF03178   CPSF_A        + More
PF00069   Pkinase

Interpro

IPR036322   WD40_repeat_dom_sf        + More
IPR031297   DDB1       
IPR004871   Cleavage/polyA-sp_fac_asu_C       
IPR015943   WD40/YVTN_repeat-like_dom_sf       
IPR011047   Quinoprotein_ADH-like_supfam       
IPR011009   Kinase-like_dom_sf       
IPR000719   Prot_kinase_dom       

SUPFAM

SSF50978   SSF50978        + More
SSF50998   SSF50998       
SSF56112   SSF56112       

Gene 3D

2.130.10.10    

ProteinModelPortal

H9J5F0   A0A2H1WKE8   S4NWY3   A0A194PP99   A0A194RJH7   A0A212FBZ7   + More
A0A2A4JZ82   A0A3S2LJK0   A0A2J7R6I6   A0A2Z5TRE2   A0A2J7R6I4   A0A067QWW9   A0A1B6IJV9   A0A1B6I554   A0A1B6ETQ7   A0A2P8YXD9   L7LV98   L7M756   A0A1B6DCC1   A0A131XUS2   A0A210PZE9   V9IJQ1   K1RKZ5   A0A232F584   A0A224YX42   K7IUN5   A0A131YKZ0   A0A131XG70   A0A1E1XLY5   A0A0C9RQP9   U5EVD6   A0A2D4KBE6   A0A0P5HHR3   A0A0P5RE31   A0A1E1XAG8   A0A0P6HGV3   A0A0P6EYQ9   E0VJ24   A0A0P5RR17   A0A0P6FCL2   A0A0P5RXC9   A0A0P6FRV4   A0A0P5R5T6   A0A0P5LWX0   A0A164LX96   E9FU30   R7UIH1   A0A151JS91   A0A195EXY0   A0A158NJ58   A0A293MTW8   A0A0P6GZA2   A0A0P5LCR1   A0A1Z5LES1   A0A195C340   A0A151X0H4   F4W766   A0A195BL46   E2BJY1   A0A0P6C9R4   A0A0P5IFL8   A0A0P5AAI7   A0A2R5L5Y4   A0A154PI86   A0A0P5KLL0   B7PIF3   A0A0N0BDG5   A0A2A3EQ74   A0A087ZZR8   A0A026WBL0   A0A1S3IIX8   A0A1S3IIM7   E2A411   A0A0J7L6L1   A0A2R7W2L8   C3ZMJ6   A8E561   U6DWG1   A0A1W4X581   A0A087SY87   V9K9R8   Q16531-2   A0A0P6GFZ4   K7G405   F7FU40   A0A0L7R1I9   C0PUD7   A0A151NYZ5   A0A0B7AQY1   A0A0F7Z6E4   A0A0B8RR16   A0A098LZ59   A0A0F7ZE80   D6WR91   A0A3Q0GSF5   A0A1W7RHX9   A0A146LUG5   T1DLK0   Q3ULS8   H9GPM9  

PDB

6H0G     E-value=6.14228e-43,     Score=434

KEGG

101741287    K10610 DNA damage-binding protein 1 | (RefSeq) DNA damage-binding protein 1

PATHWAY

03420    Nucleotide excision repair - Bombyx mori (domestic silkworm)
04120    Ubiquitin mediated proteolysis - Bombyx mori (domestic silkworm)

GO

GO:0005634   GO:0006281   GO:0003676   GO:0005524   GO:0004672   GO:0003684   GO:0043161   GO:0010564   GO:0043066   GO:0005615   GO:0070062   GO:0044877   GO:0051702   GO:0030674   GO:0045732   GO:0006295   GO:0046726   GO:0097602   GO:0010498   GO:1901990   GO:0042769   GO:0006974   GO:0006296   GO:0048511   GO:0016032   GO:0045070   GO:0006511   GO:0045722   GO:0000784   GO:0070911   GO:0000717   GO:0006289   GO:0031465   GO:0042752   GO:0016055   GO:0006283   GO:0003677   GO:0033683   GO:0016567   GO:0032991   GO:0031464   GO:0035518   GO:0000715   GO:0005737   GO:0005654   GO:0070914   GO:0043687   GO:0080008   GO:1902188   GO:0006294   GO:0071987   GO:0006293   GO:0003700   GO:0008270   GO:0043565   GO:0003707   GO:0006259   GO:0005515  

PANTHER

PTHR10644:SF3  

Subcellular location

Cytoplasm  
Nucleus  

Length:

181

Number of predicted TMHs:

0

Exp number of AAs in TMHs:

0.08141

Exp number, first 60 AAs:

0.01369

Total prob of N-in:

0.01689

outside

1  -  181

 

 

Pi

184.614469

Theta

177.968568

Tajima's D

-1.01961

CLR

0.163248

CSRT

0.126593670316484

Interpretation

Uncertain