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DNA damage-binding protein

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[[Image:3ei1.png|left|200px|thumb|Crystal structure of human DDB1 (grey) and DDB2 (green) complex with DNA [[3ei1]]]]
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<StructureSection load='3ei1' size='350' side='right' caption='Human DDB1 (cyan) and DDB2 (green) complex with DNA, and tetraethylene glycol (PDB code [[3ei1]]).' scene='54/541124/Cv/1'>
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{{STRUCTURE_3ei1| PDB=3ei1 | SIZE=350| SCENE= |right|CAPTION=Human DDB1 (grey) and DDB2 (green) complex with DNA, TMP and tetraethylene glycol [[3ei1]] }}
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== Function ==
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'''DNA damage-binding protein''' (DDB) functions in nucleotide excision repair. It prevents UV damage to DNA. <scene name='54/541124/Cv/2'>DDB is a heterodimer composed of the large DDB1 and the smaller DNA-binding DDB2</scene>.
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DNA in this complex with DDB1 and DDB2 contains modified compounds <scene name='54/541124/Cv/5'>5PY and 64T</scene> (in darkmagenta and magenta, respectively), they are derivatives from parent compound THYMIDINE-5'-MONOPHOSPHATE.<ref>PMID:18593899</ref><br /> Water molecules shown as red spheres.
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== Disease ==
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Defective activity of DDB2 causes the repair defects in patients with XPE - an autosomal disorder characterized by early onset of cancer and photosensitivity.
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</StructureSection>
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== 3D Structures of DNA damage-binding protein ==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*DDB1
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**[[3e0c]] – hDDB - human<br />
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**[[2b5m]], [[2b5n]] – hDDB BPB domain<br />
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*DDB1 binary complex
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**[[2b5l]] – hDDB + simian virus 5 protein <br />
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**[[3i7h]], [[3i7k]], [[3i7l]], [[3i7n]], [[3i7o]], [[3i7p]], [[3i89]], [[3i8c]], **[[3i8e]] – hDDB + X protein peptide<br />
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**[[6dsz]] – hDDB + DET1 peptide<br />
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**[[4a11]], [[6fcv]] – hDDB + DNA excision repair protein ERCC-8<br />
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**[[8d7x]], [[8d7y]] – hDDB + cereblon <br />
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**[[8cvp]] – hDDB + cereblon – Cryo EM<br />
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**[[6zue]] – hDDB + DCAF1<br />
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**[[8ajn]] – hDDB + DCAF1 – Cryo EM<br />
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**[[7ukn]] – hDDB + herpes virus protein br />
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**[[7p7b]] – hDDB + VPRBP – Cryo EM<br />
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*DDB1 ternary complex
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**[[4ci1]], [[4ci2]], [[4ci3]], [[4tz4]], [[8d81]] – hDDB + cereblon + thalidomide derivative<br />
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**[[5v3o]] – hDDB + cereblon + piperidine derivative<br />
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**[[5fqd]] – hDDB + cereblon + casein kinase 1<br />
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**[[5hxb]], [[6xk9]] – hDDB + cereblon + ERF3A<br />
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**[[6bn8]], [[6bn9]], [[6bnb]], [[6boy]] – hDDB + cereblon + BRD4<br />
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**[[7lps]] – hDDB + cereblon + IKAROS<br />
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**[[8d7u]], [[8d7v]], [[8d7w]] – hDDB + cereblon + mezigdomide<br />
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**[[6h0f]] – hDDB (mutant) + cereblon + IKAROS<br />
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**[[6h0g]] – hDDB (mutant) + cereblon + ZNF692<br />
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**[[6td3]] – hDDB + cyclin-dependent kinase 12 + cyclin-K<br />
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**[[7zn7]], [[7znn]] – hDDB (mutant) + herpes virus protein + STAT2 – Cryo EM<br />
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**[[6zx9]] – hDDB + SIV protein + VPRBP <br />
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**[[8ajm]], [[8ajo]] – hDDB + DCAF1 + CCT5 – Cryo EM<br />
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*DDB1 quaternary complex
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**[[6uml]] – hDDB + cereblon + ZNF797 + thalidomide derivative <br />
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**[[6bn7]] – hDDB + cereblon + BRD4 + piperidine derivative<br />
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**[[8d7z]], [[8d80]] – hDDB + cereblon + IKAROS + drug<br />
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**[[2hye]] – hDDB + simian virus 5 protein + cullin-4A + ring-box protein 1<br />
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**[[5jk7]] – hDDB + HIV protein + uracil-DNA glycosylase + VPRBP <br />
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**[[7v7c]] – hDDB + HIV protein + uracil-DNA glycosylase + VPRBP – Cryo EM<br />
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**[[7okq]] – hDDB + DCAF1 + cullin-4A + RBX1 – Cryo EM<br />
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**[[6pai]], [[6q0r]], [[6ue5]] – hDDB + DDA1 + RNA-binding protein 39 + DET1 + sulfonamide derivative<br />
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**[[6q0v]], [[6q0w]], [[6ud7]] – hDDB + DDA1 + RNA-binding protein 39 + DET1 + anti-cancer drug<br />
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**[[6sj7]] – hDDB + DDA1 + RNA-binding protein 39 + DET1 + anti-cancer drug – Cryo EM<br />
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**[[7oo3]], [[7oob]], [[7oop]], [[7opc]], [[7opd]] – hDDB in transcription-DNA repair coupling – Cryo EM<br />
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*DDB1+DDB2
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**[[3ei3]], [[3ei4]] – hDDB <br />
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**[[3ei1]], [[3ei2]], [[4a08]], [[4a09]], [[4a0a]], [[4a0b]], [[4e54]], [[4e5z]] – hDDB + DNA<br />
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**[[4a0k]] – hDDB + cullin-4A + ring-box protein 1<br />
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**[[4a0l]] – hDDB + cullin-4A + ring-box protein 1 + DNA<br />
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**[[6r8y]], [[6r8z]], [[6r90]], [[6r91]], [[6r92]] – hDDB + histones + DNA – Cryo EM<br />
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}}
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== References ==
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<references/>
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'''DNA damage-binding protein''' (DDB) functions in nucleotide excision repair. It prevents UV damage to DNA. DDB is a heterodimer composed of the large DDB1 and the smaller DNA-binding DDB2.
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== 3D Structures of DNA damage-binding protein ==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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===DDB1===
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[[2b5l]] – hDDB + simian virus 5 protein – human<br />
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[[2b5m]] – hDDB <br />
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[[2b5m]], [[2b5n]] – hDDB BPB domain<br />
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[[2hye]] – hDDB + simian virus 5 protein + cullin-4A + ring-box protein 1<br />
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[[3e0c]] – hDDB <br />
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[[3i7h]], [[3i7k]], [[3i7l]], [[3i7n]], [[3i7o]], [[3i7p]], [[3i89]], [[3i8c]], [[3i8e]] – hDDB + X protein peptide<br />
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[[4a11]] – hDDB + DNA excision repair protein ERCC-8<br />
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===DDB1+DDB2===
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[[3ei1]], [[3ei2]], [[4a08]], [[4a09]], [[4a0a]], [[4a0b]], [[4e54]], [[4e5z]] – hDDB + DNA<br />
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[[3ei3]], [[3ei4]] – hDDB <br />
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[[4a0k]] – hDDB + cullin-4A + ring-box protein 1<br />
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[[4a0l]] – hDDB + cullin-4A + ring-box protein 1 + DNA<br />
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[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Human DDB1 (cyan) and DDB2 (green) complex with DNA, and tetraethylene glycol (PDB code 3ei1).

Drag the structure with the mouse to rotate

3D Structures of DNA damage-binding protein

Updated on 30-January-2023


References

  1. ↑ Guerrero-Santoro J, Kapetanaki MG, Hsieh CL, Gorbachinsky I, Levine AS, Rapic-Otrin V. The cullin 4B-based UV-damaged DNA-binding protein ligase binds to UV-damaged chromatin and ubiquitinates histone H2A. Cancer Res. 2008 Jul 1;68(13):5014-22. PMID:18593899 doi:68/13/5014

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky

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