DNA glycosylase 3D structures

3D Structures of DNA glycosylase

Updated on 17-April-2025

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• Adenine DG or MutY
  • 3n5n – hADG catalytic domain – human
    
  • 1x51 – hADG NUDIX domain - NMR
    
  • 1wef, 1weg, 1kg4, 1kg5, 1kg6, 1kg7, 1kqj, 1mun - EcADG catalytic domain (mutant) - Escherichia coli
    
  • 1kg2, 1kg3, 1muy - EcADG catalytic domain
    
  • 1mun - EcADG catalytic domain (mutant)
    
• Adenine DG complex
  • 9lnp, 9lnq – hADG + DNA
    
  • 8fay – hADG + DNA with oxo-guanine
    
  • 7ef8, 7ef9 – mADG + DNA with oxo-guanine - mouse
    
  • 7z3y, 7z5r – mADG + inhibitor
    
  • 7efa – mADG C-terminal + PCNA
    
  • 1wei, 1mud - EcADG catalytic domain (mutant) + adenine
    
  • 6q0c, 6u7t - GsADG + DNA – Geobacillus stearothermophilus
    
  • 3g0q, 1vrl, 1rrq, 1rrs, 5kn8, 8dvy, 8dw0, 8dw4, 8dw7, 8dwd, 8dwe, 8dwf - GsADG (mutant) + DNA
    
  • 6u7t, 5kn9, 8dvp – GsADG + DNA with oxo-guanine
    
  • 9bs2 – GsADG (mutant) + DNA with oxo-guanine
    
• A/G specific adenine DG complex
  • 4ypr, 4yph, 4yoq – GsADG (mutant) + DNA
    
• Uracil DG
  • 1akz, 3tkb, 1yuo - hUDG (mutant)
    
  • 1okb – AcUDG catalytic domain – Atlantic cod
    
  • 3a7n, 4wpk, 4wrw, 4wrx – MtUDG – Mycobacterium tuberculosis
    
  • 6ail, 6ajs, 6io9 – MsUDG X – Mycobacterium smegmatis
    
  • 6ajq, 6l5a, 6l5b, 8iif, 8iih, 8iij, 8iim, 8iio, 8iiq, 8iir, 8iis – MsUDG X (mutant)
    
  • 3tr7 – UDG – Coxiella burnetii
    
  • 2jhq – UDG – Vibrio cholerae
    
  • 2owq, 3nt7, 4dof, 4dog, 4rib, 4lzb, 4qc9, 4qca, 5jx0, 8qam – VvUDG (mutant) – Vaccinia virus
    
  • 5jx3, 5jx8 – VvUDG
    
  • 2d3y, 1ui0, 1ui1 – TtUDG – Thermus thermophilus
    
  • 1lqj – EcUDG
    
  • 1flz - EcUDG (mutant)
    
  • 1udh, 1udg, 5nnh, 5nn7 – HhvUDG - Human herpesvirus
    
  • 2c2p, 2boo – DrUDG – Deinococcus radiodurans
    
  • 2c2q – DrUDG (mutant)
    
  • 1vk2, 1l9g – TmUDG - Thermotoga maritima
    
  • 3wdf – SaUDG - Staphylococcus aureus
    
  • 3zor – BsUDG – Bacillus subtilis
    
  • 4zbx, 4zbz – StUDG – Sulfolobus tokodaii
    
  • 5x3g – NsUDG – Nitratifactor salsuginis
    
  • 5x3h – NsUDG (mutant)
    
• Uracil-DNA glycosylase complex with inhibitor protein
  • 1ugh – hUDG + UDG inhibitor protein
    
  • 1uug, 1eui, 1lqg, 1lqm – EcUDG + UDG inhibitor protein
    
  • 2uug – EcUDG (mutant) + UDG inhibitor protein
    
  • 2j8x – EBvUDG + UDG inhibitor protein – Epstein-Barr virus
    
  • 2zhx – MtUDG + UDG inhibitor protein
    
  • 3wdg, 8aim, 8ain – SaUDG + UDG inhibitor protein
    
  • 4lyl – acUDG catalytic domain + UDG inhibitor protein
    
  • 4l5n – HsvUDG + PZA inhibitor protein
    
  • 1udi – HsvUDG + UDG inhibitor protein
    
• Uracil-DNA glycosylase complex with DNA
  • 4skn – hUDG (mutant) + DNA
    
  • 2oxm – hUDG + DNA
    
  • 1ssp, 1q3f – hUDG + DNA + uracil
    
  • 1emh – hUDG + DNA + deoxy pseudo-UMP
    
  • 2oyt – hUDG + DNA + abasic deoxyribose
    
  • 2ssp – hUDG (mutant) + DNA + abasic deoxyribose
    
  • 1emj – hUDG (mutant) + DNA + uracil + deoxyuridine analog
    
  • 4qcb – VvUDG (mutant) + DNA
    
  • 2ddg, 2dem, 2dp6 – TtUDG + DNA + deoxyphosphono ribose
    
  • 5nnu – HhvUDG + DNA
    
  • 1lau – HsvUDG + DNA
    
  • 6ajo, 6iod – MsUDG X + DNA
    
  • 6l6s – MsUDG X (mutant) + DNA
    
  • 4uqm – DrUDG + DNA
    
• Uracil-DNA glycosylase complex with uracil derivatives
  • 5eug, 2eug, 1flz , 3eug– EcUDG (mutant) + uracil
    
  • 1ui0 – TtUDG + Fe4S4 + uracil
    
  • 4lzb – VvUDG (mutant) + uracil
    
  • 4zby – StUDG + uracil
    
  • 5gnw – BdUDG + uracil
    
  • 4wpl, 4wru, 4wrv – MtUDG + uracil
    
  • 4wry, 4wrz, 4ws0, 4ws1, 4ws2, 4ws3, 4ws4, 4ws5, 4ws6, 4ws7, 4ws8 – MtUDG + uracil derivative
    
  • 6ajr, 6ioa, 8iie – MsUDG X + uracil
    
  • 6iob, 6ioc, 8iig, 8iil, 8iin, 8iip, 8iit – MsUDG X (mutant) + uracil
    
  • 6ajp – MsUDG X + deoxy-UMP
    
  • 2d3y – TtUDG + Fe4S4 + deoxy-UMP
    
  • 2c53 – HhvUDG (mutant) + deoxyuridine
    
  • 3cxm – UDG + Br-uracil – Leishmania naiffi
    
• Uracil-DNA glycosylase other complexes
  • 2hxm, 3fcf, 3fci, 3fck, 3fcl, 6vba – hUDG + inhibitor
    
  • 5jk7 – hUDG + DNA damage-binding protein + VPRBP + VPR
    
  • 7v7c – hUDG + DNA damage-binding protein + VPRBP + VPR – Cryo EM
    
  • 5ayr, 5ays – hUDG + protein
    
  • 3uf7 – EcUDG + single-stranded DNA-binding protein C terminal
    
  • 3ufm – DrUDG + single-stranded DNA-binding protein C terminal
    
  • 3zoq – BsUDG + phage p56
    
  • 8ail – UDG + phage p56 – Bacillus weidemannii
    
  • 5gn2, 5gn3 – BdUDG – Bradyrhizobium diazoefficiens
    
  • 5grk – BdUDG + xanthine
    
  • 8i61, 8i62, 8i63, 8i64, 8i65, 8i66, 8i67, 8i68, 8i69, 8i6a, 8i6b, 8i6c, 8i6d – MtUDG + inhibitor
    
  • 4od8, 4oda, 4ygm, 5jkr – VvUDG + DNA polymerase processivity factor component A20 N terminal
    
  • 5jks, 5jkt – VvUDG (mutant) + DNA polymerase processivity factor component A20 N terminal
    
  • 4yig – VvUDG + DNA polymerase processivity factor component A20 N terminal + DNA
    
  • 8q3r – VvUDG + DNA polymerase + DNA polymerase processivity factor – Cryo EM
    
  • 8hdz, 8hlz – mpvUDG + DNA polymerase + DNA polymerase processivity factor – monkeypox virus – Cryo EM
    
  • 8hg1, 8hm0, 8k8s, 8wpe, 8wpk, 8wpp, 9k9r, 9k9s, 9k9t, 9k9u, 9k9v – mpvUDG + DNA polymerase + DNA polymerase processivity factor + DNA –Cryo EM
    
  • 8k8u – mpvUDG + DNA polymerase + DNA polymerase processivity factor + DNA + CTP – Cryo EM
    
  • 6lyj – EBvUDG + SAUGI
    
  • 6lyv – HhvUDG + SAUGI
    
• Smug1 Uracil DG
  • 1oe4, 1oe5, 1oe6 – UDG Smug1 + DNA– Xenopus laevis
• Thymine DG
  • 2rba – hTDG core domain + DNA
    
  • 2d07, 1wyw – hTDG central region + SUMO-3
    
  • 1kea – TDG – Methanothermobacter thermautotrophicus
    
  • 1mug – EcTDG
• G/T mismatch-specific thymine DG
  • 3uo7, 4jgc, 5t2w - hTDG + DNA + carboxylcytosine
    
  • 3uob - hTDG + DNA + fluoro-cytidine
    
  • 3ufj – hTDG core domain + DNA + fluoroluridine
    
  • 4fnc, 5hf7 - hTDG + DNA + uridine derivative
    
  • 5jxy, 4z3a, 4xeg, 6u17 - hTDG + DNA + G/U analog
    
  • 6u15, 6u16 - hTDG (mutant) + DNA + G/U analog
    
  • 5ff8, 5cys, 4z7z, 4z7b, 4z47 - hTDG + DNA + deoxyribose
    
• Human 8-oxoguanine DG
  • 1ko9, 5an4 – hOgg1
    
  • 2xhi, 3ktu, 1hu0, 1fn7, 6w0m, 6w0r, 6w13 - hOgg1 + DNA
    
  • 2nob, 2noe, 2nof, 2noh, 2noi, 2nol, 2noz, 2i5w, 1yqk, 1yql, 1yqm, 1yqr, 1n39, 1n3a, 1n3c - hOgg1 (mutant) + DNA
    
  • 6rlw - hOgg1 + inhibitor
    
  • 7cfa - hOgg1 + activator
    
  • 1lwv, 1lww, 1lwy - hOgg1 + DNA
    + guanine derivative
    
  • 1m3h, 3ih7 - hOgg1 core fragment (mutant) + DNA
    
  • 1m3q, 1ebm - hOgg1 core fragment (mutant) + DNA + guanine derivative
• 8-oxoguanine (oxoG) DG or N-glycosylase/DNA ligase
  • 6g3x – mOgg1 – mouse
    
  • 6g40, 6g3y, 7pz1, 7qel, 7z5b, 7zc7, 7zg3, 8bq7, 8bvx, 8cex, 8cey – mOgg1 + ligand
    
  • 7ayz, 7az0 - mOgg1 + activator
    
  • 3n0u – TmOxDG
    
  • 3knt - MjOxDG (mutant) + DNA – Methanocaldococcus jannaschii
    
  • 3fhf - MjOxDG
    
  • 3go8, 3gp1, 3gpp, 3gpu, 3gpx, 3gpy, 3gq3, 3gq4, 3gq5 – GsOxDG (mutant) + DNA
    
  • 3f0z - CaOxDG – Clostridium acetobutylicum
    
  • 3f10 – CaOxDG + oxoG
    
  • 3i0w, 3i0x - CaOxDG (mutant) + DNA
    
  • 3fhg - OxDG (mutant) – Sulfolobus solfataricus
    
  • 1xqo, 1xqp – OxDG – Pyrobaculum aerophilum
    
  • 4ejy, 4ejz – OxDG + DNA – Thermoanaerobacter tengcongensis
    
  • 4pii – OxDG – Pyrococcus furiosus
    
  • 7ou3 – OxDG – Thermococcus gammatolerans
    
  • 7olb, 7oli – PaOxDG – Pyrococcus abyssi
    
  • 7oue, 7oy7, 7p0w, 7p8l, 7p9z – PaOxDG + DNA
    
• Methyladenine DG
  • 3bvs – BcAlkDG – Bacillus cereus
    
  • 1pvs, 1p7m, 1mpg – EcAlkDG
    
  • 1nku, 1lmz – EcAlkDG - NMR
    
  • 2ofk – StAlkDG – Salmonella typhi
    
  • 2jhj, 2jhn – AlkDG – Archaeoglobus fulgidus
    
  • 2jg6 – AlkDG – Staphylococcus aureus
    
  • 1pu6 – HpAlkDG – Helicobacter pylori
    
  • 4ai4 – SaAlkDG (mutant)
    
  • 2yg8 – DrAlkDG
    
• Methyladenine DG complex
  • 3qi5, 1ewn, 1f4r, 1f6o, 1bnk, 3uby – hAlkDG + DNA
    
  • 7xfh, 7xfj, 7xfm – hAlkDG in nucleosome – Cryo EM
    
  • 3jx7, 3jxy, 3jxz, 3jy1 - BcAlkDG + DNA
    
  • 7lxh, 7lxj - BcAlkDG + DNA + ribose derivative + inhibitor
    
  • 5uuh, 5uug, 5uuf, 5kub – BcAlkDG + damaged DNA
    
  • 3ogd, 3oh6, 3oh9 - EcAlkDG (mutant) + DNA
    
  • 3d4v, 3cvs, 3cvt, 3cw7, 3cwa, 3cws, 3cwt, 3cwu, 1diz - EcAlkDG + DNA
    
  • 2ofi – StAlkDG + DNA
    
  • 3s6i – AlkDG + DNA – fission yeast
    
  • 1pu7, 1pu8 – HpAlkDG + adenine derivative
    
  • 4aia – SaAlkDG + methyladenine
    
  • 4ai5 – SaAlkDG (mutant) + methyladenine
    
• Alkylpurine DG
  • 5vi0 – PfAlkCDG + DNA – Pseudomonas fluorescens
    
  • 5vhv – PfAlkCDG + damaged DNA
    
  • 5cl3, 5cl4, 5cl5, 5cl6, 5cl7, 5cl8, 5cl9, 5cla, 5clb, 5clc, 5cld, 5cle – BcAlkCDG + DNA
    
• Formamidopyrimidine DG
  • 1ee8 – TtFpg
    
  • 3a42, 3a45 – ApFpg – Acanthamoeba polyphaga minivirus
    
  • 3twk, 3twl – AtFpg - Arabidopsis thaliana
    
  • 6tc6 – NmFpg - Neisseria meningitidis
    
  • 6tc9 – NmFpg + DNA + DNA containing abasic analog
    
• Fpg complex with DNA
  • 1k82 – EcFpg + DNA
    
  • 4pdi, 4pdg, 4pd2, 4pcz – LlFpg + damaged DNA – Lactococcus lactis
    
  • 1kfv, 1nnj – LlFpg (mutant) + DNA
    
  • 1l1t, 1l1z, 1l2b, 1l2c – GsFpg + DNA
    
  • 2f5n, 2f5o, 2f5p, 3gpx, 3gq5 – GsFpg (mutant) + DNA
    
• Fpg complex with DNA containing a damaged base
  • 1r2y, 2f5q, 2f5s, 3jr5, 3gp1, 3gpp, 3gpu, **3gpy, 3gq3, 3gq4, 3go8, 3u6c, 3u6d – GsFpg (mutant) + DNA containing oxoG
    
  • 3u6e, 4g4o, 4g4r – GsFpg (mutant) + DNA containing oxoG and thymidine derivative
    
  • 3u6l, 3u6m, 3u6q – GsFpg (mutant) + DNA containing oxoG and cytidine derivative
    
  • 1r2z – GsFpg (mutant) + DNA containing 5,6-dihydrouracil
    
  • 3saw – GsFpg + DNA containing cytidine derivative
    
  • 3sar, 3sav, 3sbj – GsFpg (mutant) + DNA containing cytidine derivative
    
  • 1l2d, 3sau, 3u6o, 3u6p, 3u6s, 4g4n, 4g4q – GsFpg (mutant) + DNA containing thymidine derivative
    
  • 3sas, 3sat – GsFpg (mutant) + DNA containing open deoxy-ribofuranose phosphate
    
  • 1pm5 – LlFpg + DNA containing abasic dideoxyribose
    
  • 1pjj – LlFpg (mutant) + DNA containing abasic dideoxyribose
    
  • 4cis – LlFpg + DNA containing oxoG derivative
    
  • 1pji – LlFpg + DNA containing 1,3-propanediol
    
  • 2xzf, 2xzu – LlFpg + DNA containing oxidized pyrimidine
    
  • 1tdz, 1xc8, 3c58 – LlFpg + DNA containing Fapy-dG derivative
    
  • 6fl1, 6h0s – LlFpg (mutant) + DNA containing Fapy-dG derivative
    
  • 6rnm, 6rno, 6rnr, 6ro2, 6rok, 6rp0, 6rp7 – LlFpg + DNA containing abasic dideoxyribose + inhibitor
    
  • 3twm – AtFpg + DNA containing abasic dideoxyribose
    
  • 3a46 – ApFpg + DNA containing abasic dideoxyribose
    
  • 4nrw – ApFpg (mutant) + DNA containing abasic dideoxyribose
    
  • 3vk7 – ApFpg (mutant) + DNA containing 5-hydroxyuracil
    
  • 3vk8 – ApFpg (mutant) + DNA containing thymine glycol
    
  • 3jr4 – GsFpg (mutant) + DNA + guanosine derivative
    
• DNA glycosylase NEI see Endonuclease-VIII

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Michal Harel, Joel L. Sussman