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DNA glycosylase 3D structures

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Current revision (08:53, 31 January 2023) (edit) (undo)
 
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{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|
-
*Adenine DG
+
*Adenine DG or MutY
**[[3n5n]] – hADG catalytic domain – human<BR />
**[[3n5n]] – hADG catalytic domain – human<BR />
Line 14: Line 14:
*Adenine DG complex
*Adenine DG complex
 +
**[[7ef8]], [[7ef9]] – mADG + DNA with oxo-guanine - mouse<br />
 +
**[[7efa]] – mADG C-terminal + PCNA<br />
**[[1wei]], [[1mud]] - EcADG catalytic domain (mutant) + adenine<br />
**[[1wei]], [[1mud]] - EcADG catalytic domain (mutant) + adenine<br />
-
**[[6q0c]], [[5dpk]] – GsADG + DNA – ''Geobacillus stearothermophilus''<BR />
+
**[[6q0c]], [[6u7t]] - GsADG + DNA – ''Geobacillus stearothermophilus''<br />
-
**[[3g0q]], [[1vrl]], [[1rrq]], [[1rrs]], [[5kn8]] - GsADG (mutant) + DNA <BR />
+
**[[6q0c]], [[6u7t]] – GsADG + DNA <BR />
-
**[[5dpk]], [[5kn9]] – GsADG + DNA with oxo-guanine<br />
+
**[[3g0q]], [[1vrl]], [[1rrq]], [[1rrs]], [[5kn8]], [[8dvy]], [[8dw0]], [[8dw4]], [[8dw7]] - GsADG (mutant) + DNA <BR />
 +
**[[6u7t]], [[5kn9]], [[8dvp]] – GsADG + DNA with oxo-guanine<br />
*A/G specific adenine DG complex
*A/G specific adenine DG complex
Line 25: Line 28:
*Uracil DG
*Uracil DG
 +
**[[1akz]], [[3tkb]], [[1yuo]] - hUDG (mutant) <BR />
 +
**[[1okb]] – AcUDG catalytic domain – Atlantic cod<br />
**[[3a7n]], [[4wpk]], [[4wrw]], [[4wrx]] – MtUDG – ''Mycobacterium tuberculosis''<BR />
**[[3a7n]], [[4wpk]], [[4wrw]], [[4wrx]] – MtUDG – ''Mycobacterium tuberculosis''<BR />
-
**[[6ajs]] – MsUDG – ''Mycobacterium smegmatis''<br />
+
**[[6ail]], [[6ajs]], [[6io9]] – MsUDG X – ''Mycobacterium smegmatis''<br />
-
**[[6ajq]] – MsUDG (mutant)<br />
+
**[[6ajq]], [[6l5a]], [[6l5b]] – MsUDG X (mutant)<br />
-
**[[6ail]] – MsUDG X<br />
+
**[[3tr7]] – UDG – ''Coxiella burnetii''<br />
**[[3tr7]] – UDG – ''Coxiella burnetii''<br />
-
**[[1akz]], [[3tkb]], [[1yuo]] - hUDG (mutant) <BR />
 
**[[2jhq]] – UDG – ''Vibrio cholerae''<BR />
**[[2jhq]] – UDG – ''Vibrio cholerae''<BR />
**[[2owq]], [[3nt7]], [[4dof]], [[4dog]], [[4rib]], [[4lzb]], [[4qc9]], [[4qca]], [[5jx0]] – UDG (mutant) – Vaccinia virus<BR />
**[[2owq]], [[3nt7]], [[4dof]], [[4dog]], [[4rib]], [[4lzb]], [[4qc9]], [[4qca]], [[5jx0]] – UDG (mutant) – Vaccinia virus<BR />
Line 37: Line 40:
**[[1lqj]] – EcUDG<BR />
**[[1lqj]] – EcUDG<BR />
**[[1flz]] - EcUDG (mutant) <BR />
**[[1flz]] - EcUDG (mutant) <BR />
-
**[[1udh]], [[1udg]], [[5nnh]], [[5nn7]] – HsUDG - Herpes simplex virus<BR />
+
**[[1udh]], [[1udg]], [[5nnh]], [[5nn7]] – HhvUDG - Human herpesvirus<BR />
**[[2c2p]], [[2boo]] – DrUDG – ''Deinococcus radiodurans''<BR />
**[[2c2p]], [[2boo]] – DrUDG – ''Deinococcus radiodurans''<BR />
**[[2c2q]] – DrUDG (mutant) <BR />
**[[2c2q]] – DrUDG (mutant) <BR />
**[[1vk2]], [[1l9g]] – TmUDG - ''Thermotoga maritima''<BR />
**[[1vk2]], [[1l9g]] – TmUDG - ''Thermotoga maritima''<BR />
-
**[[1okb]] – AcUDG catalytic domain – Atlantic cod<br />
 
**[[3wdf]] – SaUDG - ''Staphylococcus aureus''<br />
**[[3wdf]] – SaUDG - ''Staphylococcus aureus''<br />
**[[3zor]] – BsUDG – ''Bacillus subtilis''<br />
**[[3zor]] – BsUDG – ''Bacillus subtilis''<br />
Line 50: Line 52:
*Uracil-DNA glycosylase complex with inhibitor protein
*Uracil-DNA glycosylase complex with inhibitor protein
-
**[[1udi]] – HsvUDG + UDG inhibitor protein<br />
 
**[[1ugh]] – hUDG + UDG inhibitor protein<br />
**[[1ugh]] – hUDG + UDG inhibitor protein<br />
**[[1uug]], [[1eui]], [[1lqg]], [[1lqm]] – EcUDG + UDG inhibitor protein <br />
**[[1uug]], [[1eui]], [[1lqg]], [[1lqm]] – EcUDG + UDG inhibitor protein <br />
**[[2uug]] – EcUDG (mutant) + UDG inhibitor protein <br />
**[[2uug]] – EcUDG (mutant) + UDG inhibitor protein <br />
-
**[[2j8x]] – UDG + UDG inhibitor protein – Epstein-Barr virus<br />
+
**[[2j8x]] – EBvUDG + UDG inhibitor protein – Epstein-Barr virus<br />
**[[2zhx]] – MtUDG + UDG inhibitor protein <br />
**[[2zhx]] – MtUDG + UDG inhibitor protein <br />
**[[3wdg]] – SaUDG + UDG inhibitor protein <br />
**[[3wdg]] – SaUDG + UDG inhibitor protein <br />
**[[4lyl]] – acUDG catalytic domain + UDG inhibitor protein <br />
**[[4lyl]] – acUDG catalytic domain + UDG inhibitor protein <br />
**[[4l5n]] – HsvUDG + PZA inhibitor protein <br />
**[[4l5n]] – HsvUDG + PZA inhibitor protein <br />
 +
**[[1udi]] – HsvUDG + UDG inhibitor protein<br />
*Uracil-DNA glycosylase complex with DNA
*Uracil-DNA glycosylase complex with DNA
-
**[[1lau]] – HsvUDG + DNA <br />
 
**[[4skn]] – hUDG (mutant) + DNA<br />
**[[4skn]] – hUDG (mutant) + DNA<br />
**[[2oxm]] – hUDG + DNA<br />
**[[2oxm]] – hUDG + DNA<br />
-
**[[4uqm]] – DrUDG + DNA<br />
 
**[[1ssp]], [[1q3f]] – hUDG + DNA + uracil<br />
**[[1ssp]], [[1q3f]] – hUDG + DNA + uracil<br />
**[[1emh]] – hUDG + DNA + deoxy pseudo-UMP<br />
**[[1emh]] – hUDG + DNA + deoxy pseudo-UMP<br />
Line 73: Line 73:
**[[4qcb]] – VvUDG (mutant) + DNA<br />
**[[4qcb]] – VvUDG (mutant) + DNA<br />
**[[2ddg]], [[2dem]], [[2dp6]] – TtUDG + DNA + deoxyphosphono ribose<br />
**[[2ddg]], [[2dem]], [[2dp6]] – TtUDG + DNA + deoxyphosphono ribose<br />
-
**[[5nnu]] – HhUDG + DNA <br />
+
**[[5nnu]] – HhvUDG + DNA <br />
-
**[[6ajo]] – MsUDG + DNA<br />
+
**[[1lau]] – HsvUDG + DNA <br />
 +
**[[6ajo]], [[6iod]] – MsUDG X + DNA<br />
 +
**[[6l6s]] – MsUDG X (mutant) + DNA<br />
 +
**[[4uqm]] – DrUDG + DNA<br />
*Uracil-DNA glycosylase complex with uracil derivatives
*Uracil-DNA glycosylase complex with uracil derivatives
-
**[[5eug]], [[2eug]], [[1flz]] – EcUDG (mutant) + uracil<br />
+
**[[5eug]], [[2eug]], [[1flz]] , [[3eug]]– EcUDG (mutant) + uracil<br />
**[[1ui0]] – TtUDG + Fe4S4 + uracil <br />
**[[1ui0]] – TtUDG + Fe4S4 + uracil <br />
**[[4lzb]] – VvUDG (mutant) + uracil<br />
**[[4lzb]] – VvUDG (mutant) + uracil<br />
Line 84: Line 87:
**[[4wpl]], [[4wru]], [[4wrv]] – MtUDG + uracil<br />
**[[4wpl]], [[4wru]], [[4wrv]] – MtUDG + uracil<br />
**[[4wry]], [[4wrz]], [[4ws0]], [[4ws1]], [[4ws2]], [[4ws3]], [[4ws4]], [[4ws5]], [[4ws6]], [[4ws7]], [[4ws8]] – MtUDG + uracil derivative<br />
**[[4wry]], [[4wrz]], [[4ws0]], [[4ws1]], [[4ws2]], [[4ws3]], [[4ws4]], [[4ws5]], [[4ws6]], [[4ws7]], [[4ws8]] – MtUDG + uracil derivative<br />
-
**[[6ajr]] – MsUDG + uracil<br />
+
**[[6ajr]], [[6ioa]] – MsUDG X + uracil<br />
-
**[[6ajp]] – MsUDG + deoxy-UMP <br />
+
**[[6iob]], [[6ioc]] – MsUDG X (mutant) + uracil<br />
 +
**[[6ajp]] – MsUDG X + deoxy-UMP <br />
**[[2d3y]] – TtUDG + Fe4S4 + deoxy-UMP <br />
**[[2d3y]] – TtUDG + Fe4S4 + deoxy-UMP <br />
-
**[[2c53]] – HsvUDG (mutant) + deoxyuridine<br />
+
**[[2c53]] – HhvUDG (mutant) + deoxyuridine<br />
**[[3cxm]] – UDG + Br-uracil – ''Leishmania naiffi''<br />
**[[3cxm]] – UDG + Br-uracil – ''Leishmania naiffi''<br />
*Uracil-DNA glycosylase other complexes
*Uracil-DNA glycosylase other complexes
-
**[[2hxm]], [[3fcf]], [[3fci]], [[3fck]], [[3fcl]] – hUDG + inhibitor<br />
+
**[[2hxm]], [[3fcf]], [[3fci]], [[3fck]], [[3fcl]], [[6vba]] – hUDG + inhibitor<br />
**[[5jk7]] – hUDG + DNA damage-binding protein + VPRBP + VPR <br />
**[[5jk7]] – hUDG + DNA damage-binding protein + VPRBP + VPR <br />
 +
**[[7v7c]] – hUDG + DNA damage-binding protein + VPRBP + VPR – Cryo EM<br />
**[[5ayr]], [[5ays]] – hUDG + protein<br />
**[[5ayr]], [[5ays]] – hUDG + protein<br />
**[[3uf7]] – EcUDG + single-stranded DNA-binding protein C terminal<br />
**[[3uf7]] – EcUDG + single-stranded DNA-binding protein C terminal<br />
**[[3ufm]] – DrUDG + single-stranded DNA-binding protein C terminal<br />
**[[3ufm]] – DrUDG + single-stranded DNA-binding protein C terminal<br />
**[[3zoq]] – BsUDG + p56 <br />
**[[3zoq]] – BsUDG + p56 <br />
 +
**[[5gn2]], [[5gn3]] – BdUDG – ''Bradyrhizobium diazoefficiens'' <br />
 +
**[[5grk]] – BdUDG + xanthine <br />
 +
**[[5gnw]] – BdUDG + uracil <br />
**[[4od8]], [[4oda]], [[4ygm]], [[5jkr]] – VvUDG + DNA polymerase processivity factor component A20 N terminal<br />
**[[4od8]], [[4oda]], [[4ygm]], [[5jkr]] – VvUDG + DNA polymerase processivity factor component A20 N terminal<br />
**[[5jks]], [[5jkt]] – VvUDG (mutant) + DNA polymerase processivity factor component A20 N terminal<br />
**[[5jks]], [[5jkt]] – VvUDG (mutant) + DNA polymerase processivity factor component A20 N terminal<br />
**[[4yig]] – VvUDG + DNA polymerase processivity factor component A20 N terminal + DNA<br />
**[[4yig]] – VvUDG + DNA polymerase processivity factor component A20 N terminal + DNA<br />
 +
**[[6lyj]] – EBvUDG + SAUGI <br />
 +
**[[6lyv]] – HhvUDG + SAUGI <br />
*Smug1 Uracil DG
*Smug1 Uracil DG
Line 119: Line 129:
**[[3ufj]] – hTDG core domain + DNA + fluoroluridine<br />
**[[3ufj]] – hTDG core domain + DNA + fluoroluridine<br />
**[[4fnc]], [[5hf7]] - hTDG + DNA + uridine derivative <br />
**[[4fnc]], [[5hf7]] - hTDG + DNA + uridine derivative <br />
-
**[[5jxy]], [[4z3a]], [[4xeg]] - hTDG + DNA + G/U analog<br />
+
**[[5jxy]], [[4z3a]], [[4xeg]], [[6u17]] - hTDG + DNA + G/U analog<br />
 +
**[[6u15]], [[6u16]] - hTDG (mutant) + DNA + G/U analog<br />
**[[5ff8]], [[5cys]], [[4z7z]], [[4z7b]], [[4z47]] - hTDG + DNA + deoxyribose<br />
**[[5ff8]], [[5cys]], [[4z7z]], [[4z7b]], [[4z47]] - hTDG + DNA + deoxyribose<br />
Line 125: Line 136:
**[[1ko9]], [[5an4]] – hOgg1<BR />
**[[1ko9]], [[5an4]] – hOgg1<BR />
-
**[[2xhi]], [[3ktu]], [[1hu0]], [[1fn7]] - hOgg1 + DNA<BR />
+
**[[2xhi]], [[3ktu]], [[1hu0]], [[1fn7]], [[6w0m]], [[6w0r]], [[6w13]] - hOgg1 + DNA<BR />
-
**[[1lwv]], [[1lww]], [[1lwy]] - hOgg1 + DNA<BR /> + guanine derivative<BR />
+
**[[2nob]], [[2noe]], [[2nof]], [[2noh]], [[2noi]], [[2nol]], [[2noz]], [[2i5w]], [[1yqk]], [[1yql]], [[1yqm]], [[1yqr]], [[1n39]], [[1n3a]], [[1n3c]] - hOgg1 (mutant) + DNA<BR />
**[[2nob]], [[2noe]], [[2nof]], [[2noh]], [[2noi]], [[2nol]], [[2noz]], [[2i5w]], [[1yqk]], [[1yql]], [[1yqm]], [[1yqr]], [[1n39]], [[1n3a]], [[1n3c]] - hOgg1 (mutant) + DNA<BR />
 +
**[[6rlw]] - hOgg1 + inhibitor<br />
 +
**[[7cfa]] - hOgg1 + activator<br />
 +
**[[1lwv]], [[1lww]], [[1lwy]] - hOgg1 + DNA<BR /> + guanine derivative<BR />
**[[1m3h]], [[3ih7]] - hOgg1 core fragment (mutant) + DNA<BR />
**[[1m3h]], [[3ih7]] - hOgg1 core fragment (mutant) + DNA<BR />
**[[1m3q]], [[1ebm]] - hOgg1 core fragment (mutant) + DNA + guanine derivative
**[[1m3q]], [[1ebm]] - hOgg1 core fragment (mutant) + DNA + guanine derivative
-
*8-oxoguanine (oxoG) DG
+
*8-oxoguanine (oxoG) DG or N-glycosylase/DNA ligase
**[[6g3x]] – mOgg1 – mouse<br />
**[[6g3x]] – mOgg1 – mouse<br />
-
**[[6g40]], [[6g3y]] – mOgg1 + inhibitor<br />
+
**[[6g40]], [[6g3y]], [[7pz1]], [[7qel]] – mOgg1 + inhibitor<br />
 +
**[[7ayz]], [[7az0]] - mOgg1 + activator<br />
**[[3n0u]] – TmOxDG<BR />
**[[3n0u]] – TmOxDG<BR />
**[[3knt]] - MjOxDG (mutant) + DNA – ''Methanocaldococcus jannaschii''<BR />
**[[3knt]] - MjOxDG (mutant) + DNA – ''Methanocaldococcus jannaschii''<BR />
Line 146: Line 160:
**[[4ejy]], [[4ejz]] – OxDG + DNA – ''Thermoanaerobacter tengcongensis''<br />
**[[4ejy]], [[4ejz]] – OxDG + DNA – ''Thermoanaerobacter tengcongensis''<br />
**[[4pii]] – OxDG – ''Pyrococcus furiosus''<br />
**[[4pii]] – OxDG – ''Pyrococcus furiosus''<br />
 +
**[[7ou3]] – OxDG – ''Thermococcus gammatolerans''<br />
 +
**[[7olb]], [[7oli]] – PaOxDG – ''Pyrococcus abyssi''<br />
 +
**[[7oue]], [[7oy7]], [[7p0w]], [[7p8l]], [[7p9z]] – PaOxDG + DNA <br />
*Methyladenine DG
*Methyladenine DG
Line 157: Line 174:
**[[1pu6]] – HpAlkDG – ''Helicobacter pylori''<BR />
**[[1pu6]] – HpAlkDG – ''Helicobacter pylori''<BR />
**[[4ai4]] – SaAlkDG (mutant)<br />
**[[4ai4]] – SaAlkDG (mutant)<br />
 +
**[[2yg8]] – DrAlkDG<br />
*Methyladenine DG complex
*Methyladenine DG complex
Line 162: Line 180:
**[[3qi5]], [[1ewn]], [[1f4r]], [[1f6o]], [[1bnk]], [[3uby]] – hAlkDG + DNA<BR />
**[[3qi5]], [[1ewn]], [[1f4r]], [[1f6o]], [[1bnk]], [[3uby]] – hAlkDG + DNA<BR />
**[[3jx7]], [[3jxy]], [[3jxz]], [[3jy1]] - BcAlkDG + DNA<BR />
**[[3jx7]], [[3jxy]], [[3jxz]], [[3jy1]] - BcAlkDG + DNA<BR />
 +
**[[7lxh]], [[7lxj]] - BcAlkDG + DNA + ribose derivative + inhibitor<br />
**[[5uuh]], [[5uug]], [[5uuf]], [[5kub]] – BcAlkDG + damaged DNA <br />
**[[5uuh]], [[5uug]], [[5uuf]], [[5kub]] – BcAlkDG + damaged DNA <br />
**[[3ogd]], [[3oh6]], [[3oh9]] - EcAlkDG (mutant) + DNA<BR />
**[[3ogd]], [[3oh6]], [[3oh9]] - EcAlkDG (mutant) + DNA<BR />
Line 175: Line 194:
**[[5vi0]] – PfAlkCDG + DNA – ''Pseudomonas fluorescens''<br />
**[[5vi0]] – PfAlkCDG + DNA – ''Pseudomonas fluorescens''<br />
**[[5vhv]] – PfAlkCDG + damaged DNA <br />
**[[5vhv]] – PfAlkCDG + damaged DNA <br />
-
 
+
**[[5cl3]], [[5cl4]], [[5cl5]], [[5cl6]], [[5cl7]], [[5cl8]], [[5cl9]], [[5cla]], [[5clb]], [[5clc]], [[5cld]], [[5cle]] – BcAlkCDG + DNA <br />
*Formamidopyrimidine DG
*Formamidopyrimidine DG
Line 182: Line 201:
**[[3a42]], [[3a45]] – ApFpg – ''Acanthamoeba polyphaga'' minivirus<br />
**[[3a42]], [[3a45]] – ApFpg – ''Acanthamoeba polyphaga'' minivirus<br />
**[[3twk]], [[3twl]] – AtFpg - ''Arabidopsis thaliana''<br />
**[[3twk]], [[3twl]] – AtFpg - ''Arabidopsis thaliana''<br />
 +
**[[6tc6]] – NmFpg - ''Neisseria meningitidis''<br />
 +
**[[6tc9]] – NmFpg + DNA + DNA containing abasic analog<br />
*''Fpg complex with DNA''
*''Fpg complex with DNA''
Line 204: Line 225:
**[[1pjj]] – LlFpg (mutant) + DNA containing abasic dideoxyribose<br />
**[[1pjj]] – LlFpg (mutant) + DNA containing abasic dideoxyribose<br />
**[[4cis]] – LlFpg + DNA containing oxoG derivative<br />
**[[4cis]] – LlFpg + DNA containing oxoG derivative<br />
-
**[[3twm]] – AtFpg + DNA containing abasic dideoxyribose<br />
 
**[[1pji]] – LlFpg + DNA containing 1,3-propanediol<br />
**[[1pji]] – LlFpg + DNA containing 1,3-propanediol<br />
**[[2xzf]], [[2xzu]] – LlFpg + DNA containing oxidized pyrimidine<br />
**[[2xzf]], [[2xzu]] – LlFpg + DNA containing oxidized pyrimidine<br />
**[[1tdz]], [[1xc8]], [[3c58]] – LlFpg + DNA containing Fapy-dG derivative<br />
**[[1tdz]], [[1xc8]], [[3c58]] – LlFpg + DNA containing Fapy-dG derivative<br />
 +
**[[6fl1]], [[6h0s]] – LlFpg (mutant) + DNA containing Fapy-dG derivative<br />
 +
**[[6rnm]], [[6rno]], [[6rnr]], [[6ro2]], [[6rok]], [[6rp0]], [[6rp7]] – LlFpg + DNA containing abasic dideoxyribose + inhibitor<br />
 +
**[[3twm]] – AtFpg + DNA containing abasic dideoxyribose<br />
**[[3a46]] – ApFpg + DNA containing abasic dideoxyribose<br />
**[[3a46]] – ApFpg + DNA containing abasic dideoxyribose<br />
**[[4nrw]] – ApFpg (mutant) + DNA containing abasic dideoxyribose<br />
**[[4nrw]] – ApFpg (mutant) + DNA containing abasic dideoxyribose<br />
Line 214: Line 237:
**[[3jr4]] – GsFpg (mutant) + DNA + guanosine derivative <br />
**[[3jr4]] – GsFpg (mutant) + DNA + guanosine derivative <br />
-
*DNA glycosylase NEI
+
*DNA glycosylase NEI see [[Endonuclease]]-VIII
-
**[[2ea0]], [[2opf]], [[2oq4]], [[1k3w]], [[1k3x]] – EcGD NEI + DNA<BR />
 
-
**[[2fcc]] – Pyrimidine GD + DNA – Enterobacteria phage T4<br />
 
-
**[[1q39]] – EcGD NEI<br />
 
-
**[[1q3b]], [[1q3c]] – EcGD NEI (mutant)<br />
 
-
**[[1tdh]] – hGD NEI
 
}}
}}
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

3D Structures of DNA glycosylase

Updated on 31-January-2023

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Joel L. Sussman

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