DNA glycosylase

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Line 32: Line 32:
**[[3n5n]] – hADG catalytic domain – human<BR />
**[[3n5n]] – hADG catalytic domain – human<BR />
-
**[[1yuo]] - hADG catalytic domain (mutant) <BR />
 
**[[1x51]] – hADG NUDIX domain - NMR<BR />
**[[1x51]] – hADG NUDIX domain - NMR<BR />
**[[1wef]], [[1weg]], [[1kg4]], [[1kg5]], [[1kg6]], [[1kg7]], [[1kqj]], [[1mun]] - EcADG catalytic domain (mutant) - ''Escherichia coli''<BR />
**[[1wef]], [[1weg]], [[1kg4]], [[1kg5]], [[1kg6]], [[1kg7]], [[1kqj]], [[1mun]] - EcADG catalytic domain (mutant) - ''Escherichia coli''<BR />
Line 42: Line 41:
**[[1wei]], [[1mud]] - EcADG catalytic domain (mutant) + adenine<br />
**[[1wei]], [[1mud]] - EcADG catalytic domain (mutant) + adenine<br />
**[[3fsp]], [[5dpk]] – GsADG + DNA – ''Geobacillus stearothermophilus''<BR />
**[[3fsp]], [[5dpk]] – GsADG + DNA – ''Geobacillus stearothermophilus''<BR />
-
**[[3g0q]], [[1vrl]], [[1rrq]], [[1rrs]] - GsADG (mutant) + DNA <BR />
+
**[[3g0q]], [[1vrl]], [[1rrq]], [[1rrs]], [[5kn8]] - GsADG (mutant) + DNA <BR />
 +
**[[5dpk]], [[5kn9]] – GsADG + DNA with oxo-guanine<br />
 +
 
 +
*A/G specific adenine DG complex
 +
 
 +
**[[4ypr]], [[4yph]], [[4yoq]] – GsADG (mutant) + DNA<br />
*Uracil DG
*Uracil DG
-
**[[3a7n]] – MtUDG – ''Mycobacterium tuberculosis''<BR />
+
**[[3a7n]], [[4wpk]], [[4wrw]], [[4wrx]] – MtUDG – ''Mycobacterium tuberculosis''<BR />
**[[3tr7]] – UDG – ''Coxiella burnetii''<br />
**[[3tr7]] – UDG – ''Coxiella burnetii''<br />
-
**[[1akz]], [[3tkb]] - hUDG (mutant) <BR />
+
**[[1akz]], [[3tkb]], [[1yuo]] - hUDG (mutant) <BR />
**[[2jhq]] – UDG – ''Vibrio cholerae''<BR />
**[[2jhq]] – UDG – ''Vibrio cholerae''<BR />
-
**[[2owq]], [[5jx3]], [[3nt7]], [[4dof]], [[4dog]], [[4rib]], [[4lzb]] – UDG (mutant) – Vaccinia virus<BR />
+
**[[2owq]], [[3nt7]], [[4dof]], [[4dog]], [[4rib]], [[4lzb]], [[4qc9]], [[4qca]], [[5jx0]] – UDG (mutant) – Vaccinia virus<BR />
 +
**[[5jx3]], [[5jx8]] – VvUDG<br />
**[[2d3y]], [[1ui0]], [[1ui1]] – TtUDG – ''Thermus thermophilus''<BR />
**[[2d3y]], [[1ui0]], [[1ui1]] – TtUDG – ''Thermus thermophilus''<BR />
**[[1lqj]] – EcUDG<BR />
**[[1lqj]] – EcUDG<BR />
Line 61: Line 66:
**[[3wdf]] – SaUDG - ''Staphylococcus aureus''<br />
**[[3wdf]] – SaUDG - ''Staphylococcus aureus''<br />
**[[3zor]] – BsUDG – ''Bacillus subtilis''<br />
**[[3zor]] – BsUDG – ''Bacillus subtilis''<br />
 +
**[[4zbx]], [[4zbz]] – StUDG – ''Sulfolobus tokodaii'' <br />
-
*Uracil DG complex
+
*Uracil-DNA glycosylase complex with inhibitor protein
-
**[[2zhx]] – MtDG + protein inhibitor<BR />
+
**[[1udi]] – HsvUDG + UDG inhibitor protein<br />
-
**[[2oxm]], [[2oyt]], [[1q3f]] – hUDG + DNA<BR />
+
**[[1ugh]] – hUDG + UDG inhibitor protein<br />
-
**[[1ssp]], [[2ssp]] - hUDG + DNA+ uracil<BR />
+
**[[1uug]], [[1eui]], [[1lqg]], [[1lqm]] – EcUDG + UDG inhibitor protein <br />
-
**[[1emh]], [[1emj]], [[4skn]] – hUDG (mutant) + DNA<BR />
+
**[[2uug]] – EcUDG (mutant) + UDG inhibitor protein <br />
-
**[[3fcf]], [[3fci]], [[3fck]], [[3fcl]], [[2hxm]] – hUDG + inhibitor<BR />
+
**[[2j8x]] – UDG + UDG inhibitor protein – Epstein-Barr virus<br />
-
**[[1ugh]] - hUDG (mutant) + protein inhibitor<BR />
+
**[[2zhx]] – MtUDG + UDG inhibitor protein <br />
-
**[[3cxm]] – UDG residues 129-373 + 5-bromo-uracil<BR />
+
**[[3wdg]] – SaUDG + UDG inhibitor protein <br />
-
**[[2dp6]], [[2dem]], [[2ddg]] – TtUDG + DNA<BR />
+
**[[4lyl]] – acUDG catalytic domain + UDG inhibitor protein <br />
-
**[[2j8x]] – UDG glycosylase domain + protein inhibitor – Epstein-Barr virus<BR />
+
**[[4l5n]] – HsvUDG + PZA inhibitor protein <br />
-
**[[2eug]], [[3eug]], [[1eug]], [[4eug]], [[5eug]] - EcUDG (mutant) + uracil<BR />
+
 
-
**[[1mwj]], [[1mwi]], [[1mtl]] – EcUDG + DNA<BR />
+
*Uracil-DNA glycosylase complex with DNA
-
**[[1lqg]], [[1lqm]], [[1eui]], [[1uug]] - EcUDG + protein inhibitor<BR />
+
 
-
**[[2uug]] - EcUDG (mutant) + protein inhibitor<BR />
+
**[[1lau]] – HsvUDG + DNA <br />
-
**[[3uf7]] - EcUDG + single-stranded DNA-binding protein peptide<br />
+
**[[4skn]] – hUDG (mutant) + DNA<br />
-
**[[3ufm]] - DrUDG + single-stranded DNA-binding protein peptide<br />
+
**[[2oxm]] – hUDG + DNA<br />
-
**[[2c53]], [[2c56]] – HhUDG (mutant) – Human herpesvirus<BR />
+
**[[4uqm]] – DrUDG + DNA<br />
-
**[[1lau]] – HhUDG + DNA<BR />
+
**[[1ssp]], [[1q3f]] – hUDG + DNA + uracil<br />
-
**[[1udi]] - HsUDG + protein inhibitor<BR />
+
**[[1emh]] – hUDG + DNA + deoxy pseudo-UMP<br />
-
**[[3wdg]] – SaUDG + protein<br />
+
**[[2oyt]] – hUDG + DNA + abasic deoxyribose<br />
 +
**[[2ssp]] – hUDG (mutant) + DNA + abasic deoxyribose<br />
 +
**[[1emj]] – hUDG (mutant) + DNA + uracil + deoxyuridine analog<br />
 +
**[[4qcb]] – VvUDG (mutant) + DNA<br />
 +
**[[2ddg]], [[2dem]], [[2dp6]] – TtUDG + DNA + deoxyphosphono ribose<br />
 +
 
 +
*Uracil-DNA glycosylase complex with uracil derivatives
 +
 
 +
**[[5eug]], [[2eug]], [[1flz]] – EcUDG (mutant) + uracil<br />
 +
**[[1ui0]] – TtUDG + Fe4S4 + uracil <br />
 +
**[[4lzb]] – VvUDG (mutant) + uracil<br />
 +
**[[4zby]] – StUDG + uracil<br />
 +
**[[4wpl]], [[4wru]], [[4wrv]] – MtUDG + uracil<br />
 +
**[[4wry]], [[4wrz]], [[4ws0]], [[4ws1]], [[4ws2]], [[4ws3]], [[4ws4]], [[4ws5]], [[4ws6]], [[4ws7]], [[4ws8]] – MtUDG + uracil derivative<br />
 +
**[[2d3y]] – TtUDG + Fe4S4 + deoxy-UMP <br />
 +
**[[2c53]] – HsvUDG (mutant) + deoxyuridine<br />
 +
**[[3cxm]] – UDG + Br-uracil – ''Leishmania naiffi''<br />
 +
 
 +
*Uracil-DNA glycosylase other complexes
 +
 
 +
**[[2hxm]], [[3fcf]], [[3fci]], [[3fck]], [[3fcl]] – hUDG + inhibitor<br />
 +
**[[5jk7]] – hUDG + DNA damage-binding protein + VPRBP + VPR <br />
 +
**[[5ayr]], [[5ays]] – hUDG + protein<br />
 +
**[[3uf7]] – EcUDG + 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 />
-
**[[4l5n]] – HsUDG + p56 <br />
+
**[[4od8]], [[4oda]], [[4ygm]], [[5jkr]] – VvUDG + DNA polymerase processivity factor component A20 N terminal<br />
-
**[[4lyl]] - AcUDG + protein inhibitor<br />
+
**[[5jks]], [[5jkt]] – VvUDG (mutant) + DNA polymerase processivity factor component A20 N terminal<br />
-
**[[4od8]], [[4oda]] - VvUDG + DNA polymerase processivity factor<br />
+
**[[4yig]] – VvUDG + DNA polymerase processivity factor component A20 N terminal + DNA<br />
*Smug1 Uracil DG
*Smug1 Uracil DG
Line 92: Line 122:
**[[1oe4]], [[1oe5]], [[1oe6]] – UDG Smug1 + DNA– ''Xenopus laevis''
**[[1oe4]], [[1oe5]], [[1oe6]] – UDG Smug1 + DNA– ''Xenopus laevis''
-
*Thymine DG (G/T mismatch-specific thymine DG)
+
*Thymine DG
**[[2rba]] – hTDG core domain + DNA<BR />
**[[2rba]] – hTDG core domain + DNA<BR />
Line 98: Line 128:
**[[1kea]] – TDG – ''Methanothermobacter thermautotrophicus''<BR />
**[[1kea]] – TDG – ''Methanothermobacter thermautotrophicus''<BR />
**[[1mug]] – EcTDG
**[[1mug]] – EcTDG
-
**[[3uo7]], [[4jgc]] - hTDG + DNA + carboxylcytosine<br />
+
 
 +
*G/T mismatch-specific thymine DG
 +
 
 +
**[[3uo7]], [[4jgc]], [[5t2w]] - hTDG + DNA + carboxylcytosine<br />
**[[3uob]] - hTDG + DNA + fluoro-cytidine<br />
**[[3uob]] - hTDG + DNA + fluoro-cytidine<br />
**[[3ufj]] – hTDG core domain + DNA + fluoroluridine<br />
**[[3ufj]] – hTDG core domain + DNA + fluoroluridine<br />
-
**[[4fnc]] - hTDG + DNA + hydroxymethyluracil<br />
+
**[[4fnc]], [[5hf7]] - hTDG + DNA + uridine derivative <br />
 +
**[[5jxy]], [[4z3a]], [[4xeg]] - hTDG + DNA + G/U analog<br />
 +
**[[5ff8]], [[5cys]], [[4z7z]], [[4z7b]], [[4z47]] - hTDG + DNA + deoxyribose<br />
*Human 8-oxoguanine DG
*Human 8-oxoguanine DG

Revision as of 10:42, 23 April 2017

Structure of adenine DNA glycosylase containing Fe4S4 cluster complex with DNA containing an oxoG base, deoxy-ribofuranose phosphate and Ca+2 ion (green) (PDB code 1rrs).

Drag the structure with the mouse to rotate

3D Structures of DNA glycosylate

Updated on 23-April-2017

References

  1. ↑ Fromme JC, Banerjee A, Verdine GL. DNA glycosylase recognition and catalysis. Curr Opin Struct Biol. 2004 Feb;14(1):43-9. PMID:15102448 doi:http://dx.doi.org/10.1016/j.sbi.2004.01.003
  2. ↑ Willetts KE, Rey F, Agostini I, Navarro JM, Baudat Y, Vigne R, Sire J. DNA repair enzyme uracil DNA glycosylase is specifically incorporated into human immunodeficiency virus type 1 viral particles through a Vpr-independent mechanism. J Virol. 1999 Feb;73(2):1682-8. PMID:9882380
  3. ↑ Fromme JC, Banerjee A, Huang SJ, Verdine GL. Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature. 2004 Feb 12;427(6975):652-6. PMID:14961129 doi:10.1038/nature02306

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman, Jaime Prilusky

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