DNA glycosylase

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: Crystal Structure of DNA glycosylate, 1akz {{STRUCTURE_1akz| PDB=1akz | SIZE=300| SCENE=DNA_glycosylagte/Dna_glycosylate/3 |right|CAPTION=Human ur...)
Line 7: Line 7:
== 3D Structures of DNA glycosylate ==
== 3D Structures of DNA glycosylate ==
 +
 +
===Adenine DG===
 +
 +
[[3n5n]] – hADG catalytic domain – human<BR />
 +
[[1yuo]] - hADG catalytic domain (mutant) <BR />
 +
[[1x51]] – hADG NUDIX domain]] - NMR<BR />
 +
[[3fsp]], [[3fsq]] – GsADG + DNA– Geobacillus stearothermophilus<BR />
 +
[[3g0q]], [[1vrl]], [[1rrq]], [[1rrs]] - GsADG (mutant) + DNA – Bacillus stearothermophilus<BR />
 +
[[1wef]], [[1weg]], [[1kg4]], [[1kg5]], [[1kg6]], [[1kg7]], [[1kqj]] - EcADG catalytic domain (mutant)]] - Escherichia coli<BR />
 +
[[1kg2]], [[1kg3]], [[1muy]] - EcADG catalytic domain<BR />
 +
[[1mun]] - EcADG catalytic domain (mutant) <BR />
 +
[[1wei]], [[1mud]] - EcADG catalytic domain (mutant) + adenine
 +
 +
===Uracil DG===
 +
 +
[[3a7n]] – MtUDG – Mycobacterium tuberculosis<BR />
 +
[[2zhx]] – MtDG + protein inhibitor<BR />
 +
[[1akz]] - hUDG (mutant) <BR />
 +
[[2oxm]], [[2oyt]], [[1q3f]] – hUDG + DNA<BR />
 +
[[1ssp]], [[2ssp]] - hUDG + DNA+ uracil<BR />
 +
[[1emh]], [[1emj]], [[4skn]] – hUDG (mutant) + DNA<BR />
 +
[[3fcf]], [[3fci]], [[3fck]], [[3fcl]], [[2hxm]] – hUDG + inhibitor<BR />
 +
[[1ugh]] - hUDG (mutant) + protein inhibitor<BR />
 +
[[2jhq]] – UDG – Vibrio cholerae<BR />
 +
[[3cxm]] – UDG residues 129-373 + 5-bromo-uracil<BR />
 +
[[2owq]], [[2owr]] – UDG (mutant) – Vaccinia virus<BR />
 +
[[2d3y]], [[1ui0]], [[1ui1]] – TtUDG – Thermus thermophilus<BR />
 +
[[2dp6]], [[2dem]], [[2ddg]] – TtUDG + DNA<BR />
 +
[[2j8x]] – UDG glycosylase domain + protein inhibitor – Epstein-Barr virus<BR />
 +
[[1lqj]] – EcUDG<BR />
 +
[[1flz]] - EcUDG (mutant) <BR />
 +
[[2eug]], [[3eug]], [[1eug]], [[4eug]], [[5eug]] - EcUDG (mutant) + uracil<BR />
 +
[[1mwj]], [[1mwi]], [[1mtl]] – EcUDG + DNA<BR />
 +
[[1lqg]], [[1lqm]], [[1eui]], [[1uug]] - EcUDG + protein inhibitor<BR />
 +
[[2uug]] - EcUDG (mutant) + protein inhibitor<BR />
 +
[[2c53]], [[2c56]] – HhUDG (mutant) – Human herpesvirus<BR />
 +
[[1lau]] – HhUDG + DNA<BR />
 +
[[1udh]], [[1udg]] – HsUDG _ Herpes simplex virus<BR />
 +
[[1udi]] - HsUDG + protein inhibitor<BR />
 +
[[2c2p]], [[2boo]] – DrUDG – Deinococcus radiodurans<BR />
 +
[[2c2q]] – DrUDG (mutant) <BR />
 +
[[1vk2]], [[1l9g]] – TmUDG - Thermotoga maritime<BR />
 +
[[1okb]] – UDG catalytic domain – Atlantic cod
 +
 +
===Smug1 Uracil DG===
 +
 +
[[1oe4]], [[1oe5]], [[1oe6]] – UDG Smug1 + DNA– Xenopus laevis
 +
 +
===Thymine DG===
 +
 +
[[2rba]] – hTDG core domain + DNA<BR />
 +
[[2d07]], [[1wyw]] – hTDG central region + SUMO-3<BR />
 +
[[1kea]] – TDG – Methanothermobacter thermautotrophicus<BR />
 +
[[1mug]] – EcTDG
 +
 +
===Human 8-oxoguanine DG===
 +
 +
[[1ko9]] – hOgg1<BR />
 +
[[2xhi]], [[3ih7]], [[3ktu]], [[1hu0]], [[1fn7]] - 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 />
 +
[[1m3h]] - hOgg1 core fragment (mutant) + DNA<BR />
 +
[[1m3q]], [[1ebm]] - hOgg1 core fragment (mutant) + DNA + guanine derivative
 +
 +
===8-oxoguanine DG===
 +
 +
[[3n0u]] – TmOxDG<BR />
 +
[[3knt]] - MjOxDG (mutant) + DNA – Methanocaldococcus jannaschii<BR />
 +
[[3fhf]] - MjOxDG<BR />
 +
[[3go8]], [[3gp1]], [[3gpp]], [[3gpu]], [[3gpx]], [[3gpy]], [[3gq3]], [[3gq4]], [[3gq5]] – GsOxDG (mutant) + DNA<BR />
 +
[[3f0z]] - CaOxDG – Clostridium acetobutylicum<BR />
 +
[[3f10]] – CaOxDG + 8-oxoguanosine<BR />
 +
[[3i0w]], [[3i0x]] - CaOxDG (mutant) + DNA<BR />
 +
[[3fhg]] - OxDG (mutant) – Sulfolobus solfataricus<BR />
 +
[[1xqo]], [[1xqp]] – OxDG – Pyrobaculum aerophilum
 +
 +
===Methyladenine DG===
 +
 +
[[3qi5]], [[1ewn]], [[1f4r]], [[1f6o]], [[1bnk]] – hAlkDG + DNA<BR />
 +
[[3bvs]] – BcAlkDG – Bacillus cereus<BR />
 +
[[3jx7]], [[3jxy]], [[3jxz]], [[3jy1]] - BcAlkDG + DNA<BR />
 +
[[1pvs]], [[1p7m]], [[1mpg]] – EcAlkDG<BR />
 +
[[1nku]], [[1lmz]] – EcAlkDG]] - NMR<BR />
 +
[[3ogd]], [[3oh6]], [[3oh9]] - EcAlkDG (mutant) + DNA<BR />
 +
[[3d4v]], [[3cvs]], [[3cvt]], [[3cw7]], [[3cwa]], [[3cws]], [[3cwt]], [[3cwu]], [[1diz]] - EcAlkDG + DNA<BR />
 +
[[2ofk]] – StAlkDG – Salmonella typhi<BR />
 +
[[2ofi]] – StAlkDG + DNA<BR />
 +
[[2jhj]], [[2jhn]] – AlkDG – Archaeoglobus fulgidus<BR />
 +
[[2jg6]] – AlkDG – Staphylococcus aureus<BR />
 +
[[1pu6]] – HpAlkDG – Helicobacter pylori<BR />
 +
[[1pu7]], [[1pu8]] – HpAlkDG + adenine derivative
 +
 +
===Formamidopyrimidine DG===
 +
 +
[[3c58]], [[1xc8]], [[1tdz]], [[1pji]], [[1pm5]], [[1nnj]] - LlFpg+ DNA – Lactococcus lactis<BR />
 +
[[1pjj]], [[1kfv]] - LlFpg (mutant) + DNA<BR />
 +
[[1k82]] - EcFpg+ DNA<BR />
 +
[[3jr4]], [[3jr5]], [[2f5n]], [[2f5o]], [[2f5p]], [[2f5q]], [[2f5s]], [[1r2y]], [[1r2z]] – GsFpg (mutant) + DNA<BR />
 +
[[1l1t]], [[1l1z]], [[1l2b]], [[1l2c]], [[1l2d]] - GsFpg + DNA<BR />
 +
[[3a42]], [[3a45]], [[3a46]] – Fpg – Acanthamoeba polyphaga minivirus<BR />
 +
 +
[[2ea0]], [[2opf]], [[2oq4]] – EcGD NEI + DNA<BR />
 +
[[2fcc]] – Pyrimidine GD + DNA – Enterobacteria phage T4

Revision as of 10:15, 17 April 2011

Image:1akz.png
Crystal Structure of DNA glycosylate, 1akz

Template:STRUCTURE 1akz

DNA glycosylase (DG) are enzymes which remove damaged DNA bases by flipping them out of the double helix followed by their cleavage. Monofunctional DG have only glycosylase activity; bifunctional DG also act as lysates; ADG, UDG, TDG remove adenine, uracil, thymine from DNA. ADG is also called MutY. Smug1 is a single-strand selective monofunctional UDG. OxDG recognize oxidized bases. The human 8-oxoguanine GD is named hOgg1. AlkDG recognize methylated adenine. Formamidopyrimidine DG (FPG) or MutM removes oxidized purines from damaged DNA.

Contents

3D Structures of DNA glycosylate

Adenine DG

3n5n – hADG catalytic domain – human
1yuo - hADG catalytic domain (mutant)
1x51 – hADG NUDIX domain]] - NMR
3fsp, 3fsq – GsADG + DNA– Geobacillus stearothermophilus
3g0q, 1vrl, 1rrq, 1rrs - GsADG (mutant) + DNA – Bacillus stearothermophilus
1wef, 1weg, 1kg4, 1kg5, 1kg6, 1kg7, 1kqj - EcADG catalytic domain (mutant)]] - Escherichia coli
1kg2, 1kg3, 1muy - EcADG catalytic domain
1mun - EcADG catalytic domain (mutant)
1wei, 1mud - EcADG catalytic domain (mutant) + adenine

Uracil DG

3a7n – MtUDG – Mycobacterium tuberculosis
2zhx – MtDG + protein inhibitor
1akz - hUDG (mutant)
2oxm, 2oyt, 1q3f – hUDG + DNA
1ssp, 2ssp - hUDG + DNA+ uracil
1emh, 1emj, 4skn – hUDG (mutant) + DNA
3fcf, 3fci, 3fck, 3fcl, 2hxm – hUDG + inhibitor
1ugh - hUDG (mutant) + protein inhibitor
2jhq – UDG – Vibrio cholerae
3cxm – UDG residues 129-373 + 5-bromo-uracil
2owq, 2owr – UDG (mutant) – Vaccinia virus
2d3y, 1ui0, 1ui1 – TtUDG – Thermus thermophilus
2dp6, 2dem, 2ddg – TtUDG + DNA
2j8x – UDG glycosylase domain + protein inhibitor – Epstein-Barr virus
1lqj – EcUDG
1flz - EcUDG (mutant)
2eug, 3eug, 1eug, 4eug, 5eug - EcUDG (mutant) + uracil
1mwj, 1mwi, 1mtl – EcUDG + DNA
1lqg, 1lqm, 1eui, 1uug - EcUDG + protein inhibitor
2uug - EcUDG (mutant) + protein inhibitor
2c53, 2c56 – HhUDG (mutant) – Human herpesvirus
1lau – HhUDG + DNA
1udh, 1udg – HsUDG _ Herpes simplex virus
1udi - HsUDG + protein inhibitor
2c2p, 2boo – DrUDG – Deinococcus radiodurans
2c2q – DrUDG (mutant)
1vk2, 1l9g – TmUDG - Thermotoga maritime
1okb – UDG catalytic domain – Atlantic cod

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

Human 8-oxoguanine DG

1ko9 – hOgg1
2xhi, 3ih7, 3ktu, 1hu0, 1fn7 - hOgg1 + DNA
1lwv, 1lww, 1lwy - hOgg1 + DNA
+ guanine derivative
2nob, 2noe, 2nof, 2noh, 2noi, 2nol, 2noz, 2i5w, 1yqk, 1yql, 1yqm, 1yqr, 1n39, 1n3a, 1n3c - hOgg1 (mutant) + DNA
1m3h - hOgg1 core fragment (mutant) + DNA
1m3q, 1ebm - hOgg1 core fragment (mutant) + DNA + guanine derivative

8-oxoguanine DG

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 + 8-oxoguanosine
3i0w, 3i0x - CaOxDG (mutant) + DNA
3fhg - OxDG (mutant) – Sulfolobus solfataricus
1xqo, 1xqp – OxDG – Pyrobaculum aerophilum

Methyladenine DG

3qi5, 1ewn, 1f4r, 1f6o, 1bnk – hAlkDG + DNA
3bvs – BcAlkDG – Bacillus cereus
3jx7, 3jxy, 3jxz, 3jy1 - BcAlkDG + DNA
1pvs, 1p7m, 1mpg – EcAlkDG
1nku, 1lmz – EcAlkDG]] - NMR
3ogd, 3oh6, 3oh9 - EcAlkDG (mutant) + DNA
3d4v, 3cvs, 3cvt, 3cw7, 3cwa, 3cws, 3cwt, 3cwu, 1diz - EcAlkDG + DNA
2ofk – StAlkDG – Salmonella typhi
2ofi – StAlkDG + DNA
2jhj, 2jhn – AlkDG – Archaeoglobus fulgidus
2jg6 – AlkDG – Staphylococcus aureus
1pu6 – HpAlkDG – Helicobacter pylori
1pu7, 1pu8 – HpAlkDG + adenine derivative

Formamidopyrimidine DG

3c58, 1xc8, 1tdz, 1pji, 1pm5, 1nnj - LlFpg+ DNA – Lactococcus lactis
1pjj, 1kfv - LlFpg (mutant) + DNA
1k82 - EcFpg+ DNA
3jr4, 3jr5, 2f5n, 2f5o, 2f5p, 2f5q, 2f5s, 1r2y, 1r2z – GsFpg (mutant) + DNA
1l1t, 1l1z, 1l2b, 1l2c, 1l2d - GsFpg + DNA
3a42, 3a45, 3a46 – Fpg – Acanthamoeba polyphaga minivirus

2ea0, 2opf, 2oq4 – EcGD NEI + DNA
2fcc – Pyrimidine GD + DNA – Enterobacteria phage T4

Proteopedia Page Contributors and Editors (what is this?)

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

Retrieved from "http://52.214.119.220/wiki/index.php/DNA_glycosylase"
Personal tools