DNA glycosylase

From Proteopedia

Revision as of 08:39, 10 August 2014

Template:STRUCTURE 3fsp

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.

• Adenine DNA glycosylase is also called MutY.
  
• Smug1 is a single-strand selective monofunctional UDG.
  
• 8-oxoguanine DNA glycosylase recognize oxidized bases.
  
• Human 8-oxoguanine GD is named hOgg1. See details on Ogg1 in 8-Oxoguanine Glycosylase.
  
• AlkDG recognize methylated adenine; for details see Alka1.
  
• Formamidopyrimidine DG (FPG) or MutM removes oxidized purines from damaged DNA. More about FPG in
  
• Fpg Nei Protein Family
  
• Fpg Nei Protein Superfamily.

3D Structures of DNA glycosylate

Updated on 10-August-2014

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, 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, 3ih7 - hOgg1 core fragment (mutant) + DNA
1m3q, 1ebm - hOgg1 core fragment (mutant) + DNA + guanine derivative

8-oxoguanine (oxoG) 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 + oxoG
3i0w, 3i0x - CaOxDG (mutant) + DNA
3fhg - OxDG (mutant) – Sulfolobus solfataricus
1xqo, 1xqp – OxDG – Pyrobaculum aerophilum
4ejy, 4ejz – OxDG + DNA – Thermoanaerobacter tengcongensis

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

1ee8 – TtFpg
3a42, 3a45 – ApFpg – Acanthamoeba polyphaga minivirus
3twk, 3twl – AtFpg - Arabidopsis thaliana

Fpg complex with DNA

1k82 – EcFpg + DNA
1kfv, 1nnj – LlFpg (mutant) + DNA – Lactococcus lactis
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
3twm – AtFpg + DNA containing abasic dideoxyribose
1pji – LlFpg + DNA containing 1,3-propanediol
2xzf, 2xzu – LlFpg + DNA containing oxidized pyrimidine
1tdz, 1xc8, 3c58 – LlFpg + DNA containing Fapy-dG derivative
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 <br /

DNA glycosylase NEI

2ea0, 2opf, 2oq4, 1k3w, 1k3x – EcGD NEI + DNA
2fcc – Pyrimidine GD + DNA – Enterobacteria phage T4
1q39 – EcGD NEI
1q3b, 1q3c – EcGD NEI (mutant)
1tdh – hGD NEI