DNA methyltransferase 3D structures

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**[[1eh8]] - hO6-methylguanine DNMT benzylated<br />
**[[1eh8]] - hO6-methylguanine DNMT benzylated<br />
**[[1mgt]] - O6-methylguanine DNMT – ''Thermococcus kodakarensis''<br />
**[[1mgt]] - O6-methylguanine DNMT – ''Thermococcus kodakarensis''<br />
-
**[[1wrj]] - O6-methylguanine DNMT - ''Sulfolobus tokodaii''
+
**[[1wrj]], [[7dkn]] - O6-methylguanine DNMT - ''Sulfolobus tokodaii''<br />
-
 
+
**[[7csm]], [[7d4v]], [[7dqr]], [[7dqt]] - StO6-methylguanine DNMT (mutant) <br />
 +
**[[7e1p]] - StO6-methylguanine DNMT (mutant) + purine derivative<br />
 +
**[[7dqq]] - StO6-methylguanine DNMT (mutant) + methyldeoxyguanosine<br />
**[[2g7h]] - O6-methylguanine DNMT – ''Methanocaldococcus jannaschii''
**[[2g7h]] - O6-methylguanine DNMT – ''Methanocaldococcus jannaschii''
- 
**[[2kif]], [[2kim]] - O6-methylguanine DNMT – ''Vibrio parahaemolyticus'' - NMR<br />
**[[2kif]], [[2kim]] - O6-methylguanine DNMT – ''Vibrio parahaemolyticus'' - NMR<br />
**[[4bhb]], [[4bhc]], [[4wxd]], [[4wxc]] - MtO6-methylguanine DNMT (mutant) – ''Mycobacterium tuberculosis''<br />
**[[4bhb]], [[4bhc]], [[4wxd]], [[4wxc]] - MtO6-methylguanine DNMT (mutant) – ''Mycobacterium tuberculosis''<br />
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**[[1sfe]] – O6-methylguanine DNMT C terminal – ''Escherichia coli''<br />
**[[1sfe]] – O6-methylguanine DNMT C terminal – ''Escherichia coli''<br />
-
*Methylcytosine DNMT; Domains – RFTS 351-599; ADD 476-611; PWWP 206-355
+
*Methylcytosine DNMT; Domains – N-terminal 16-93; RFTS 351-599; ADD 476-611; PWWP 206-355; methyltransferase 628-912
-
**[[3epz]] - h-cytosine DNMT 1 replication foci-targeting sequence
+
**[[8v9u]] - h-cytosine DNMT 1 N-terminal domain - NMR<br />
-
**[[4yoc]] - h-cytosine DNMT 1 residues 600-1600 + ubiquitin carboxyl-terminal hydrolase 7<br />
+
**[[3epz]] - h-cytosine DNMT 1 RFTS domain<br />
-
**[[4z97]], [[4z96]] - h-cytosine DNMT 1 residues 1097-1129 + ubiquitin carboxyl-terminal hydrolase 7<br />
+
**[[1g55]] - h-cytosine DNMT 2 (mutant) <br />
-
**[[5ydr]] - h-cytosine DNMT 1 RFTS domain residues 351-599 + ubiquitin<br />
+
-
**[[5wvo]] - h-cytosine DNMT 1 RFTS domain + ubiquitin + histone H3.1<br />
+
-
**[[4wxx]] - h-cytosine DNMT 1 residues 351-1600 + SAH<br />
+
-
**[[1g55]] - h-cytosine DNMT 2 (mutant)<br />
+
**[[2qrv]] - h-cytosine DNMT 3A C-terminal domain<br />
**[[2qrv]] - h-cytosine DNMT 3A C-terminal domain<br />
-
**[[3a1a]] - h-cytosine DNMT 3A ADD domain<br />
+
**[[3a1a]], [[8ba5]] - h-cytosine DNMT 3A ADD domain<br />
-
**[[3a1b]], [[4qbq]] - h-cytosine DNMT 3A ADD domain + histone H3<br />
+
**[[8tdr]] - h-cytosine DNMT 3A methyltransferase domain<br />
-
**[[4qbr]], [[4qbs]] - h-cytosine DNMT 3A ADD domain (mutant) + histone H3<br />
+
**[[8te1]], [[8te3]], [[8te4]] - h-cytosine DNMT 3A methyltransferase domain (mutant)<br />
-
**[[4u7p]] - h-cytosine DNMT 3A residues 455-912 + h-cytosine DNMT 3-like residues 178-379 + SAH<br />
+
**[[7v0e]] - h-cytosine DNMT 3B methyltransferase domain<br />
-
**[[6pa7]] - h-cytosine DNMT 3A residues 224-912 + h-cytosine DNMT 3B residues 1-770 + SAH + histones + DNA – Cryo EM<br />
+
**[[7o45]] - h-cytosine DNMT 3B ADD domain<br />
-
**[[4u7t]] - h-cytosine DNMT 3A residues 455-912 + h-cytosine DNMT 3-like residues 178-379 + histone 3.3 + SAH<br />
+
**[[3flg]], [[8zlk]], - h-cytosine DNMT 3B PWWP domain<br />
-
**[[6w89]], [[6w8b]], [[6w8d]], [[6w6j]] - h-cytosine DNMT 3A residues 628-912 + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor<br />
+
-
**[[6f57]], [[5yx2]], [[6brr]] - h-cytosine DNMT 3A residues 628-912 + h-cytosine DNMT 3-like residues 178-379 + DNA + SAH + pyrimidine derivative<br />
+
-
**[[3flg]] - h-cytosine DNMT 3B PWWP domain<br />
+
-
**[[6r3e]] - h-cytosine DNMT 3B PWWP domain + inhibitor<br />
+
**[[3qkj]] - h-cytosine DNMT 3B residues 293-442<br />
**[[3qkj]] - h-cytosine DNMT 3B residues 293-442<br />
-
**[[5nvo]] - h-cytosine DNMT 3B PWWP domain + choline<br />
+
**[[3av4]], [[1khc]] - m-cytosine DNMT residues 291-1620 – mouse<br />
-
**[[5nv7]], [[5nv2]], [[5nv0]], [[5nrv]], [[5nrs]], [[5nrr]], [[5nr3]] - h-cytosine DNMT 3B PWWP domain + inhibitor<br />
+
-
**[[5ciu]] - h-cytosine DNMT 3B residues 206-355 + histone H3.2<br />
+
-
**[[6u8p]], [[6u8v]], [[6u8w]], [[6u8x]], [[6u90]], [[6u91]] - h-cytosine DNMT 3B residues 563-853 + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor<br />
+
-
**[[3swr]] - h-cytosine DNMT + sinefungin<br />
+
-
**[[6pzv]] - cytosine DNMT 1 RFTS domain + histone H3.3 + ubiquitin - bovine<br />
+
-
**[[3av4]], [[1khc]] - m-cytosine DNMT – mouse<br />
+
**[[5wy1]] - m-cytosine DNMT (mutant) <br />
**[[5wy1]] - m-cytosine DNMT (mutant) <br />
**[[5guv]], [[5gut]] - m-cytosine DNMT residues 731-1600 (mutant) <br />
**[[5guv]], [[5gut]] - m-cytosine DNMT residues 731-1600 (mutant) <br />
-
**[[6w8v]], [[6w8w]] - m-cytosine DNMT1 residues 731-1600 + SAH + CMP derivative<br />
+
**[[1boo]] - cytosine DNMT (mutant) – ''Proteus vulgaris''<br />
-
**[[3pt6]], [[3pt9]], [[4da4]] – m-cytosine DNMT residues 650-1602 + DNA
+
**[[1svu]] - Hh-cytosine DNMT (mutant) - ''Haemophilus haemolyticus''<br />
-
+
**[[4h0n]] - cytosine DNMT (mutant) – ''Spodoptera frugiperda''<br />
-
**[[3av5]] - m-cytosine DNMT + SAH residues 291-1620
+
-
**[[3av6]] - m-cytosine DNMT + SAM residues 291-1620
+
*Methylcytosine DNMT complex with DNA
-
**[[4fsx]] – c-cytosine DNMT + SAH – corn<br />
+
**[[6pa7]] - h-cytosine DNMT 3A residues 224-912 + h-cytosine DNMT 3B residues 1-770 + SAH + histones + DNA – Cryo EM<br />
-
**[[4ft2]], [[4ft4]] – c-cytosine DNMT + histone H3 peptide<br />
+
**[[6w89]], [[6w8b]], [[6w8d]], [[6w8j]] - h-cytosine DNMT 3A residues 628-912 (mutant) + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor<br />
-
**[[6fdf]] - cytosine DNMT2 + SAH – fission yeast<br/>
+
**[[6f57]], [[5yx2]] - h-cytosine DNMT 3A residues 628-912 + h-cytosine DNMT 3L residues 178-379 + DNA + SAH + pyrimidine derivative<br />
-
**[[1boo]] - cytosine DNMT (mutant) – ''Proteus vulgaris''<br />
+
**[[6brr]] - h-cytosine DNMT 3A residues 439-723 + h-cytosine DNMT 3L residues 178-379 + DNA + SAH + pyrimidine derivative<br />
-
**[[3qv2]] - cytosine DNMT + SAH – ''Entamoeba histolytica''<br />
+
**[[6w8b]] - h-cytosine DNMT 3A residues 628-912 + h-cytosine DNMT 3L residues 178-379 + DNA + SAH<br />
-
**[[2uyc]], [[2uyh]], [[2uz4]], [[1fjx]] – Hh-cytosine DNMT (mutant) + DNA + SAH - ''Haemophilus haemolyticus''<br />
+
**[[6kda]], [[6kdb]], [[6kdl]] - h-cytosine DNMT 3B residues 563-853 + h-cytosine DNMT 3L residues 178-386 + DNA + SAH <br />
-
**[[2c7o]], [[2c7p]], [[2c7q]], [[2c7r]], [[3pta]] – Hh-cytosine DNMT + DNA + S-adenonosyl cysteine<br />
+
**[[6u8p]], [[6u8v]], [[6u8x]] - h-cytosine DNMT 3B residues 563-853 + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor<br />
-
**[[1hmy]] – Hh-cytosine Haeiii DNMT + SAM
+
**[[6u8w]], [[6u90]], [[6u91]] - h-cytosine DNMT 3B residues 563-853 (mutant) + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor<br />
 +
**[[6w8v]], [[6w8w]] - m-cytosine DNMT1 residues 731-1600 + SAH + DNA<br />
 +
**[[3pt6]], [[3pt9]], [[4da4]] – m-cytosine DNMT residues 650-1602 + DNA<br />
 +
**[[2uyc]], [[2uyh]], [[2uz4]], [[1fjx]] – Hh-cytosine DNMT (mutant) + DNA + SAH<br />
 +
**[[2c7o]], [[2c7p]], [[2c7q]], [[2c7r]], [[3pta]], [[4da4]] – Hh-cytosine DNMT + DNA + SAH<br />
 +
**[[1m0e]] - Hh-cytosine DNMT (mutant) + DNA + inhibitor<br />
 +
**[[2i9k]] – Hh-cytosine DNMT (mutant) + DNA<br />
 +
**[[2hr1]] - Hh-cytosine DNMT + DNA + ADOHCY<br />
 +
**[[2z6q]], [[2z6u]], [[2zcj]] - Hh-cytosine DNMT (mutant) + DNA + ADOHCY<br />
-
**[[1m0e]] - Hh-cytosine DNMT (mutant) + DNA + inhibitor
+
*Methylcytosine DNMT complex with protein
-
**[[2i9k]] - Hh-cytosine DNMT (mutant) + DNA
+
**[[4yoc]] - h-cytosine DNMT 1 residues 600-1600 + ubiquitin carboxyl-terminal hydrolase 7<br />
 +
**[[4z97]], [[4z96]] - h-cytosine DNMT 1 residues 1097-1129 + ubiquitin carboxyl-terminal hydrolase 7<br />
 +
**[[5ydr]] - h-cytosine DNMT 1 RFTS domain + ubiquitin<br />
 +
**[[5wvo]] - h-cytosine DNMT 1 RFTS domain + ubiquitin + histone H3.1<br />
 +
**[[8xqc]] - h-cytosine DNMT 1 351-1616 + ubiquitin + PAF15 + DNA – Cryo EM<br />
 +
**[[7xi9]] – hDNMT 1 351-1600 + H3 – Cryo EM <BR />
 +
**[[3a1b]], [[4qbq]] - h-cytosine DNMT 3A ADD domain + histone H3
 +
**[[4qbr]], [[4qbs]] - h-cytosine DNMT 3A ADD domain (mutant) + histone H3<br />
 +
**[[4u7t]] - h-cytosine DNMT 3A residues 455-912 + h-cytosine DNMT 3L residues 178-379 + histone 3.3 peptide + SAH<br />
 +
**[[8uw1]] - h-cytosine DNMT 3A residues 159-228 in nucleosome – Cryo EM<br />
 +
**[[5ciu]], [[5ciy]] - h-cytosine DNMT 3B PWWP domain + histone H3.2<br />
 +
**[[6pzv]] – b-cytosine DNMT 1 RFTS domain + histone H3.3 + ubiquitin - bovine<br />
 +
**[[7lmk]], [[7lmm]] – b-cytosine DNMT 1 BAH1 domain + histone H4 <br />
 +
**[[4ft2]], [[4ft4]] – c-cytosine DNMT + histone H3 peptide – corn<br />
-
**[[2hr1]] - Hh-cytosine DNMT + DNA + ADOHCY
+
*Methylcytosine DNMT complex with small molecule
-
**[[2z6q]], [[2z6u]], [[2zcj]] - Hh-cytosine DNMT (mutant) + DNA + ADOHCY
+
**[[4wxx]] - h-cytosine DNMT 1 residues 351-1600 + SAH<br />
-
 
+
**[[7sfc]], [[7sfd]], [[7sfe]], [[7sff]], [[7sfg]] – hDNMT 1 729-1600 + DNA + CMP + pyrimidine derivative + SAM <BR />
-
**[[1svu]] - Hh-cytosine DNMT (mutant)<br />
+
**[[6x9j]], [[6x9k]], [[6x9i]] – hDNMT 1 729-1600 + DNA + CMP + pyrimidine derivative + SAH <BR />
-
**[[4h0n]] - cytosine DNMT (mutant) – ''Spodoptera frugiperda''<br/>
+
**[[7xi9]] – hDNMT 1 351-1600 + H3 – Cryo EM <BR />
 +
**[[4u7p]] - h-cytosine DNMT 3A residues 455-912 + h-cytosine DNMT 3L residues 178-379 + SAH<br />
 +
**[[5nvo]] - h-cytosine DNMT 3B PWWP domain + choline<br />
 +
**[[5nv7]], [[5nv2]], [[5nv0]], [[5nrv]], [[5nrs]], [[5nrr]], [[5nr3]], [[6r3e]] - h-cytosine DNMT 3B PWWP domain + inhibitor<br />
 +
**[[6kdp]] - h-cytosine DNMT 3B residues 563-853 + h-cytosine DNMT 3L residues 178-386 + SAH <br />
 +
**[[6kdt]] - h-cytosine DNMT 3B residues 563-853 (mutant) + h-cytosine DNMT 3L residues 178-386 + SAH <br />
 +
**[[8eih]], [[8eii]], [[8eij]], [[8eik]] - h-cytosine DNMT 3B residues 206-853 + SAH – Cryo EM<br />
 +
**[[7x9d]] - h-cytosine DNMT 3B residues 571-853 + harmine<br />
 +
**[[8xee]] - h-cytosine DNMT 3B residues 571-853 (mutant) + SAH<br />
 +
**[[3swr]] - h-cytosine DNMT + sinefungin<br />
 +
**[[6w8v]], [[6w8w]] - m-cytosine DNMT1 residues 731-1600 + SAH + CMP derivative<br />
 +
**[[3av5]] - m-cytosine DNMT residues 291-1620 + SAH<br />
 +
**[[3av6]] - m-cytosine DNMT residues 650-1620 + SAM<br />
 +
**[[4fsx]] – c-cytosine DNMT + SAH <br />
 +
**[[3qv2]] - cytosine DNMT + SAH – ''Entamoeba histolytica<''br />
 +
**[[1hmy]] – HhHaeiii DNMT + SAM<br />
*Methyladenine DNMT
*Methyladenine DNMT
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**[[6khs]] – hN6AMT1 + TRMT112 + SAH + methylGln<br />
**[[6khs]] – hN6AMT1 + TRMT112 + SAH + methylGln<br />
**[[1nw5]] – RsN6-adenine DNMT + SAM – ''Rhodobacter sphaeroides''
**[[1nw5]] – RsN6-adenine DNMT + SAM – ''Rhodobacter sphaeroides''
- 
**[[1nw6]] - RsN6-adenine DNMT + sinefungin<br />
**[[1nw6]] - RsN6-adenine DNMT + sinefungin<br />
**[[1nw7]] - RsN6-adenine DNMT + SAH<br />
**[[1nw7]] - RsN6-adenine DNMT + SAH<br />
**[[1nw8]] - RsN6-adenine DNMT (mutant)<br />
**[[1nw8]] - RsN6-adenine DNMT (mutant)<br />
**[[5hek]] - HpN6-adenine DNMT – ''Helicobacter pylori''<br />
**[[5hek]] - HpN6-adenine DNMT – ''Helicobacter pylori''<br />
-
**[[5hfj]] - HpN6-adenine DNMT + SAM<br />
+
**[[5hfj]], [[6k0x]] - HpN6-adenine DNMT + sinefungin<br />
-
**[[6k0w]] - HpN6-adenine DNMT + sinefungin<br />
+
**[[2ibs]], [[2ibt]], [[2ih2]], [[2ih4]], [[2ih5]], [[2np6]], [[2np7]], [[1g38]] - Ta-adenine DNMT Taqi + DNA + cofactor analog – ''Thermus aquaticus''<br />
**[[2ibs]], [[2ibt]], [[2ih2]], [[2ih4]], [[2ih5]], [[2np6]], [[2np7]], [[1g38]] - Ta-adenine DNMT Taqi + DNA + cofactor analog – ''Thermus aquaticus''<br />
**[[1aqi]] – Ta-adenine DNMT Taqi + SAH<br />
**[[1aqi]] – Ta-adenine DNMT Taqi + SAH<br />
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**[[4rtm]], [[4rtp]], [[4rtr]], [[4rts]] - Ec-adenine DNMT + DNA + AdoMet<br />
**[[4rtm]], [[4rtp]], [[4rtr]], [[4rts]] - Ec-adenine DNMT + DNA + AdoMet<br />
**[[4rtn]], [[4rtq]] - Ec-adenine DNMT + DNA + AdoHcy<br />
**[[4rtn]], [[4rtq]] - Ec-adenine DNMT + DNA + AdoHcy<br />
 +
**[[7m6b]] - adenine DNMT + SAM + SAH – ''Caldicellulosiraptor bescii''<br />
 +
**[[7lni]], [[7lnj]] – Cd-adenine DNMT + DNA – ''Clostridioides difficile''<br />
 +
**[[7lnj]], [[7lt5]] – Cd-adenine DNMT + DNA + SAH<br />
 +
**[[7rfk]], [[7rfl]], [[7rfm]], [[7rfn]], [[8cy2]], [[8fs1]], [[8fs2]] – Cd-adenine DNMT + DNA + inhibitor<br />
 +
**[[8cxs]], [[8cxt]], [[8cxu]], [[8cxv]], [[8cxw]], [[8cxx]], [[8cxy]], [[8cxz]], [[8cy0]], [[8cy1]], [[8cy2j]], [[8cy3]], [[8cy4]], [[8cy5]] – Cd-adenine DNMT + DNA + inhibitor<br />
 +
**[[7lo5]], [[7lvv]] - adenine DNMT + DNA + SAM – ''Deinococcus wulumuquiensis'' – Cryo EM<br />
 +
**[[7qw5]], [[7qw6]], [[7qw7]], [[7qw8]] – adenine DNMT + DNA + SAH – ''Geobacillus stearothermophilus''<br />
 +
**[[7vru]], [[7vs4]] – adenine DNMT + DNA + AMP + SAH – ''Pseudomonas alcaligenes''<br />
 +
**[[8q56]] – adenine DNMT + OCR + SAM – ''Salmonella enterica'' <br />
*HhaI DNA methyltransferase
*HhaI DNA methyltransferase
 +
**[[5lod]] – HhHDMT <BR />
**[[1fjx]], [[2hmy]] – HhHDMT + SAM – ''Haemophilus haemolyticus'' <BR />
**[[1fjx]], [[2hmy]] – HhHDMT + SAM – ''Haemophilus haemolyticus'' <BR />
**[[1svu]] – HhHDMT (mutant) + SAH <BR />
**[[1svu]] – HhHDMT (mutant) + SAH <BR />

Current revision

3D Structures of DNA methyltransferase

Updated on 20-April-2025

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel

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