DNA methyltransferase 3D structures

3D Structures of DNA methyltransferase

Updated on 20-April-2025

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• Methylguanine DNMT
  • 1qnt, 1eh6, 3llr - hO6-methylguanine DNMT – human
  • 1t38 - hO6-methylguanine DNMT (mutant) + DNA
  • 1t39, 1yfh - hO6-methylguanine DNMT + DNA
  • 1eh7 - hO6-methylguanine DNMT methylated
  • 1eh8 - hO6-methylguanine DNMT benzylated
    
  • 1mgt - O6-methylguanine DNMT – Thermococcus kodakarensis
    
  • 1wrj, 7dkn - O6-methylguanine DNMT - Sulfolobus tokodaii
    
  • 7csm, 7d4v, 7dqr, 7dqt - StO6-methylguanine DNMT (mutant)
    
  • 7e1p - StO6-methylguanine DNMT (mutant) + purine derivative
    
  • 7dqq - StO6-methylguanine DNMT (mutant) + methyldeoxyguanosine
    
  • 2g7h - O6-methylguanine DNMT – Methanocaldococcus jannaschii
  • 2kif, 2kim - O6-methylguanine DNMT – Vibrio parahaemolyticus - NMR
    
  • 4bhb, 4bhc, 4wxd, 4wxc - MtO6-methylguanine DNMT (mutant) – Mycobacterium tuberculosis
    
  • 4wx9 - MtO6-methylguanine DNMT (mutant) + modified DNA
    
  • 4zyg, 4zye, 6ga0 - SsO6-methylguanine DNMT – Sulfolobus solfataricus
    
  • 5llq, 4zyh - SsO6-methylguanine DNMT (mutant)
    
  • 4zyd - SsO6-methylguanine DNMT (mutant) + modified DNA
    
  • 1sfe – O6-methylguanine DNMT C terminal – Escherichia coli
    
• Methylcytosine DNMT; Domains – N-terminal 16-93; RFTS 351-599; ADD 476-611; PWWP 206-355; methyltransferase 628-912
  • 8v9u - h-cytosine DNMT 1 N-terminal domain - NMR
    
  • 3epz - h-cytosine DNMT 1 RFTS domain
    
  • 1g55 - h-cytosine DNMT 2 (mutant)
    
  • 2qrv - h-cytosine DNMT 3A C-terminal domain
    
  • 3a1a, 8ba5 - h-cytosine DNMT 3A ADD domain
    
  • 8tdr - h-cytosine DNMT 3A methyltransferase domain
    
  • 8te1, 8te3, 8te4 - h-cytosine DNMT 3A methyltransferase domain (mutant)
    
  • 7v0e - h-cytosine DNMT 3B methyltransferase domain
    
  • 7o45 - h-cytosine DNMT 3B ADD domain
    
  • 3flg, 8zlk, - h-cytosine DNMT 3B PWWP domain
    
  • 3qkj - h-cytosine DNMT 3B residues 293-442
    
  • 3av4, 1khc - m-cytosine DNMT residues 291-1620 – mouse
    
  • 5wy1 - m-cytosine DNMT (mutant)
    
  • 5guv, 5gut - m-cytosine DNMT residues 731-1600 (mutant)
    
  • 1boo - cytosine DNMT (mutant) – Proteus vulgaris
    
  • 1svu - Hh-cytosine DNMT (mutant) - Haemophilus haemolyticus
    
  • 4h0n - cytosine DNMT (mutant) – Spodoptera frugiperda
    
• Methylcytosine DNMT complex with DNA
  • 6pa7 - h-cytosine DNMT 3A residues 224-912 + h-cytosine DNMT 3B residues 1-770 + SAH + histones + DNA – Cryo EM
    
  • 6w89, 6w8b, 6w8d, 6w8j - h-cytosine DNMT 3A residues 628-912 (mutant) + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor
    
  • 6f57, 5yx2 - h-cytosine DNMT 3A residues 628-912 + h-cytosine DNMT 3L residues 178-379 + DNA + SAH + pyrimidine derivative
    
  • 6brr - h-cytosine DNMT 3A residues 439-723 + h-cytosine DNMT 3L residues 178-379 + DNA + SAH + pyrimidine derivative
    
  • 6w8b - h-cytosine DNMT 3A residues 628-912 + h-cytosine DNMT 3L residues 178-379 + DNA + SAH
    
  • 6kda, 6kdb, 6kdl - h-cytosine DNMT 3B residues 563-853 + h-cytosine DNMT 3L residues 178-386 + DNA + SAH
    
  • 6u8p, 6u8v, 6u8x - h-cytosine DNMT 3B residues 563-853 + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor
    
  • 6u8w, 6u90, 6u91 - h-cytosine DNMT 3B residues 563-853 (mutant) + h-cytosine DNMT 3L residues 178-386 + DNA + SAH + inhibitor
    
  • 6w8v, 6w8w - m-cytosine DNMT1 residues 731-1600 + SAH + DNA
    
  • 3pt6, 3pt9, 4da4 – m-cytosine DNMT residues 650-1602 + DNA
    
  • 2uyc, 2uyh, 2uz4, 1fjx – Hh-cytosine DNMT (mutant) + DNA + SAH
    
  • 2c7o, 2c7p, 2c7q, 2c7r, 3pta, 4da4 – Hh-cytosine DNMT + DNA + SAH
    
  • 1m0e - Hh-cytosine DNMT (mutant) + DNA + inhibitor
    
  • 2i9k – Hh-cytosine DNMT (mutant) + DNA
    
  • 2hr1 - Hh-cytosine DNMT + DNA + ADOHCY
    
  • 2z6q, 2z6u, 2zcj - Hh-cytosine DNMT (mutant) + DNA + ADOHCY
    
• Methylcytosine DNMT complex with protein
  • 4yoc - h-cytosine DNMT 1 residues 600-1600 + ubiquitin carboxyl-terminal hydrolase 7
    
  • 4z97, 4z96 - h-cytosine DNMT 1 residues 1097-1129 + ubiquitin carboxyl-terminal hydrolase 7
    
  • 5ydr - h-cytosine DNMT 1 RFTS domain + ubiquitin
    
  • 5wvo - h-cytosine DNMT 1 RFTS domain + ubiquitin + histone H3.1
    
  • 8xqc - h-cytosine DNMT 1 351-1616 + ubiquitin + PAF15 + DNA – Cryo EM
    
  • 7xi9 – hDNMT 1 351-1600 + H3 – Cryo EM
    
  • 3a1b, 4qbq - h-cytosine DNMT 3A ADD domain + histone H3
  • 4qbr, 4qbs - h-cytosine DNMT 3A ADD domain (mutant) + histone H3
    
  • 4u7t - h-cytosine DNMT 3A residues 455-912 + h-cytosine DNMT 3L residues 178-379 + histone 3.3 peptide + SAH
    
  • 8uw1 - h-cytosine DNMT 3A residues 159-228 in nucleosome – Cryo EM
    
  • 5ciu, 5ciy - h-cytosine DNMT 3B PWWP domain + histone H3.2
    
  • 6pzv – b-cytosine DNMT 1 RFTS domain + histone H3.3 + ubiquitin - bovine
    
  • 7lmk, 7lmm – b-cytosine DNMT 1 BAH1 domain + histone H4
    
  • 4ft2, 4ft4 – c-cytosine DNMT + histone H3 peptide – corn
    
• Methylcytosine DNMT complex with small molecule
  • 4wxx - h-cytosine DNMT 1 residues 351-1600 + SAH
    
  • 7sfc, 7sfd, 7sfe, 7sff, 7sfg – hDNMT 1 729-1600 + DNA + CMP + pyrimidine derivative + SAM
    
  • 6x9j, 6x9k, 6x9i – hDNMT 1 729-1600 + DNA + CMP + pyrimidine derivative + SAH
    
  • 7xi9 – hDNMT 1 351-1600 + H3 – Cryo EM
    
  • 4u7p - h-cytosine DNMT 3A residues 455-912 + h-cytosine DNMT 3L residues 178-379 + SAH
    
  • 5nvo - h-cytosine DNMT 3B PWWP domain + choline
    
  • 5nv7, 5nv2, 5nv0, 5nrv, 5nrs, 5nrr, 5nr3, 6r3e - h-cytosine DNMT 3B PWWP domain + inhibitor
    
  • 6kdp - h-cytosine DNMT 3B residues 563-853 + h-cytosine DNMT 3L residues 178-386 + SAH
    
  • 6kdt - h-cytosine DNMT 3B residues 563-853 (mutant) + h-cytosine DNMT 3L residues 178-386 + SAH
    
  • 8eih, 8eii, 8eij, 8eik - h-cytosine DNMT 3B residues 206-853 + SAH – Cryo EM
    
  • 7x9d - h-cytosine DNMT 3B residues 571-853 + harmine
    
  • 8xee - h-cytosine DNMT 3B residues 571-853 (mutant) + SAH
    
  • 3swr - h-cytosine DNMT + sinefungin
    
  • 6w8v, 6w8w - m-cytosine DNMT1 residues 731-1600 + SAH + CMP derivative
    
  • 3av5 - m-cytosine DNMT residues 291-1620 + SAH
    
  • 3av6 - m-cytosine DNMT residues 650-1620 + SAM
    
  • 4fsx – c-cytosine DNMT + SAH
    
  • 3qv2 - cytosine DNMT + SAH – Entamoeba histolytica<br />
  • 1hmy – HhHaeiii DNMT + SAM
    
• Methyladenine DNMT
  • 6ped – hN6AMT1 + tRNA methyltransferase
    
  • 6h1d – hN6AMT1 + TRMT112
    
  • 6kmr, 6kms – hN6AMT1 + TRMT112 + SAM
    
  • 6h1e – hN6AMT1 + TRMT112 + SAH + histone H4 peptide
    
  • 6khs – hN6AMT1 + TRMT112 + SAH + methylGln
    
  • 1nw5 – RsN6-adenine DNMT + SAM – Rhodobacter sphaeroides
  • 1nw6 - RsN6-adenine DNMT + sinefungin
    
  • 1nw7 - RsN6-adenine DNMT + SAH
    
  • 1nw8 - RsN6-adenine DNMT (mutant)
    
  • 5hek - HpN6-adenine DNMT – Helicobacter pylori
    
  • 5hfj, 6k0x - HpN6-adenine DNMT + sinefungin
    
  • 2ibs, 2ibt, 2ih2, 2ih4, 2ih5, 2np6, 2np7, 1g38 - Ta-adenine DNMT Taqi + DNA + cofactor analog – Thermus aquaticus
    
  • 1aqi – Ta-adenine DNMT Taqi + SAH
    
  • 1aqj – Ta-adenine DNMT Taqi + sinefungin
    
  • 2adm - Ta-adenine DNMT Taqi + SAM
    
  • 1g60 - adenine DNMT + SAM – Moraxella bovis
    
  • 4rtj, 4rtl, 4rto - Ec-adenine DNMT + DNA + sinefungin
    
  • 4rtk - Ec-adenine DNMT + DNA + SAH
    
  • 4gbe - Ec-adenine DNMT + SAH
    
  • 4gol, 4gom, 4gon, 4goo - Ec-adenine DNMT + SAM derivative
    
  • 4rtm, 4rtp, 4rtr, 4rts - Ec-adenine DNMT + DNA + AdoMet
    
  • 4rtn, 4rtq - Ec-adenine DNMT + DNA + AdoHcy
    
  • 7m6b - adenine DNMT + SAM + SAH – Caldicellulosiraptor bescii
    
  • 7lni, 7lnj – Cd-adenine DNMT + DNA – Clostridioides difficile
    
  • 7lnj, 7lt5 – Cd-adenine DNMT + DNA + SAH
    
  • 7rfk, 7rfl, 7rfm, 7rfn, 8cy2, 8fs1, 8fs2 – Cd-adenine DNMT + DNA + inhibitor
    
  • 8cxs, 8cxt, 8cxu, 8cxv, 8cxw, 8cxx, 8cxy, 8cxz, 8cy0, 8cy1, 8cy2j, 8cy3, 8cy4, 8cy5 – Cd-adenine DNMT + DNA + inhibitor
    
  • 7lo5, 7lvv - adenine DNMT + DNA + SAM – Deinococcus wulumuquiensis – Cryo EM
    
  • 7qw5, 7qw6, 7qw7, 7qw8 – adenine DNMT + DNA + SAH – Geobacillus stearothermophilus
    
  • 7vru, 7vs4 – adenine DNMT + DNA + AMP + SAH – Pseudomonas alcaligenes
    
  • 8q56 – adenine DNMT + OCR + SAM – Salmonella enterica
    
• HhaI DNA methyltransferase
  • 5lod – HhHDMT
    
  • 1fjx, 2hmy – HhHDMT + SAM – Haemophilus haemolyticus
    
  • 1svu – HhHDMT (mutant) + SAH
    
  • 1hmy, 1mht, 3mht, 4mht, 5mht, 7mht, 8mht, 2hr1, 3eeo – HhHDMT + DNA + SAH
    
  • 2i9k, 2z6a, 2z6u, 2zcj – HhHDMT (mutant) + DNA + SAH
    
  • 6mht – HhHDMT + DNA + SAH + thiodeoxycytidine
    
  • 9mht – HhHDMT + DNA + SAH + abasic dideoxyribose
    
  • 1skm – HhHDMT + DNA + SAH + bicyclohexane
    
  • 10mh – HhHDMT + DNA + SAH + dihydroazacytosine
    
  • 1m0e – HhHDMT + DNA + SAH + zebularine
    
  • 2c7o, 2c7p, 2c7q – HhHDMT + DNA + SAH + methyl cytosine + aminopurine
    
  • 2c7r – HhHDMT (mutant) + DNA + SAH + methyl cytosine + aminopurine
    
  • 2z6q – HhHDMT (mutant) + DNA + SAH + deoxycytidine
    
  • 2uyc, 2uyh, 2uz4 – HhHDMT (mutant) + DNA + SAH + methyl cytosine
    
• DNA methyltransferase
  • 4onj – tHDMT catalytic domain + sinefungin – tobacco
    
  • 4onq – tHDMT catalytic domain (mutant) + sinefungin
    

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Michal Harel