Structural Classification of Proteins

Fold: S-adenosyl-L-methionine-dependent methyltransferases

: core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold: S-adenosyl-L-methionine-dependent methyltransferases [53334]
core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest

Superfamilies:

S-adenosyl-L-methionine-dependent methyltransferases [53335] (52)
1. COMT-like [53336] (3)
  1. Catechol O-methyltransferase, COMT [53337]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [53338] (5)
  2. COMT domain-containing protein 1, COMTD1 [142571]
    1. Human (Homo sapiens) [TaxId: 9606] [142572] (2)
  3. Caffeoyl-CoA O-methyltransferase [142573]
    1. Alfalfa (Medicago sativa) [TaxId: 3879] [142574] (8)
2. Plant O-methyltransferase, C-terminal domain [64111] (5)
  1. Chalcone O-methyltransferase [64112]
    1. Alfalfa (Medicago sativa) [TaxId: 3879] [64113] (2)
  2. Isoflavone O-methyltransferase [64114]
    1. Alfalfa (Medicago sativa) [TaxId: 3879] [64115] (2)
  3. Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase [75259]
    1. Alfalfa (Medicago sativa) [TaxId: 3879] [75260] (2)
  4. Aclacinomycin-10-hydroxylase RdmB [102554]
    evolved a different function; binds SAM and SAH
    1. Streptomyces purpurascens [TaxId: 1924] [102555] (4)
  5. Carminomycin 4-O-methyltransferase [110660]
    1. Streptomyces peucetius [TaxId: 1950] [110661] (2)
3. RNA methyltransferase FtsJ [53339] (1)
  1. RNA methyltransferase FtsJ [53340]
    1. Escherichia coli [TaxId: 562] [53341] (2)
4. Fibrillarin homologue [53342] (3)
  1. Fibrillarin homologue [53343]
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53344] (2)
    2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [89737] (1)
      AF2087
    3. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102556] (2)
5. rRNA methyltransferase RlmA [102557] (1)
  1. rRNA methyltransferase RlmA [102558]
    23S rRNA N1-G745 methyltransferase
    1. Escherichia coli [TaxId: 562] [102559] (1)
6. rRNA methyltransferase AviRa [89738] (1)
  1. rRNA methyltransferase AviRa [89739]
    1. Streptomyces viridochromogenes [TaxId: 1938] [89740] (2)
7. rRNA adenine dimethylase-like [88784] (5)
  1. rRNA adenine dimethylase [53363]
    contains additional all-alpha C-terminal domain (res.181-248)
    1. Streptococcus pneumoniae, Ermam [TaxId: 1313] [53364] (1)
    2. Bacillus subtilis, Ermc' [TaxId: 1423] [53365] (5)
  2. Transcription factor sc-mtTFB [69555]
    overall structure is very similar to those of Ermc' and Ermam
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [69556] (1)
  3. High level kasugamycin resistance protein KsgA [110662]
    1. Escherichia coli [TaxId: 562] [110663] (1)
  4. Probable dimethyladenosine transferase [142575]
    1. Human (Homo sapiens) [TaxId: 9606] [142576] (2)
8. mRNA cap methylase [88785] (2)
  1. Polymerase regulatory subunit VP39 [53361]
    1. Vaccinia virus [TaxId: 10245] [53362] (19)
  2. An RNA cap (nucleoside-2'-O-)-methyltransferase domain of RNA polymerase NS5 [89741]
    structurally and functionally similar to VP39
    1. Flavivirus (Dengue virus type 2) [TaxId: 12637] [89742] (3)
9. mRNA cap (Guanine N-7) methyltransferase [102560] (1)
  mRNA capping enzyme
  1. mRNA cap (Guanine N-7) methyltransferase [102561]
    1. Fungus (Encephalitozoon cuniculi) [TaxId: 6035] [102562] (7)
10. Hypothetical protein MJ0882 [53345] (1)
  1. Hypothetical protein MJ0882 [53346]
    1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53347] (1)
11. Hypothetical protein HI0319 (YecO) [69544] (1)
  1. Hypothetical protein HI0319 (YecO) [69545]
    1. Haemophilus influenzae [TaxId: 727] [69546] (1)
      structural genomics
12. Glycine N-methyltransferase [53348] (3)
  1. Glycine N-methyltransferase [53349]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [53350] (16)
    2. Human (Homo sapiens) [TaxId: 9606] [110664] (1)
    3. Mouse (Mus musculus) [TaxId: 10090] [110665] (2)
13. Arylamine N-methyltransferase [69547] (2)
  1. Phenylethanolamine N-methyltransferase, PNMTase [69548]
    1. Human (Homo sapiens) [TaxId: 9606] [69549] (19)
  2. Indolethylamine N-methyltransferase, INMT [142577]
    1. Human (Homo sapiens) [TaxId: 9606] [142578] (1)
14. Histamine methyltransferase [75261] (1)
  1. Histamine methyltransferase [75262]
    1. Human (Homo sapiens) [TaxId: 9606] [75263] (12)
15. Hypothetical Protein YjhP [82469] (1)
  1. Hypothetical Protein YjhP [82470]
    1. Escherichia coli [TaxId: 562] [82471] (1)
16. Salicylic acid carboxyl methyltransferase (SAMT) [102563] (1)
  1. Salicylic acid carboxyl methyltransferase (SAMT) [102564]
    1. Clarkia breweri [TaxId: 36903] [102565] (1)
17. Thiopurine S-methyltransferase [102566] (2)
  1. Thiopurine S-methyltransferase [102567]
    1. Pseudomonas syringae [TaxId: 317] [102568] (1)
    2. Human (Homo sapiens) [TaxId: 9606] [142579] (3)
18. Leucine carboxy methyltransferase Ppm1 [102569] (1)
  1. Leucine carboxy methyltransferase Ppm1 [102570]
    involved in the regulation of protein phosphatase 2a activity
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [102571] (7)
19. Precorrin-6Y methyltransferase (CbiT) [82472] (1)
  1. Precorrin-6Y methyltransferase (CbiT) [82473]
    1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [82474] (5)
      MTH146
20. MraW-like putative methyltransferases [82475] (2)
  1. TM0872, methyltransferase domain [82476]
    contains an inserted alpha helical subdomain
    1. Thermotoga maritima [TaxId: 2336] [82477] (2)
    2. Thermus thermophilus [TaxId: 274] [117678] (1)
21. N5-glutamine methyltransferase, HemK [89743] (2)
  1. N5-glutamine methyltransferase, HemK [89744]
    contains an N-terminal alpha helical subdomain; res. 13-84
    1. Thermotoga maritima [TaxId: 2336] [89745] (5)
    2. Escherichia coli [TaxId: 562] [110666] (2)
22. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89746] (2)
  1. Catalytic, N-terminal domain of histone methyltransferase Dot1l [89747]
    a non-SET domain nucleosomal histone methyltransferase
    1. Human (Homo sapiens) [TaxId: 9606] [89748] (1)
    2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110667] (1)
23. Guanidinoacetate methyltransferase [69550] (2)
  1. Guanidinoacetate methyltransferase [69551]
    a template structure of protein arginine methyltransferase
    1. Rat (Rattus norvegicus) [TaxId: 10116] [69552] (5)
    2. Human (Homo sapiens) [TaxId: 9606] [142580] (3)
24. Arginine methyltransferase [53351] (4)
  lacks the last two strands of the common fold replaced with a beta-sandwich oligomerisation subdomain
  1. Arginine methyltransferase, HMT1 [53352]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53353] (1)
    2. Rat (Rattus norvegicus) [TaxId: 10116] [64116] (1)
  2. Protein arginine N-methyltransferase 1, PRMT1 [89749]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [89750] (3)
  3. Protein arginine N-methyltransferase 3, PRMT3 [142581]
    1. Human (Homo sapiens) [TaxId: 9606] [142582] (1)
25. Protein-L-isoaspartyl O-methyltransferase [53354] (5)
  topological variant; strand order 3214567; strand 6 is antiparallel to the rest
  1. Protein-L-isoaspartyl O-methyltransferase [68927]
    1. Thermotoga maritima [TaxId: 2336] [68928] (1)
    2. Archaeon Pyrococcus furiosus [TaxId: 2261] [69553] (4)
    3. Human (Homo sapiens) [TaxId: 9606] [69554] (2)
    4. Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102572] (1)
    5. Sulfolobus tokodaii [TaxId: 111955] [110668] (1)
26. Glucose-inhibited division protein B (GidB) [75264] (2)
  1. Glucose-inhibited division protein B (GidB) [75265]
    function unknown
    1. Escherichia coli [TaxId: 562] [75266] (1)
    2. Bacillus subtilis [TaxId: 1423] [117679] (1)
27. tRNA(1-methyladenosine) methyltransferase-like [64117] (4)
  contains additional N-terminal beta-sandwich domain
  1. Probable methyltransferase Rv2118c [64118]
    1. Mycobacterium tuberculosis [TaxId: 1773] [64119] (1)
  2. Hypothetical protein TM0748 [102573]
    1. Thermotoga maritima [TaxId: 2336] [102574] (1)
  3. Hypothetical protein FLJ20628 [142583]
    1. Human (Homo sapiens) [TaxId: 9606] [142584] (2)
  4. Hypothetical protein Ta0852 [142585]
    forms dimer similar to half-tetramer of the other members but with swapped N-terminal domains; variant topology of the N-terminal domain
    1. Thermoplasma acidophilum [TaxId: 2303] [142586] (1)
28. NOL1/NOP2/sun [102575] (3)
  Pfam 01189; contains additional N-terminal 3-helical and ferredoxin-like domains
  1. Hypothetical methyltransferase PH1374 [102576]
    1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [102577] (1)
  2. Ribosomal RNA small subunit methyltransferase B, RsmB (Sun, Fmu/Fmv), C-terminal domain [110669]
    1. Escherichia coli [TaxId: 562] [110670] (2)
  3. NOL1R [142587]
    1. Human (Homo sapiens) [TaxId: 9606] [142588] (1)
29. Ribosomal protein L11 methyltransferase PrmA [102578] (1)
  contains additional N-terminal ferredoxin-like domain
  1. PrmA-like protein TTHA0656 (TT0836) [102579]
    1. Thermus thermophilus [TaxId: 274] [102580] (7)
30. (Uracil-5-)-methyltransferase [102581] (1)
  Pfam 05958
  1. rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain [102582]
    includes an iron-sulfur cluster-binding, alpha+beta sudbomain
    1. Escherichia coli [TaxId: 562] [102583] (3)
31. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53357] (1)
  contains additional N-terminal all-alpha domain, res. 11-91
  1. Chemotaxis receptor methyltransferase CheR, C-terminal domain [53358]
    1. Salmonella typhimurium [TaxId: 602] [53359] (2)
32. C5 cytosine-specific DNA methylase, DCM [88786] (3)
  1. DNA methylase HhaI [53367]
    1. Haemophilus haemolyticus [TaxId: 726] [53368] (20)
  2. DNA methylase HaeIII [53371]
    1. Haemophilus aegyptius [TaxId: 197575] [53372] (1)
  3. DNMT2 [53375]
    an enigmatic DNA methyltransferase homologue from mitochondria
    1. Human (Homo sapiens) [TaxId: 9606] [53376] (1)
33. DNA methylase TaqI, N-terminal domain [88787] (1)
  1. DNA methylase TaqI, N-terminal domain [53369]
    1. Thermus aquaticus [TaxId: 271] [53370] (8)
34. N6 adenine-specific DNA methylase, DAM [88788] (2)
  1. DNA methylase DpnM [53373]
    1. Streptococcus pneumoniae [TaxId: 1313] [53374] (1)
  2. DNA methylase T4DAM [102584]
    1. Bacteriophage T4 [TaxId: 10665] [102585] (14)
35. Type II DNA methylase [53377] (3)
  circularly permuted version of the common fold
  1. m.PvuII N4 cytosine-specific DNA methyltransferase [53378]
    1. Proteus vulgaris [TaxId: 585] [53379] (1)
  2. m.RsrI N6 adenosine-specific DNA methyltransferase [53380]
    1. Rhodobacter sphaeroides [TaxId: 1063] [53381] (5)
  3. Methyltransferase mboII [75267]
    1. Moraxella bovis [TaxId: 476] [75268] (1)
36. Spermidine synthase [69557] (7)
  contains additional N-terminal tetramerisation all-beta domain, res. 1-71
  1. Spermidine synthase [69558]
    polyamine aminopropyltransferase
    1. Thermus thermophilus [TaxId: 274] [102586] (1)
    2. Thermotoga maritima [TaxId: 2336] [69559] (2)
    3. Bacillus subtilis [TaxId: 1423] [82478] (1)
    4. Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117680] (5)
    5. Caenorhabditis elegans [TaxId: 6239] [142589] (2)
    6. Human (Homo sapiens) [TaxId: 9606] [142590] (8)
  2. Putative spermidine synthetase PF0127 (SpeE) [82479]
    1. Archaeon Pyrococcus furiosus [TaxId: 2261] [82480] (1)
37. Mycolic acid cyclopropane synthase [69560] (5)
  1. CmaA1 [69561]
    1. Mycobacterium tuberculosis [TaxId: 1773] [69562] (3)
  2. CmaA2 [116723]
    1. Mycobacterium tuberculosis [TaxId: 1773] [116724] (1)
  3. PccA [75269]
    1. Mycobacterium tuberculosis [TaxId: 1773] [75270] (1)
  4. Methoxy mycolic acid synthase 2, Mma2 [117681]
    1. Mycobacterium tuberculosis [TaxId: 1773] [117682] (1)
  5. Methoxy mycolic acid synthase 4, Mma4 [142591]
    1. Mycobacterium tuberculosis [TaxId: 1773] [142592] (2)
38. Ta1320-like [89751] (2)
  1. Hypothetical protein Ta1320 [89752]
    1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [89753] (1)
  2. Hypothetical protein PH1948 [142593]
    1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142594] (4)
39. UbiE/COQ5-like [110671] (4)
  Pfam 01209
  1. Hypothetical protein BH2331 [110672]
    1. Bacillus halodurans [TaxId: 86665] [110673] (1)
  2. Possible histamine N-methyltransferase TM1293 [110674]
    1. Thermotoga maritima [TaxId: 2336] [110675] (1)
  3. Hypothetical protein YcgJ [117683]
    1. Bacillus subtilis [TaxId: 1423] [117684] (3)
  4. Hypothetical methyltransferase TM1389 [142595]
    1. Thermotoga maritima [TaxId: 2336] [142596] (2)
40. AD-003 protein-like [117685] (2)
  Pfam 05891; DUF858
  1. Hypothetical protein Lmaj004091aaa (LmjF30.0810) [117686]
    1. Leishmania major [TaxId: 5664] [117687] (1)
  2. Adrenal gland protein AD-003 (C9orf32) [142597]
    1. Human (Homo sapiens) [TaxId: 9606] [142598] (2)
41. CAC2371-like [117688] (3)
  similar overall fold to the Glycine N-methyltransferase (scop_fa 53348) and mRNA cap (Guanine N-7) methyltransferase (scop_fa 102560) families
  1. Putative methyltransferase CAC2371 [117689]
    1. Clostridium acetobutylicum [TaxId: 1488] [117690] (1)
  2. Hypothetical protein PH0226 [142599]
    1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142600] (2)
  3. Hypothetical methyltransferase PH1305 [142601]
    the beta-sheet insertion makes trimerization subdomain
    1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142602] (3)
42. TehB-like [142603] (1)
  Pfam 03848; overall structural similarity to Thiopurine S-methyltransferase (Pfam 05724)
  1. Putative methyltransferase TehB [142604]
    Tellurite resistance protein
    1. Salmonella typhimurium [TaxId: 602] [142605] (2)
      sequence similarity to Hypothetical methyltransferase PH1305 of the CAC2371-like family (scop_fa 117688)
43. N-6 DNA Methylase-like [142606] (2)
  Pfam 02384; contains C-terminal extension to the canonical fold and extra N-terminal all-alpha domain similar to the insert domain of the DAM family (scop_fa 88788)
  1. Hypothetical protein Lmo1582 [142607]
    1. Listeria monocytogenes [TaxId: 1639] [142608] (1)
  2. M.EcoKI [142609]
    contains extra C-terminal structured region
    1. Escherichia coli [TaxId: 562] [142610] (2)
44. YhhF-like [142611] (5)
  Pfam 03602
  1. Putative methylase EF2452 [142612]
    1. Enterococcus faecalis [TaxId: 1351] [142613] (2)
  2. Methyltransferase TTHA0928 [142614]
    1. Thermus thermophilus [TaxId: 274] [142615] (1)
  3. Putative methylase HI0767 [142616]
    YhhF homologue
    1. Haemophilus influenzae [TaxId: 727] [142617] (1)
  4. Putative methyltransferase SPy1538 [142618]
    1. Streptococcus pyogenes [TaxId: 1314] [142619] (2)
  5. Methylase YhhF [142620]
    1. Escherichia coli [TaxId: 562] [142621] (6)
45. Met-10+ protein-like [142622] (1)
  Pfam 02475; contains extra N-terminal alpha+beta domain: beta(2)-alpha-beta(2); mixed beta-sheet; order: 1234; cf scop_fold 102740
  1. Hypothetical protein PH0793 [142623]
    1. Pyrococcus horikoshii [TaxId: 53953] [142624] (1)
46. Nsp15 N-terminal domain-like [142625] (2)
  rudiment methyltransferase fold that probably has lost the enzymatic activity; contains extra N-terminal alpha+beta subdomain
  1. Nsp15 [142626]
    1. Murine hepatitis virus, MHV [TaxId: 11138] [142627] (2)
    2. SARS coronavirus [TaxId: 227859] [142628] (1)
47. BC2162-like [142629] (1)
  contains extra helical regions inserted after strands 5 and 6 of the canonical fold
  1. Methyltransferase BC2162 [142630]
    1. Bacillus cereus [TaxId: 1396] [142631] (2)
48. CmcI-like [142632] (1)
  Pfam 04989; may have evolved different enzymatic activity
  1. Cephalosporin hydroxylase CmcI [142633]
    1. Streptomyces clavuligerus [TaxId: 1901] [142634] (34)
49. hypothetical RNA methyltransferase [142635] (4)
  C-terminal part of Pfam 03602; similar to (Uracil-5-)-methyltransferase (Pfam 05958)
  1. Putative methyltransferase Atu0340 [142636]
    there is no associated PUA domain; rudiment extra N-terminal subdomain
    1. Agrobacterium tumefaciens [TaxId: 358] [142637] (3)
  2. Hypothetical protein TTHA1280, middle and C-terminal domains [142638]
    1. Thermus thermophilus [TaxId: 274] [142639] (10)
  3. Hypothetical protein SMu776, middle and C-terminal domains [142640]
    1. Streptococcus mutans [TaxId: 1309] [142641] (1)
  4. Hypothetical protein PH1915, middle and C-terminal domains [142642]
    1. Archaeon Pyrococcus horikoshii [TaxId: 53953] [142643] (2)
50. RPA4359-like [142644] (1)
  Pfam 02636; DUF185
  1. Hypothetical protein RPA4359 [142645]
    1. Rhodopseudomonas palustris [TaxId: 1076] [142646] (2)
51. TrmB-like [142647] (2)
  Pfam 02390
  1. tRNA (guanine-N(7)-)-methyltransferase TrmB [142648]
    1. Streptococcus pneumoniae [TaxId: 1313] [142649] (2)
    2. Bacillus subtilis [TaxId: 1423] [142650] (2)
52. Methyltransferase 10 domain [142651] (1)
  Pfam 05971; DUF890
  1. Methyltransferase 10 domain containing protein METT10D [142652]
    1. Human (Homo sapiens) [TaxId: 9606] [142653] (3)