Structural Classification of Proteins
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Fold: alpha/beta knot

core: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: alpha/beta knot [75216]
    core: 3 layers: a/b/a, parallel beta-sheet of 5 strands, order 21435; contains a deep trefoil knot

Superfamilies:

  1. alpha/beta knot [75217] (8)
    known or predicted SAM-dependent methytransferases including the SPOUT 'sequence' superfamily
    all known members have dimeric structures
    link to SUPERFAMILY database - Superfamily
    1. YbeA-like [82371] (4)
      Pfam 02590
      1. Hypothetical protein YbeA [82372]
        1. Escherichia coli [TaxId: 562] [82373] (1)
          1. 1ns5 picpic
            structural genomics; NESG target ER45
            complexed with mse
            1. chain a [80705] picpiclink
            2. chain b [80706] picpiclink
      2. Hypothetical protein TM0844 [102274]
        1. Thermotoga maritima [TaxId: 2336] [102275] (1)
          1. 1o6d picpic
            structural genomics
            1. chain a [92567] picpiclink
      3. Hypothetical protein SAV0024/SA0023 [102276]
        1. Staphylococcus aureus [TaxId: 1280] [102277] (1)
          1. 1vh0 picpic
            structural genomics
            1. chain a [100626] picpiclink
            2. chain b [100627] picpiclink
            3. chain c [100628] picpiclink
            4. chain d [100629] picpiclink
            5. chain e [100630] picpiclink
            6. chain f [100631] picpiclink
      4. Hypothetical protein YydA [110497]
        1. Bacillus subtilis [TaxId: 1423] [110498] (1)
          SQ Q45601
          1. 1to0 picpic
            1. chain a [107153] picpiclink
            2. chain b [107154] picpiclink
            3. chain c [107155] picpiclink
            4. chain d [107156] picpiclink
            5. chain e [107157] picpiclink
            6. chain f [107158] picpiclink
            7. chain g [107159] picpiclink
            8. chain h [107160] picpiclink
    2. tRNA(m1G37)-methyltransferase TrmD [89629] (3)
      fold and dimerisation mode are similar to those of the YbeA-like family; contains additional C-terminal all-alpha subdomain
      1. tRNA(m1G37)-methyltransferase TrmD [89630]
        1. Haemophilus influenzae [TaxId: 727] [89631] (4)
          1. 1ual picpic
            complexed with sah
            1. chain a [88383] picpiclink
          2. 1uaj picpic
            1. chain a [88381] picpiclink
          3. 1uak picpic
            complexed with sam
            1. chain a [88382] picpiclink
          4. 1uam picpic
            complexed with po4, sah
            1. chain a [88384] picpiclink
        2. Aquifex aeolicus [TaxId: 63363] [102278] (1)
          1. 1oy5 picpic
            a TrmD topoisomer that lacks the knot; misfolded inactive structure?
            1. chain a [93718] picpiclink
            2. chain b [93719] picpiclink
            3. chain c [93720] picpiclink
        3. Escherichia coli [TaxId: 562] [110499] (1)
          SQ P07020
          1. 1p9p picpic
            complexed with sah
            1. chain a [104092] picpiclink
    3. SpoU-like RNA 2'-O ribose methyltransferase [75218] (4)
      contains extra strand (3) in the parallel beta-sheet, order 321546
      1. tRNA (Gm18) methyltransferase TrmH [102279]
        1. Thermus thermophilus [TaxId: 274] [102280] (1)
          1. 1v2x picpic
            complexed with po4, sam
            1. chain a [100274] picpiclink
      2. Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) [82374]
        1. Haemophilus influenzae [TaxId: 727] [82375] (2)
          1. 1mxi picpic
            complexed with iod, sah
            1. chain a [79646] picpiclink
          2. 1j85 picpic
            1. chain a [77100] picpiclink
      3. RrmA (RrmH), C-terminal domain [75219]
        23S rRNA methyltransferase; proposed gene names are as appear in the original publication (and the PDB entry)
        1. Thermus thermophilus [TaxId: 274] [75220] (1)
          1. 1ipa picpicxref
            1. region a:106-263 [71254] picpiclink
      4. RlmB, C-terminal domain [82376]
        23S rRNA G2251 2'O-methytransferase
        1. Escherichia coli [TaxId: 562] [82377] (1)
          1. 1gz0 picpicxref
            complexed with mse
            1. region a:78-243 [76391] picpiclink
            2. region b:78-243 [76393] picpiclink
            3. region c:78-243 [76395] picpiclink
            4. region d:78-243 [76397] picpiclink
            5. region e:78-243 [76399] picpiclink
            6. region f:78-243 [76400] picpiclink
            7. region g:78-243 [76402] picpiclink
            8. region h:78-243 [76403] picpiclink
    4. Hypothetical protein MTH1 (MT0001), dimerisation domain [75221] (1)
      contains extra strand (3) in the parallel beta-sheet, order 321546; interrupted by an insert OB-fold domain
      1. Hypothetical protein MTH1 (MT0001), dimerisation domain [75222]
        1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [75223] (1)
          1. 1k3r picpicxref
            1. region a:1-92,a:164-262 [72019] picpiclink
            2. region b:1-92,b:164-264 [72021] picpiclink
    5. YggJ C-terminal domain-like [89632] (3)
      contains extra strand (3) in the parallel beta-sheet, order 321546; similar dimerisation to the MTH1 domain
      1. Hypothetical protein HI0303 [89633]
        1. Haemophilus influenzae [TaxId: 727] [89634] (2)
          1. 1vhy picpicxref
            structural genomics
            1. region a:74-247 [100715] picpiclink
            2. region b:74-247 [100717] picpiclink
          2. 1nxz picpicxref
            structural genomics
            complexed with mse
            1. region a:74-247 [86392] picpiclink
            2. region b:74-246 [86394] picpiclink
      2. Hypothetical protein YqeU [102281]
        1. Bacillus subtilis [TaxId: 1423] [102282] (1)
          1. 1vhk picpicxref
            structural genomics
            1. region a:74-253 [100681] picpiclink
            2. region b:74-253 [100683] picpiclink
            3. region c:74-253 [100685] picpiclink
            4. region d:74-253 [100687] picpiclink
      3. Hypothetical protein TTHA0657 (TT1575) [117494]
        1. Thermus thermophilus [TaxId: 274] [117495] (3)
          SQ Q5SKI6
          1. 1v6z picpicxref
            Structural genomics target
            1. region a:67-228 [113552] picpiclink
            2. region b:67-228 [113554] picpiclink
          2. 2cx8 picpicxref
            complexed with sah
            1. region a:67-228 [130984] picpiclink
          3. 2z0y picpicxref
            automatically matched to d1v6za2
            complexed with sam
            1. region a:67-228 [153919] picpiclink
    6. EMG1/NEP1-like [159513] (2)
      Pfam 03587; structurally most similar to the AF1056-like family, but more decorated
      1. Ribosome biogenesis protein NEP1 [159514]
        1. Methanococcus jannaschii [TaxId: 2190] [159515] (6)
          SQ Q57977 2-205
          1. 3bbd picpic
            complexed with gol, sah
            1. region a:2-205 [155061] picpiclink
          2. 3bbd picpic
            automatically matched to 3BBD A:2-205
            complexed with gol, sah
            1. region b:2-205 [155062] picpiclink
          3. 3bbe picpic
            automatically matched to 3BBD A:2-205
            complexed with gol
            1. region a:2-205 [155063] picpiclink
          4. 3bbe picpic
            automatically matched to 3BBD A:2-205
            complexed with gol
            1. region b:2-205 [155064] picpiclink
          5. 3bbh picpic
            automatically matched to 3BBD A:2-205
            complexed with gol, sfg
            1. region a:2-205 [155071] picpiclink
          6. 3bbh picpic
            automatically matched to 3BBD A:2-205
            complexed with gol, sfg
            1. region b:2-205 [155072] picpiclink
      2. Essential for mitotic growth 1, EMG1 [159516]
        1. Saccharomyces cerevisiae [TaxId: 4932] [159517] (2)
          SQ Q06287 23-251
          1. 2v3k picpic
            automatically matched to 2V3J A:23-251
            complexed with sam, so4
            1. region a:25-251 [152460] picpiclink
          2. 2v3j picpic
            complexed with so4
            1. region a:23-251 [152459] picpiclink
    7. AF1056-like [159518] (2)
      Pfam 04013; DUF358
      1. Uncharacterized protein AF1056 [159519]
        1. Archaeoglobus fulgidus [TaxId: 2234] [159520] (2)
          SQ O29206 95-288
          1. 2qmm picpic
            complexed with sam
            1. region a:95-288 [150886] picpiclink
          2. 2qmm picpic
            automatically matched to 2QMM A:95-288
            complexed with sam
            1. region b:95-288 [150887] picpiclink
      2. Uncharacterized protein VCA1059 [159521]
        1. Vibrio cholerae [TaxId: 666] [159522] (2)
          SQ Q9KKP3 1-201
          1. 2qwv picpic
            complexed with acy
            1. region a:5-205 [151439] picpiclink
          2. 2qwv picpic
            automatically matched to 2QWV A:5-205
            complexed with acy
            1. region b:5-205 [151440] picpiclink
    8. AF0751-like [159523] (1)
      Pfam 01994; DUF127
      1. Uncharacterized protein AF0751 [159524]
        1. Archaeoglobus fulgidus [TaxId: 2234] [159525] (2)
          SQ O29507 1-167
          1. 2o3a picpic
            1. region a:1-167 [148570] picpiclink
          2. 2o3a picpic
            automatically matched to 2O3A A:1-167
            1. region b:1-167 [148571] picpiclink
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MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk