Structural Classification of Proteins

Fold: alpha/beta knot

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

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
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:

alpha/beta knot [75217] (8)
known or predicted SAM-dependent methytransferases including the SPOUT 'sequence' superfamily
all known members have dimeric structures
uperfamily
1. YbeA-like [82371] (4)
  Pfam 02590
  1. Hypothetical protein YbeA [82372]
    1. Escherichia coli [TaxId: 562] [82373] (1)
  2. Hypothetical protein TM0844 [102274]
    1. Thermotoga maritima [TaxId: 2336] [102275] (1)
  3. Hypothetical protein SAV0024/SA0023 [102276]
    1. Staphylococcus aureus [TaxId: 1280] [102277] (1)
  4. Hypothetical protein YydA [110497]
    1. Bacillus subtilis [TaxId: 1423] [110498] (1)
      SQ Q45601
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)
    2. Aquifex aeolicus [TaxId: 63363] [102278] (1)
    3. Escherichia coli [TaxId: 562] [110499] (1)
      SQ P07020
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)
  2. Hypothetical tRNA/rRNA methyltransfease HI0766 (YibK homologue) [82374]
    1. Haemophilus influenzae [TaxId: 727] [82375] (2)
  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)
  4. RlmB, C-terminal domain [82376]
    23S rRNA G2251 2'O-methytransferase
    1. Escherichia coli [TaxId: 562] [82377] (1)
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)
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)
  2. Hypothetical protein YqeU [102281]
    1. Bacillus subtilis [TaxId: 1423] [102282] (1)
  3. Hypothetical protein TTHA0657 (TT1575) [117494]
    1. Thermus thermophilus [TaxId: 274] [117495] (3)
      SQ Q5SKI6
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
  2. Essential for mitotic growth 1, EMG1 [159516]
    1. Saccharomyces cerevisiae [TaxId: 4932] [159517] (2)
      SQ Q06287 23-251
7. AF1056-like [159518] (2)
  Pfam 04013; DUF358
  1. Uncharacterized protein AF1056 [159519]
    1. Archaeoglobus fulgidus [TaxId: 2234] [159520] (2)
      SQ O29206 95-288
  2. Uncharacterized protein VCA1059 [159521]
    1. Vibrio cholerae [TaxId: 666] [159522] (2)
      SQ Q9KKP3 1-201
8. AF0751-like [159523] (1)
  Pfam 01994; DUF127
  1. Uncharacterized protein AF0751 [159524]
    1. Archaeoglobus fulgidus [TaxId: 2234] [159525] (2)
      SQ O29507 1-167