SCOP 1.63: Family c.1.8.1: Amylase, catalytic domain

Lineage for Family c.1.8.1: Amylase, catalytic domain

1. Root: SCOP 1.63

2. Class c: Alpha and beta proteins (a/b) [51349] (117 folds)

3. Fold c.1: TIM beta/alpha-barrel [51350] (26 superfamilies)
   contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678
   the first seven superfamilies have similar phosphate-binding sites

4. Superfamily c.1.8: (Trans)glycosidases [51445] (9 families)

5. Family c.1.8.1: Amylase, catalytic domain [51446] (21 proteins)
   members of the family may contain various insert subdomains
   in alpha-amylases and closer relatives this domain is usually followed by a common all-beta domain

Proteins:

1. 1,4-alpha-glucan branching enzyme, central domain [82244] (1 species)

   • Species Escherichia coli [TaxId:562] [82245] (1 PDB entry)

2. 4-alpha-glucanotransferase [75062] (1 species)

   • Species Thermotoga maritima [TaxId:243274] [75063] (2 PDB entries)

3. A4 beta-galactosidase [82246] (1 species)
   the catalytic domain is very similar to that of the bacterial beta-amylase; but contains a typical alpha-amylase extra domain

   • Species Thermus thermophilus [TaxId:274] [82247] (2 PDB entries)

4. alpha-N-acetylgalactosaminidase [75064] (1 species)

   • Species Chicken (Gallus gallus) [TaxId:9031] [75065] (2 PDB entries)

5. Amylomaltase MalQ [51478] (1 species)
   single-domain amylase with several insertions in the common fold

   • Species Thermus aquaticus [TaxId:271] [51479] (2 PDB entries)

6. Amylosucrase [69384] (1 species)

   • Species Neisseria polysaccharea [TaxId:489] [69385] (8 PDB entries)

7. Animal alpha-amylase [51458] (3 species)
   contains Ca2+-binding subdomain, residues 100-170

   1. Species Human (Homo sapiens) [TaxId:9606] [51460] (18 PDB entries)

   2. Species Pig (Sus scrofa) [TaxId:9823] [51459] (11 PDB entries)

   3. Species Yellow mealworm (Tenebrio molitor), larva [TaxId:7067] [51461] (4 PDB entries)

8. Bacterial alpha-amylase [51447] (5 species)

   1. Species Bacillus licheniformis [TaxId:1402] [51448] (4 PDB entries)

   2. Species Bacillus stearothermophilus [TaxId:1422] [51451] (1 PDB entry)

   3. Species Bacillus subtilis [TaxId:1423] [51450] (1 PDB entry)

   4. Species Chimera (Bacillus amyloliquefaciens) and (Bacillus licheniformis) [TaxId:1390] [63903] (4 PDB entries)
      the N-terminal 300 residues are from B. amyloliquefaciens

   5. Species Pseudoalteromonas haloplanctis (Alteromonas haloplanctis) [51449] (9 PDB entries)

9. Bacterial beta-amylase [51485] (1 species)
   protein contains additional starch-binding domain

   • Species Bacillus cereus [TaxId:1396] [51486] (3 PDB entries)

10. beta-Amylase [51481] (3 species)
    Common fold covers whole protein structure

    1. Species Barley (Hordeum vulgare) [TaxId:4513] [51483] (1 PDB entry)

    2. Species Soybean (Glycine max) [TaxId:3847] [51482] (6 PDB entries)

    3. Species Sweet potato (Ipomoea batatas) [TaxId:4120] [51484] (1 PDB entry)

11. Cyclodextrin glycosyltransferase [51452] (5 species)
    contains two more all-beta domains, one is Immunoglobulin-like and the other is trasthyretin-like

    1. Species Alkalophilic bacillus sp., strain 1011 [51456] (4 PDB entries)

    2. Species Bacillus circulans, different strains [TaxId:1397] [51453] (29 PDB entries)

    3. Species Bacillus stearothermophilus [TaxId:1422] [51454] (1 PDB entry)

    4. Species Bacillus stearothermophilus, maltogenic alpha-amylase [TaxId:1422] [51455] (2 PDB entries)

    5. Species Thermoanaerobacterium thermosulfurigenes, EM1 [TaxId:33950] [51457] (2 PDB entries)

12. Fungal alpha-amylases [51462] (2 species)

    1. Species Aspergillus niger, acid amylase [TaxId:5061] [51463] (1 PDB entry)

    2. Species Aspergillus oryzae, Taka-amylase [TaxId:5062] [51464] (3 PDB entries)

13. G4-amylase (1,4-alpha-D-glucan maltotetrahydrolase) [51472] (1 species)

    • Species Pseudomonas stutzeri [TaxId:316] [51473] (9 PDB entries)

14. Glycosyltrehalose trehalohydrolase, central domain [51468] (1 species)
    contains an additional N-terminal domain

    • Species Archaeon Sulfolobus solfataricus, km1 [TaxId:2287] [51469] (2 PDB entries)

15. Isoamylase, central domain [51470] (1 species)

    • Species Pseudomonas amyloderamosa [TaxId:32043] [51471] (1 PDB entry)

16. Maltogenic amylase, central domain [51465] (4 species)
    contains an additional N-terminal domain

    1. Species Bacillus sp., cyclomaltodextrinase [TaxId:1409] [75060] (1 PDB entry)

    2. Species Thermoactinomyces vulgaris, TVAI [TaxId:2026] [75061] (1 PDB entry)

    3. Species Thermoactinomyces vulgaris, TVAII [TaxId:2026] [51467] (7 PDB entries)

    4. Species Thermus sp. [TaxId:275] [51466] (2 PDB entries)

17. Maltooligosyl trehalose synthase [82242] (1 species)
    elaborated with several large insertions in the common fold

    • Species Archaeon Sulfolobus acidocaldarius [TaxId:2285] [82243] (1 PDB entry)

18. Maltosyltransferase [63904] (1 species)
    similar to bacterial alpha-amylase; contains larger insertion domain

    • Species Thermotoga maritima [TaxId:243274] [63905] (2 PDB entries)

19. Neopullulanase, central domain [82240] (1 species)
    homologous to Maltogenic amylase

    • Species Bacillus stearothermophilus [TaxId:1422] [82241] (4 PDB entries)

20. Oligo-1,6, glucosidase [51476] (1 species)

    • Species Bacillus cereus [TaxId:1396] [51477] (1 PDB entry)

21. Plant alpha-amylase [51474] (1 species)

    • Species Barley (Hordeum vulgare), seeds, AMY2 isozyme [TaxId:4513] [51475] (3 PDB entries)

More info for Family c.1.8.1: Amylase, catalytic domain

Timeline for Family c.1.8.1: Amylase, catalytic domain:

• Family c.1.8.1: Amylase, catalytic domain first appeared (with stable ids) in SCOP 1.55, called Family c.1.8.1: alpha-Amylases, N-terminal domain
  
• Family c.1.8.1: Amylase, catalytic domain was called Family c.1.8.1: alpha-Amylases, N-terminal domain in SCOP 1.61
  
• Family c.1.8.1: Amylase, catalytic domain appears in SCOP 1.65
  
• Family c.1.8.1: Amylase, catalytic domain appears in the current release, SCOPe 2.08