SCOPe 2.06: Family c.1.8.1: Amylase, catalytic domain

Lineage for Family c.1.8.1: Amylase, catalytic domain

1. Root: SCOPe 2.06

2. Class c: Alpha and beta proteins (a/b) [51349] (148 folds)

3. Fold c.1: TIM beta/alpha-barrel [51350] (33 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] (15 families)

5. Family c.1.8.1: Amylase, catalytic domain [51446] (26 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:2336] [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. Amylomaltase MalQ [51478] (3 species)
   4-alpha-glucanotransferase; single-domain amylase with several insertions in the common fold

   1. Species Aquifex aeolicus [TaxId:63363] [141770] (1 PDB entry)
      Uniprot O66937 1-485

   2. Species Potato (Solanum tuberosum) [TaxId:4113] [141771] (1 PDB entry)
      Uniprot Q06801 54-576

   3. Species Thermus aquaticus [TaxId:271] [51479] (4 PDB entries)
      synonym: Thermus thermophilus

5. Amylosucrase [69384] (1 species)

   • Species Neisseria polysaccharea [TaxId:489] [69385] (10 PDB entries)

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

   1. Species Human (Homo sapiens) [TaxId:9606] [51460] (53 PDB entries)
      Uniprot P04746 16-511 ! SQ 04746

   2. Species Pig (Sus scrofa) [TaxId:9823] [51459] (13 PDB entries)

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

7. Bacterial alpha-amylase [51447] (10 species)

   1. Species Bacillus halmapalus [TaxId:79882] [141768] (1 PDB entry)
      Uniprot P19571 38-431

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

   3. Species Bacillus sp. 707 [TaxId:1416] [117366] (4 PDB entries)
      Uniprot P19571 38-518

   4. Species Bacillus sp., ksm-k38 [TaxId:1409] [89463] (6 PDB entries)

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

   6. Species Bacillus subtilis [TaxId:1423] [51450] (2 PDB entries)
      Uniprot P00691

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

   8. Species Halothermothrix orenii [TaxId:31909] [141767] (1 PDB entry)
      Uniprot Q8GPL8 28-436

   9. Species Pseudoalteromonas haloplanktis [TaxId:228] [51449] (9 PDB entries)

   10. Species Pyrococcus woesei [TaxId:2262] [89464] (3 PDB entries)

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

   • Species Bacillus cereus [TaxId:1396] [51486] (11 PDB entries)

9. 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] (18 PDB entries)
      Uniprot P10538

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

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

    1. Species Bacillus circulans, different strains [TaxId:1397] [51453] (36 PDB entries)

    2. Species Bacillus sp. 1011, alkaliphilic [TaxId:1410] [51456] (8 PDB entries)
       Uniprot P05618

    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] (4 PDB entries)

11. Cyclomaltodextrinase, central domain [102058] (1 species)
    protein shares similar domain organization with maltogenic amylases but differs in the spatial arrangement of its domains

    • Species Flavobacterium sp. 92 [TaxId:197856] [102059] (1 PDB entry)

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] (8 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] (2 species)
    contains an additional N-terminal domain

    1. Species Deinococcus radiodurans [TaxId:1299] [141769] (9 PDB entries)
       Uniprot Q9RX51 111-528

    2. Species Sulfolobus solfataricus, km1 [TaxId:2287] [51469] (8 PDB entries)

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

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

16. Isomaltulose synthase PalI [89466] (2 species)

    1. Species Erwinia rhapontici [TaxId:55212] [254869] (5 PDB entries)

    2. Species Klebsiella sp., lx3 [TaxId:576] [89467] (1 PDB entry)

17. 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] (8 PDB entries)

    3. Species Thermoactinomyces vulgaris, TVAII [TaxId:2026] [51467] (12 PDB entries)

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

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

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

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

    • Species Thermotoga maritima [TaxId:2336] [63905] (2 PDB entries)

20. Melibiase [75064] (4 species)

    1. Species Chicken (Gallus gallus) [TaxId:9031] [75065] (2 PDB entries)
       alpha-N-acetylgalactosaminidase

    2. Species Human (Homo sapiens) [TaxId:9606] [102062] (17 PDB entries)
       alpha-galactosidase A

    3. Species Rice (Oryza sativa) [TaxId:4530] [89468] (1 PDB entry)
       alpha-galactosidase

    4. Species Trichoderma reesei [TaxId:51453] [110349] (2 PDB entries)
       Alpha-galactosidase agl1
       Uniprot Q92456

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

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

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

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

23. Plant alpha-amylase [51474] (2 species)

    1. Species Barley (Hordeum vulgare), AMY1 isozyme [TaxId:4513] [89465] (7 PDB entries)

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

24. Pullulanase PulA [159381] (1 species)

    • Species Klebsiella pneumoniae [TaxId:573] [159382] (6 PDB entries)
      Uniprot P07206 410-972

25. Sucrose phosphorylase [102060] (1 species)
    sequence and close structural relationship to amylosucrase; variations in the C-terminal domain fold

    • Species Bifidobacterium adolescentis [TaxId:1680] [102061] (2 PDB entries)

26. automated matches [190099] (25 species)
    not a true protein

    1. Species Bacillus cereus [TaxId:1396] [254917] (3 PDB entries)

    2. Species Bacillus halmapalus [TaxId:79882] [255187] (2 PDB entries)

    3. Species Bacillus sp. [225222] (1 PDB entry)

    4. Species Bacillus sp. [TaxId:535911] [225472] (1 PDB entry)

    5. Species Bacillus subtilis [TaxId:224308] [228099] (4 PDB entries)

    6. Species Barley (Hordeum vulgare) [TaxId:4513] [255684] (8 PDB entries)

    7. Species Bifidobacterium adolescentis [TaxId:1680] [255183] (4 PDB entries)

    8. Species Escherichia coli [TaxId:331111] [311496] (3 PDB entries)

    9. Species Escherichia coli [TaxId:562] [270950] (4 PDB entries)

    10. Species Flavobacterium sp. [TaxId:197856] [255816] (5 PDB entries)

    11. Species Geobacillus stearothermophilus [TaxId:1422] [311444] (1 PDB entry)

    12. Species Human (Homo sapiens) [TaxId:9606] [225770] (13 PDB entries)

    13. Species Listeria monocytogenes [TaxId:169963] [277525] (1 PDB entry)

    14. Species Neisseria polysaccharea [TaxId:489] [226280] (6 PDB entries)

    15. Species Oryzias latipes [TaxId:8090] [226401] (1 PDB entry)

    16. Species Pig (Sus scrofa) [TaxId:9823] [225875] (3 PDB entries)

    17. Species Protaminobacter rubrum [TaxId:126825] [225680] (2 PDB entries)

    18. Species Pseudomonas mesoacidophila [TaxId:265293] [224875] (9 PDB entries)

    19. Species Pyrococcus woesei [TaxId:2262] [226292] (1 PDB entry)

    20. Species Soybean (Glycine max) [TaxId:3847] [186821] (2 PDB entries)

    21. Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [278910] (6 PDB entries)

    22. Species Thermoactinomyces vulgaris [TaxId:2026] [254920] (6 PDB entries)

    23. Species Thermus aquaticus [TaxId:271] [328921] (1 PDB entry)

    24. Species Thermus brockianus [TaxId:56956] [189542] (1 PDB entry)

    25. Species Thermus thermophilus [TaxId:274] [188525] (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 appears in SCOPe 2.05
  
• Family c.1.8.1: Amylase, catalytic domain appears in SCOPe 2.07
  
• Family c.1.8.1: Amylase, catalytic domain appears in the current release, SCOPe 2.08