SCOPe 2.08: Family c.2.1.7: Aminoacid dehydrogenase-like, C-terminal domain

Lineage for Family c.2.1.7: Aminoacid dehydrogenase-like, C-terminal domain

1. Root: SCOPe 2.08

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

3. Fold c.2: NAD(P)-binding Rossmann-fold domains [51734] (1 superfamily)
   core: 3 layers, a/b/a; parallel beta-sheet of 6 strands, order 321456
   The nucleotide-binding modes of this and the next two folds/superfamilies are similar

4. Superfamily c.2.1: NAD(P)-binding Rossmann-fold domains [51735] (13 families)

5. Family c.2.1.7: Aminoacid dehydrogenase-like, C-terminal domain [51883] (12 proteins)
   extra N-terminal helix displaces the C-terminal helix (following strand 6) from its usual position creating a family nicotineamide-binding site

Proteins:

1. Glutamate dehydrogenase [51884] (8 species)

   1. Species Clostridium symbiosum [TaxId:1512] [51885] (4 PDB entries)

   2. Species Cow (Bos taurus) [TaxId:9913] [51889] (6 PDB entries)

   3. Species Human (Homo sapiens) [TaxId:9606] [75115] (2 PDB entries)

   4. Species Pyrobaculum islandicum [TaxId:2277] [117436] (1 PDB entry)
      Uniprot Q9Y8I4

   5. Species Pyrococcus furiosus [TaxId:2261] [51886] (1 PDB entry)

   6. Species Thermococcus litoralis [TaxId:2265] [51887] (1 PDB entry)

   7. Species Thermococcus profundus [TaxId:49899] [63943] (1 PDB entry)

   8. Species Thermotoga maritima [TaxId:2336] [51888] (3 PDB entries)

2. Glutamyl tRNA-reductase middle domain [69413] (1 species)
   other domains of this protein are distinct from those usually associated with the family domain

   • Species Methanopyrus kandleri [TaxId:2320] [69414] (1 PDB entry)

3. Leucine dehydrogenase [51890] (1 species)

   • Species Bacillus sphaericus [TaxId:1421] [51891] (1 PDB entry)

4. Malate oxidoreductase (malic enzyme) [110434] (1 species)

   • Species Thermotoga maritima [TaxId:2336] [110435] (1 PDB entry)
     Uniprot Q9WZ12

5. Methylene-tetrahydromethanopterin dehydrogenase [82303] (1 species)

   • Species Methylobacterium extorquens [TaxId:408] [82304] (2 PDB entries)

6. Methylenetetrahydrofolate dehydrogenase/cyclohydrolase [51894] (3 species)
   the two-domain organization is similar to that of aminoacid dehydrogenases, but both domains are truncated

   1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [51897] (2 PDB entries)

   2. Species Escherichia coli [TaxId:562] [51896] (1 PDB entry)

   3. Species Human (Homo sapiens) [TaxId:9606] [51895] (7 PDB entries)

7. Mitochondrial NAD(P)-dependent malic enzyme [51898] (3 species)
   includes C-terminal additional subdomains

   1. Species Domestic pigeon (Columba livia) [TaxId:8932] [75116] (1 PDB entry)

   2. Species Human (Homo sapiens) [TaxId:9606] [51899] (10 PDB entries)

   3. Species Pig roundworm (Ascaris suum) [TaxId:6253] [75117] (2 PDB entries)

8. Phenylalanine dehydrogenase [51892] (1 species)

   • Species Rhodococcus sp., M4 [TaxId:1831] [51893] (4 PDB entries)

9. Putative shikimate dehydrogenase YdiB [82305] (1 species)

   • Species Escherichia coli [TaxId:562] [82306] (3 PDB entries)

10. Shikimate 5-dehydrogenase AroE [89538] (6 species)

    1. Species Aquifex aeolicus [TaxId:63363] [225281] (3 PDB entries)

    2. Species Escherichia coli [TaxId:562] [89539] (1 PDB entry)

    3. Species Geobacillus kaustophilus [TaxId:1462] [225426] (1 PDB entry)

    4. Species Haemophilus influenzae [TaxId:727] [102173] (2 PDB entries)

    5. Species Methanococcus jannaschii [TaxId:2190] [89540] (1 PDB entry)
       MJ1084

    6. Species Staphylococcus epidermidis [TaxId:176279] [225658] (2 PDB entries)

11. Shikimate 5-dehydrogenase-like protein HI0607 [89536] (1 species)

    • Species Haemophilus influenzae [TaxId:727] [89537] (1 PDB entry)

12. automated matches [227005] (6 species)
    not a true protein

    1. Species Cow (Bos taurus) [TaxId:9913] [225674] (6 PDB entries)

    2. Species Escherichia coli [TaxId:83333] [346973] (3 PDB entries)

    3. Species Geobacillus stearothermophilus [TaxId:272567] [361597] (1 PDB entry)

    4. Species Human (Homo sapiens) [TaxId:9606] [353659] (2 PDB entries)

    5. Species Salmonella enterica [TaxId:90371] [226190] (1 PDB entry)

    6. Species Thermotoga maritima [TaxId:2336] [255206] (1 PDB entry)

More info for Family c.2.1.7: Aminoacid dehydrogenase-like, C-terminal domain

Timeline for Family c.2.1.7: Aminoacid dehydrogenase-like, C-terminal domain:

• Family c.2.1.7: Aminoacid dehydrogenase-like, C-terminal domain first appeared (with stable ids) in SCOP 1.55, called Family c.2.1.7: Amino-acid dehydrogenase-like, C-terminal domain
  
• Family c.2.1.7: Aminoacid dehydrogenase-like, C-terminal domain appears in SCOPe 2.07