Structural Classification of Proteins
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Superfamily: Thiamin diphosphate-binding fold (THDP-binding)

there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules
two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules
link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: Thiamin diphosphate-binding fold (THDP-binding) [52517]
    3 layers: a/b/a; parallel beta-sheet of 6 strands, order 213465
  4. Superfamily: Thiamin diphosphate-binding fold (THDP-binding) [52518]
    there are two different functional modules of this fold: pyridine-binding (Pyr) and pyrophosphate-binding (PP) modules
    two Pyr and two PP modules assemble together in a conserved heterotetrameric core that binds two THDP coenzyme molecules
    link to SUPERFAMILY database - Superfamily

Families:

  1. Pyruvate oxidase and decarboxylase Pyr module [88724] (12)
    the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpha/beta domain of Rossmann-like topology
    1. Pyruvate decarboxylase [88725]
      1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [88726] (1) picpic
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88727] (2) picpic
      3. Zymomonas mobilis [TaxId: 542] [88728] (1) picpic
    2. Indole-3-pyruvate decarboxylase [89648]
      1. Enterobacter cloacae [TaxId: 550] [89649] (1) picpic
    3. Pyruvate oxidase [88729]
      1. Lactobacillus plantarum [TaxId: 1590] [88730] (12) picpic
      2. Aerococcus viridans [TaxId: 1377] [142203] (4) picpic
    4. Benzoylformate decarboxylase [88731]
      1. Pseudomonas putida [TaxId: 303] [88732] (12) picpic
        SQ P20906
    5. Acetohydroxyacid synthase catalytic subunit [88733]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88734] (6) picpic
        SQ P07342 84-687
      2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142204] (6) picpic
        SQ P17597 86-280
    6. Catabolic acetolactate synthase [102328]
      1. Klebsiella pneumoniae [TaxId: 573] [102329] (3) picpic
    7. Carboxyethylarginine synthase [102330]
      1. Streptomyces clavuligerus [TaxId: 1901] [102331] (11) picpic
    8. Oxalyl-CoA decarboxylase [142205]
      1. Oxalobacter formigenes [TaxId: 847] [142206] (12) picpic
        SQ P40149 7-194
  2. TK-like Pyr module [88735] (5)
    different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
    1. Transketolase (TK), Pyr module [88736]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88737] (7) picpic
      2. Maize (Zea mays) [TaxId: 4577] [88738] (1) picpic
      3. Escherichia coli [TaxId: 562] [89650] (7) picpic
      4. Leishmania mexicana mexicana [TaxId: 44270] [117521] (1) picpic
        SQ Q8MPM3
    2. Pyruvate dehydrogenase E1 component, Pyr module [88739]
      E1A and E1B fused together in a single-chain protein
      1. Escherichia coli [TaxId: 562] [88740] (14) picpic
  3. Branched-chain alpha-keto acid dehydrogenase Pyr module [88741] (6)
    parent family to TK and PFOR
    heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
    1. Branched-chain alpha-keto acid dehydrogenase, Pyr module [88742]
      1. Human (Homo sapiens) [TaxId: 9606] [88743] (21) picpic
        SQ P21953 52-392
      2. Thermus thermophilus [TaxId: 274] [102332] (4) picpic
    2. 2-oxoisovalerate dehydrogenase (E1B), Pyr module [88744]
      chain A is alpha-subunit and chain B is beta-subunit
      1. Pseudomonas putida [TaxId: 303] [88745] (5) picpic
    3. E1-beta subunit of pyruvate dehydrogenase, Pyr module [69472]
      1. Archaeon Pyrobaculum aerophilum [TaxId: 13773] [69473] (1) picpic
      2. Human (Homo sapiens) [TaxId: 9606] [89653] (3) picpic
    4. Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain [117522]
      1. Bacillus stearothermophilus [TaxId: 1422] [117523] (2) picpic
        SQ P21874
  4. PFOR Pyr module [88746] (1)
    domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
    1. Pyruvate-ferredoxin oxidoreductase, PFOR, domain I [88747]
      1. Desulfovibrio africanus [TaxId: 873] [88748] (17) picpic
  5. Pyruvate oxidase and decarboxylase PP module [88749] (12)
    the N-terminal, Pyr module is separated from the C-terminal, PP module by an alpa/beta domain of Rossmann-like topology
    1. Pyruvate decarboxylase [88750]
      1. Brewer's yeast (Saccharomyces), uvarum strain [TaxId: 4932] [88751] (1) picpic
      2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88752] (2) picpic
      3. Zymomonas mobilis [TaxId: 542] [88753] (1) picpic
    2. Indole-3-pyruvate decarboxylase [89654]
      1. Enterobacter cloacae [TaxId: 550] [89655] (1) picpic
    3. Pyruvate oxidase [88754]
      1. Lactobacillus plantarum [TaxId: 1590] [88755] (12) picpic
      2. Aerococcus viridans [TaxId: 1377] [142207] (4) picpic
    4. Benzoylformate decarboxylase [88756]
      1. Pseudomonas putida [TaxId: 303] [88757] (12) picpic
        SQ P20906
    5. Acetohydroxyacid synthase catalytic subunit [88758]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88759] (6) picpic
        SQ P07342 84-687
      2. Thale cress (Arabidopsis thaliana), chloroplast [TaxId: 3702] [142208] (6) picpic
        SQ P17597 460-667
    6. Catabolic acetolactate synthase [102333]
      1. Klebsiella pneumoniae [TaxId: 573] [102334] (3) picpic
    7. Carboxyethylarginine synthase [102335]
      1. Streptomyces clavuligerus [TaxId: 1901] [102336] (11) picpic
    8. Oxalyl-CoA decarboxylase [142209]
      1. Oxalobacter formigenes [TaxId: 847] [142210] (12) picpic
        SQ P40149 370-552
  6. TK-like PP module [88760] (5)
    different order of the modules, PP module is N-terminal, Pyr module is next to it followed by a Rossmann-like domain
    1. Transketolase (TK), PP module [88761]
      1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [88762] (7) picpic
      2. Maize (Zea mays) [TaxId: 4577] [88763] (1) picpic
      3. Escherichia coli [TaxId: 562] [89656] (7) picpic
      4. Leishmania mexicana mexicana [TaxId: 44270] [117524] (1) picpic
        SQ Q8MPM3
    2. Pyruvate dehydrogenase E1 component, PP module [88764]
      E1A and E1B fused together in a single-chain protein
      1. Escherichia coli [TaxId: 562] [88765] (14) picpic
  7. Branched-chain alpha-keto acid dehydrogenase PP module [88766] (5)
    parent family to TK and PFOR
    heterodimeric protein related to TK; alpha-subunit is the PP module and the N-terminal domain of beta-subunit is the Pyr module
    1. Branched-chain alpha-keto acid dehydrogenase, PP module [88767]
      1. Human (Homo sapiens) [TaxId: 9606] [88768] (23) picpic
        SQ P12694 52-445
      2. Thermus thermophilus [TaxId: 274] [102337] (4) picpic
    2. E1-beta subunit of pyruvate dehydrogenase (PP module) [89651]
      1. Human (Homo sapiens) [TaxId: 9606] [89652] (3) picpic
    3. 2-oxoisovalerate dehydrogenase (E1B), PP module [88769]
      chain A is alpha-subunit and chain B is beta-subunit
      1. Pseudomonas putida [TaxId: 303] [88770] (5) picpic
    4. Pyruvate dehydrogenase E1-alpha, PdhA [117525]
      1. Bacillus stearothermophilus [TaxId: 1422] [117526] (2) picpic
        SQ P21873
  8. PFOR PP module [88771] (1)
    domains VI, I and II are arranged in the same way as the TK PP, Pyr and C domains
    1. Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI [88772]
      1. Desulfovibrio africanus [TaxId: 873] [88773] (17) picpic
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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