SCOPe 2.02: Family c.1.4.1: FMN-linked oxidoreductases

Lineage for Family c.1.4.1: FMN-linked oxidoreductases

1. Root: SCOPe 2.02

2. Class c: Alpha and beta proteins (a/b) [51349] (147 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.1.4: FMN-linked oxidoreductases [51395] (2 families)

5. Family c.1.4.1: FMN-linked oxidoreductases [51396] (19 proteins)

Proteins:

1. (S)-3-O-geranylgeranylglyceryl phosphate synthase [141765] (1 species)

   • Species Archaeoglobus fulgidus [TaxId:2234] [141766] (2 PDB entries)
     Uniprot O29844 1-231
     PcrB homolog AF0403

2. 12-oxophytodienoate reductase (OPR, OYE homolog) [63896] (3 species)

   1. Species Thale cress (Arabidopsis thaliana), OPR1 [TaxId:3702] [102040] (1 PDB entry)
      At1G76680

   2. Species Thale cress (Arabidopsis thaliana), OPR3 [TaxId:3702] [102041] (2 PDB entries)

   3. Species Tomato (Lycopersicon esculentum), OPR1 [TaxId:4081] [63897] (4 PDB entries)

3. 2,4-dienoyl-CoA reductase, N-terminal domain [102042] (1 species)

   • Species Escherichia coli [TaxId:562] [102043] (1 PDB entry)

4. Alpha subunit of glutamate synthase, central and FMN domains [69381] (2 species)
   Central domain (residues 423-780) may be a rudiment form of the FMN domain

   1. Species Azospirillum brasilense [TaxId:192] [69382] (2 PDB entries)

   2. Species Synechocystis sp. [TaxId:1143] [75055] (5 PDB entries)

5. Dihydroorotate dehydrogenase [51397] (7 species)

   1. Species Escherichia coli [TaxId:562] [82239] (1 PDB entry)

   2. Species Human (Homo sapiens) [TaxId:9606] [51400] (11 PDB entries)

   3. Species Lactococcus lactis, isozyme A [TaxId:1358] [51398] (9 PDB entries)

   4. Species Lactococcus lactis, isozyme B [TaxId:1358] [51399] (3 PDB entries)
      PyrD subunit

   5. Species Malaria parasite (Plasmodium falciparum) [TaxId:5833] [141759] (1 PDB entry)
      Uniprot Q08210 158-566
      homolog, mitochonrial

   6. Species Norway rat (Rattus norvegicus) [TaxId:10116] [102039] (2 PDB entries)

   7. Species Trypanosome (Trypanosoma brucei) [TaxId:5691] [141758] (1 PDB entry)
      Uniprot Q57U83 2-313

6. Dihydropyrimidine dehydrogenase, domain 4 [51410] (1 species)

   • Species Pig (Sus scrofa) [TaxId:9823] [51411] (5 PDB entries)

7. Flavocytochrome b2, C-terminal domain [51408] (1 species)

   • Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [51409] (11 PDB entries)
     Uniprot P00175
     N-terminal domain homologous to cytochrome b5

8. Glycolate oxidase [51404] (1 species)

   • Species Spinach (Spinacia oleracea) [TaxId:3562] [51405] (4 PDB entries)

9. Hydroxyacid oxidase [141761] (1 species)

   • Species Norway rat (Rattus norvegicus) [TaxId:10116] [141762] (1 PDB entry)
     Uniprot Q07523 1-349

10. Isopentenyl-diphosphate delta-isomerase [89454] (3 species)

    1. Species Bacillus subtilis [TaxId:1423] [89455] (2 PDB entries)

    2. Species Thermus thermophilus HB8 [TaxId:300852] [159377] (1 PDB entry)

    3. Species Thermus thermophilus [TaxId:274] [141760] (2 PDB entries)
       Uniprot Q53W52 23-332

11. Membrane-associated (S)-mandelate dehydrogenase [63898] (1 species)

    • Species Pseudomonas putida [TaxId:303] [63899] (3 PDB entries)

12. Morphinone reductase [75053] (1 species)

    • Species Pseudomonas putida [TaxId:303] [75054] (3 PDB entries)

13. NADPH dehydrogenase NamA [141763] (1 species)
    OYE homolog

    • Species Bacillus subtilis [TaxId:1423] [141764] (4 PDB entries)
      Uniprot P54550 1-337
      probable NADH-dependent flavin oxidoreductase YqjM

14. Old yellow enzyme (OYE) [51401] (2 species)

    1. Species Lager yeast (Saccharomyces pastorianus) [TaxId:27292] [51402] (12 PDB entries)

    2. Species Yeast (Candida albicans) [TaxId:5476] [51403] (2 PDB entries)

15. PcrB protein homolog YerE [102046] (2 species)
    provisional classification; it is not known whether this protein binds FMN or not

    1. Species Bacillus subtilis [TaxId:1423] [102047] (2 PDB entries)

    2. Species Staphylococcus aureus [TaxId:418127] [194170] (2 PDB entries)

16. Pentaerythritol tetranirate reductase [63900] (1 species)

    • Species Enterobacter cloacae [TaxId:550] [63901] (27 PDB entries)
      Uniprot P71278

17. Putative flavin oxidoreducatase TM0096 [102044] (1 species)
    Dihydrouridine synthase (Dus) homologue; contains extra C-terminal alpha-helical domain

    • Species Thermotoga maritima [TaxId:2336] [102045] (1 PDB entry)

18. Trimethylamine dehydrogenase, N-terminal domain [51406] (1 species)
    two other domains are alpha/beta Rossmann-like fold and beta/beta/alpha fold

    • Species Methylophilus methylotrophus, w3a1 [TaxId:17] [51407] (5 PDB entries)

19. automated matches [190228] (8 species)
    not a true protein

    1. Species Human (Homo sapiens) [TaxId:9606] [187000] (7 PDB entries)

    2. Species Lactococcus lactis [TaxId:1358] [186992] (2 PDB entries)

    3. Species Leishmania donovani [TaxId:5661] [188354] (1 PDB entry)

    4. Species Plasmodium falciparum [TaxId:36329] [189697] (1 PDB entry)

    5. Species Rattus norvegicus [TaxId:10116] [195883] (1 PDB entry)

    6. Species Solanum lycopersicum [TaxId:4081] [187823] (5 PDB entries)

    7. Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [187180] (2 PDB entries)

    8. Species Trypanosoma cruzi [TaxId:5693] [187324] (7 PDB entries)

More info for Family c.1.4.1: FMN-linked oxidoreductases

Timeline for Family c.1.4.1: FMN-linked oxidoreductases:

• Family c.1.4.1: FMN-linked oxidoreductases first appeared (with stable ids) in SCOP 1.55
  
• Family c.1.4.1: FMN-linked oxidoreductases appears in SCOPe 2.01
  
• Family c.1.4.1: FMN-linked oxidoreductases appears in SCOPe 2.03
  
• Family c.1.4.1: FMN-linked oxidoreductases appears in the current release, SCOPe 2.08