SCOPe 2.01: Family c.2.1.2: Tyrosine-dependent oxidoreductases

Lineage for Family c.2.1.2: Tyrosine-dependent oxidoreductases

1. Root: SCOPe 2.01

2. Class c: Alpha and beta proteins (a/b) [51349] (147 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.2.1.2: Tyrosine-dependent oxidoreductases [51751] (71 proteins)
   also known as short-chain dehydrogenases and SDR family
   parallel beta-sheet is extended by 7th strand, order 3214567; left-handed crossover connection between strands 6 and 7

Proteins:

1. (3R)-hydroxyacyl-CoA dehydrogenase domain of estradiol 17 beta-Dehydrogenase 4 [82294] (1 species)
   peroxisomal multifunctional enzyme type 2
   segment swapping involving a C-terminal extension to the family fold

   • Species Norway rat (Rattus norvegicus) [TaxId:10116] [82295] (1 PDB entry)

2. (s)-1-phenylethanol dehydrogenase [141902] (1 species)

   • Species Azoarcus sp. ebn1 [TaxId:76114] [141903] (2 PDB entries)
     Uniprot Q5P5I4 3-249

3. 1,3,6,8-tetrahydroxynaphthalene reductase [63929] (1 species)

   • Species Fungus (Magnaporthe grisea) [TaxId:148305] [63930] (1 PDB entry)

4. 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase) [51798] (1 species)

   • Species Fungus (Magnaporthe grisea) [TaxId:148305] [51799] (4 PDB entries)

5. 11-beta-hydroxysteroid dehydrogenase 1 [117423] (3 species)

   1. Species Guinea pig (Cavia porcellus) [TaxId:10141] [117425] (4 PDB entries)
      Uniprot Q6QLL4 23-296

   2. Species Human (Homo sapiens) [TaxId:9606] [117424] (19 PDB entries)
      Uniprot P28845

   3. Species Mouse (Mus musculus) [TaxId:10090] [141879] (3 PDB entries)
      Uniprot P50172 24-298

6. 15-hydroxyprostaglandin dehydrogenase, PGDH [141888] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [141889] (1 PDB entry)
     Uniprot P15428 3-256

7. 17-beta-hydroxysteroid dehydrogenase type XI [117426] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117427] (1 PDB entry)
     Uniprot Q8NBQ5 30-273

8. 2,4-dienoyl-CoA reductase, mitochondrial (DECR) [117421] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [117422] (3 PDB entries)
     Uniprot Q16698 35-328

9. 3-alpha,20-beta-hydroxysteroid dehydrogenase [51776] (1 species)

   • Species Streptomyces hydrogenans [TaxId:1905] [51777] (2 PDB entries)

10. 3-alpha-hydroxysteroid dehydrogenase [51778] (1 species)

    • Species Comamonas testosteroni [TaxId:285] [51779] (2 PDB entries)

11. 3beta/17beta hydroxysteroid dehydrogenase [82290] (1 species)

    • Species Comamonas testosteroni [TaxId:285] [82291] (1 PDB entry)

12. 7-alpha-hydroxysteroid dehydrogenase [51774] (1 species)

    • Species Escherichia coli [TaxId:562] [51775] (3 PDB entries)

13. ADP-L-glycero-D-mannoheptose 6-epimerase [51761] (1 species)

    • Species Escherichia coli [TaxId:562] [51762] (1 PDB entry)

14. Aldehyde reductase II [117413] (1 species)

    • Species Sporobolomyces salmonicolor [TaxId:5005] [117414] (3 PDB entries)
      Uniprot Q9UUN9

15. Bacterial sepiapterin reductase [141892] (1 species)

    • Species Chlorobium tepidum [TaxId:1097] [141893] (1 PDB entry)
      Uniprot Q8KES3 2-241
      CT0609

16. beta-keto acyl carrier protein reductase [51788] (8 species)

    1. Species Escherichia coli [TaxId:562] [51790] (3 PDB entries)

    2. Species Malaria parasite (Plasmodium falciparum) [TaxId:5833] [141877] (1 PDB entry)
       Uniprot Q86RB1 54-304

    3. Species Mycobacterium tuberculosis [TaxId:1773] [141875] (2 PDB entries)
       Uniprot P0A5Y4 9-245! Uniprot P0A5Y4 9-247

    4. Species Oil seed rape (Brassica napus) [TaxId:3708] [51789] (2 PDB entries)

    5. Species Streptomyces coelicolor [TaxId:1902] [117408] (8 PDB entries)
       Uniprot P16544 #SP

    6. Species Thermotoga maritima [TaxId:2336] [102150] (1 PDB entry)
       TM1169

    7. Species Thermus thermophilus [TaxId:274] [117407] (1 PDB entry)
       Uniprot Q5SK98

    8. Species Thermus thermophilus, TTHB020 [TaxId:274] [141876] (1 PDB entry)
       Uniprot Q53WH2 2-242

17. Biliverdin IX beta reductase [63931] (1 species)
    Histidine in the active site instead of the Tyr-Lys dyad

    • Species Human (Homo sapiens) [TaxId:9606] [63932] (5 PDB entries)

18. Carbonyl reductase [51765] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [102144] (1 PDB entry)
       dicarbonyl/L-xylulose reductase

    2. Species Mouse (Mus musculus) [TaxId:10090] [51766] (1 PDB entry)

19. Carbonyl reductase sniffer [110413] (2 species)

    1. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [110414] (1 PDB entry)
       Uniprot Q9W3H4 # cg10964-pa

    2. Species Nematode (Caenorhabditis elegans) [TaxId:6239] [186880] (1 PDB entry)

20. Carbonyl reductase/20beta-hydroxysteroid dehydrogenase [63935] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [141878] (5 PDB entries)
       Uniprot P16152 2-276

    2. Species Pig (Sus scrofa) [TaxId:9823] [63936] (1 PDB entry)

21. CDP-glucose-4,6-dehydratase [102136] (3 species)

    1. Species Salmonella enterica [TaxId:220341] [190019] (1 PDB entry)

    2. Species Salmonella typhimurium [TaxId:90371] [141873] (1 PDB entry)
       Uniprot P26397 2-356

    3. Species Yersinia pseudotuberculosis [TaxId:633] [102137] (1 PDB entry)

22. CDP-tyvelose-2-epimerase [102138] (1 species)

    • Species Salmonella typhi [TaxId:90370] [102139] (1 PDB entry)

23. Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase [51780] (1 species)

    • Species Pseudomonas sp., lb400 [TaxId:306] [51781] (1 PDB entry)

24. D(-)-3-hydroxybutyrate dehydrogenase [141886] (1 species)

    • Species Pseudomonas fragi [TaxId:296] [141887] (1 PDB entry)
      Uniprot Q5KST5 1-260

25. Dehydrogenase/reductase SDR family member 6, DHRS6 [141894] (1 species)
    Oxidoreductase UCPA

    • Species Human (Homo sapiens) [TaxId:9606] [141895] (1 PDB entry)
      Uniprot Q9BUT1 1-245

26. Dihydropteridin reductase (pteridine reductase) [51769] (6 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [51771] (1 PDB entry)

    2. Species Leishmania major [TaxId:5664] [63926] (10 PDB entries)
       Uniprot Q01782

    3. Species Leishmania tarentolae [TaxId:5689] [102145] (1 PDB entry)

    4. Species Nematode (Caenorhabditis elegans) [TaxId:6239] [89520] (1 PDB entry)

    5. Species Norway rat (Rattus norvegicus) [TaxId:10116] [51770] (2 PDB entries)

    6. Species Trypanosoma cruzi [TaxId:5693] [102146] (2 PDB entries)

27. Drosophila alcohol dehydrogenase [51782] (2 species)

    1. Species Fly (Drosophila lebanonensis) [TaxId:7225] [51783] (6 PDB entries)

    2. Species Fruit fly (Drosophila melanogaster) [TaxId:7227] [102147] (1 PDB entry)

28. DTDP-4-dehydrorhamnose reductase RfbD [110409] (1 species)

    • Species Clostridium acetobutylicum [TaxId:1488] [110410] (1 PDB entry)
      Uniprot Q97GQ1

29. dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) [75102] (1 species)

    • Species Salmonella typhimurium [TaxId:90371] [75103] (4 PDB entries)

30. dTDP-glucose 4,6-dehydratase (RmlB) [51755] (4 species)

    1. Species Escherichia coli [TaxId:562] [51756] (1 PDB entry)

    2. Species Salmonella enterica [TaxId:28901] [63925] (1 PDB entry)

    3. Species Streptococcus suis, serotype 2 [TaxId:1307] [69406] (6 PDB entries)

    4. Species Streptomyces venezuelae [TaxId:54571] [102133] (2 PDB entries)

31. Enoyl-ACP reductase [51791] (10 species)

    1. Species Anthrax bacillus (Bacillus anthracis) [TaxId:1392] [188487] (1 PDB entry)

    2. Species Bacillus subtilis [TaxId:1423] [189591] (2 PDB entries)

    3. Species Escherichia coli [TaxId:562] [51794] (13 PDB entries)

    4. Species Helicobacter pylori [TaxId:210] [102151] (2 PDB entries)

    5. Species Malaria parasite (Plasmodium falciparum) [TaxId:5833] [82296] (23 PDB entries)
       Uniprot Q9BJJ9 96-424 # fragment

    6. Species Mycobacterium leprae [TaxId:1769] [187924] (1 PDB entry)

    7. Species Mycobacterium tuberculosis, TB, gene InhA [TaxId:1773] [51793] (36 PDB entries)

    8. Species Oil seed rape (Brassica napus) [TaxId:3708] [51792] (4 PDB entries)

    9. Species Staphylococcus aureus [TaxId:1280] [189086] (3 PDB entries)

    10. Species Thermus thermophilus [TaxId:274] [117409] (1 PDB entry)
        Uniprot Q5SLI9

32. Erythromycin synthase, eryAI, 1st ketoreductase module [141909] (1 species)
    tandem repeat of two SDR-like modules resembling a dimer commonly founf in the family; only the second module retains the coenzyme-binding site

    • Species Saccharopolyspora erythraea [TaxId:1836] [141910] (2 PDB entries)
      Uniprot Q5UNP6 1448-1656! Uniprot Q5UNP6 1657-1915

33. GDP-4-keto-6-deoxy-d-mannose epimerase/reductase (GDP-fucose synthetase) [51757] (1 species)

    • Species Escherichia coli [TaxId:562] [51758] (8 PDB entries)

34. GDP-mannose 4,6-dehydratase [51759] (4 species)

    1. Species Escherichia coli [TaxId:562] [51760] (1 PDB entry)

    2. Species Human (Homo sapiens) [TaxId:9606] [102135] (1 PDB entry)

    3. Species Pseudomonas aeruginosa [TaxId:287] [102134] (1 PDB entry)

    4. Species Thale-cress (Arabidopsis thaliana) [TaxId:3702] [82289] (2 PDB entries)

35. GDP-mannose-3', 5'-epimerase [141890] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [141891] (4 PDB entries)
      Uniprot Q93VR3 13-374! Uniprot Q93VR3 13-375

36. Gluconate 5-dehydrogenase [110411] (1 species)

    • Species Thermotoga maritima [TaxId:2336] [110412] (1 PDB entry)
      Uniprot Q9WYS2

37. Glucose dehydrogenase [51784] (1 species)

    • Species Bacillus megaterium [TaxId:1404] [51785] (4 PDB entries)

38. Glucose dehydrogenase (5l265) [102155] (1 species)

    • Species Nematode (Caenorhabditis elegans) [TaxId:6239] [102156] (1 PDB entry)

39. Halohydrin dehalogenase HheC [102153] (1 species)
    haloalcohol dehalogenase: evolved a new activity; lost the NAD-binding site

    • Species Agrobacterium tumefaciens [TaxId:358] [102154] (5 PDB entries)

40. Human estrogenic 17beta-hydroxysteroid dehydrogenase [51772] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [51773] (16 PDB entries)
      Uniprot P14061

41. Hypothetical protein At5g02240 (T7H20_290) [117417] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [117418] (4 PDB entries)
      Uniprot Q94EG6

42. Hypothetical protein F25D1.5 [110415] (1 species)

    • Species Nematode (Caenorhabditis elegans) [TaxId:6239] [110416] (1 PDB entry)
      Uniprot Q19774

43. Hypothetical protein PA4017 [141911] (1 species)
    unknown function; the active site region is blocked by a loop; strong sequence similarity to mammalian TAT-interacting protein TIP30

    • Species Pseudomonas aeruginosa [TaxId:287] [141912] (1 PDB entry)
      Uniprot Q9HX10 4-215

44. Hypothetical protein R05D8.7 [117415] (1 species)

    • Species Nematode (Caenorhabditis elegans) [TaxId:6239] [117416] (1 PDB entry)
      Uniprot Q9N5G4

45. Hypothetical protein TTHA0369 [141896] (1 species)
    TT0321

    • Species Thermus thermophilus [TaxId:274] [141897] (1 PDB entry)
      Uniprot Q5SLC4 2-249

46. Levodione reductase [89523] (1 species)

    • Species Corynebacterium aquaticum [TaxId:144185] [89524] (1 PDB entry)

47. Mannitol dehydrogenase [63927] (1 species)

    • Species Mushroom (Agaricus bisporus) [TaxId:5341] [63928] (1 PDB entry)

48. meso-2,3-butanediol dehydrogenase [51786] (1 species)

    • Species Klebsiella pneumoniae [TaxId:573] [51787] (1 PDB entry)

49. Negative transcriptional regulator NmrA [69407] (1 species)
    has an UDP-galactose 4-epimerase-like structure but evolved a different function

    • Species Emericella nidulans (Aspergillus nidulans) [TaxId:162425] [69408] (5 PDB entries)
      Uniprot O59919

50. Peroxisomal multifunctional enzyme type 2 [141900] (1 species)
    17-beta-hydroxysteroid dehydrogenase 4

    • Species Human (Homo sapiens) [TaxId:9606] [141901] (1 PDB entry)
      Uniprot P51659 2-303
      the structure of C-terminal domain is also known, PDB entry 1S9C

51. Peroxisomal trans 2-enoyl CoA reductase [141884] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [141885] (1 PDB entry)
      Uniprot Q9BY49 7-303

52. Phenylcoumaran benzylic ether reductase [102140] (1 species)

    • Species Loblolly pine (Pinus taeda) [TaxId:3352] [102141] (1 PDB entry)

53. Pinoresinol-lariciresinol reductase [102142] (1 species)

    • Species Giant arborvitae (Thuja plicata) [TaxId:3316] [102143] (1 PDB entry)

54. Polymyxin resistance protein ArnA (PrmI) [117419] (1 species)
    evolved new activities: UDP-glucuronic acid decarboxylase, UDP-4-amino-4-deoxy-L-arabinose formyltransferase

    • Species Escherichia coli [TaxId:562] [117420] (7 PDB entries)
      Uniprot P77398

55. Putative carbonyl reductase sniffer [141913] (1 species)

    • Species Nematode (Caenorhabditis elegans) [TaxId:6239] [141914] (1 PDB entry)
      Uniprot P90780 1-250

56. Putative dehydrogenase ARPG836 (MGC4172) [117411] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [117412] (1 PDB entry)
      Uniprot Q6UWP2

57. Putative oxidoreductase Rv2002 [82292] (1 species)

    • Species Mycobacterium tuberculosis [TaxId:1773] [82293] (3 PDB entries)

58. R-specific alcohol dehydrogenase [89521] (1 species)

    • Species Lactobacillus brevis [TaxId:1580] [89522] (2 PDB entries)

59. Retinal dehydrogenase/reductase 3 [141907] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [141908] (1 PDB entry)
      Uniprot Q9BPX1 4-253

60. Rhizome secoisolariciresinol dehydrogenase [141898] (1 species)

    • Species Mayapple (Podophyllum peltatum) [TaxId:35933] [141899] (1 PDB entry)
      Uniprot Q94KL8 11-278

61. Sepiapterin reductase [51767] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [141874] (1 PDB entry)
       Uniprot P35270 5-261

    2. Species Mouse (Mus musculus) [TaxId:10090] [51768] (3 PDB entries)

62. Sorbitol dehydrogenase [102148] (1 species)

    • Species Rhodobacter sphaeroides [TaxId:1063] [102149] (1 PDB entry)

63. Sulfolipid biosynthesis protein SQD1 [51763] (1 species)

    • Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [51764] (4 PDB entries)

64. TAT-interacting protein TIP30 [141904] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [141905] (1 PDB entry)
       Uniprot Q9BUP3 5-236

    2. Species Mouse (Mus musculus) [TaxId:10090] [141906] (1 PDB entry)
       Uniprot Q9Z2G9 7-236

65. Tropinone reductase [51795] (3 species)

    1. Species Jimsonweed (Datura stramonium), I [TaxId:4076] [51796] (1 PDB entry)

    2. Species Jimsonweed (Datura stramonium), II [TaxId:4076] [51797] (4 PDB entries)

    3. Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [117410] (1 PDB entry)
       Uniprot Q9ASX2

66. Type II 3-hydroxyacyl-CoA dehydrogenase [63933] (3 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [102152] (2 PDB entries)
       Uniprot Q99714

    2. Species Norway rat (Rattus norvegicus) [TaxId:10116] [63934] (3 PDB entries)

    3. Species Thermus thermophilus [TaxId:274] [89525] (1 PDB entry)

67. UDP-glucuronate decarboxylase 1 [141880] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [141881] (1 PDB entry)
      Uniprot Q8NBZ7 87-398

68. UDP-N-acetylglucosamine 4-epimerase WbpP [110407] (1 species)

    • Species Pseudomonas aeruginosa [TaxId:287] [110408] (2 PDB entries)
      Uniprot Q8KN66 # list: Q8GGB8 Q9RHD6 99% identity

69. Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase) [51752] (4 species)

    1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [141872] (1 PDB entry)
       Uniprot P04397 11-357
       N-terminal domain of bifunctional Gal10 protein

    2. Species Escherichia coli [TaxId:562] [51753] (17 PDB entries)

    3. Species Human (Homo sapiens) [TaxId:9606] [51754] (7 PDB entries)

    4. Species Trypanosome (Trypanosoma brucei) [TaxId:5691] [89519] (1 PDB entry)

70. Xylitol dehydrogenase [141882] (1 species)

    • Species Gluconobacter oxydans [TaxId:442] [141883] (1 PDB entry)
      Uniprot Q8GR61 3-262

71. automated matches [190085] (29 species)
    not a true protein

    1. Species Alcaligenes faecalis [TaxId:511] [188427] (1 PDB entry)

    2. Species Alfalfa (Medicago sativa) [TaxId:3879] [187740] (1 PDB entry)

    3. Species Aquifex aeolicus [TaxId:224324] [188271] (2 PDB entries)

    4. Species Bacillus anthracis [TaxId:198094] [188031] (1 PDB entry)

    5. Species Burkholderia pseudomallei [TaxId:320372] [188614] (1 PDB entry)

    6. Species Comamonas testosteroni [TaxId:285] [189779] (3 PDB entries)

    7. Species Eimeria tenella [TaxId:413949] [187997] (1 PDB entry)

    8. Species Emericella nidulans [TaxId:162425] [187249] (3 PDB entries)

    9. Species Escherichia coli K-12 [TaxId:83333] [189924] (3 PDB entries)

    10. Species Francisella tularensis [TaxId:177416] [189289] (1 PDB entry)

    11. Species Francisella tularensis [TaxId:263] [188795] (1 PDB entry)

    12. Species Human (Homo sapiens) [TaxId:9606] [186828] (5 PDB entries)

    13. Species Lactobacillus brevis [TaxId:1580] [186912] (6 PDB entries)

    14. Species Leishmania donovani [TaxId:5661] [189607] (1 PDB entry)

    15. Species Malaria parasite (Plasmodium falciparum) [TaxId:5833] [186807] (1 PDB entry)

    16. Species Pandoraea pnomenusa [TaxId:93220] [189780] (3 PDB entries)

    17. Species Plasmodium berghei [TaxId:5821] [189246] (1 PDB entry)

    18. Species Plesiomonas shigelloides [TaxId:703] [189972] (8 PDB entries)

    19. Species Pseudomonas fragi [TaxId:296] [188080] (6 PDB entries)

    20. Species Pseudomonas putida [TaxId:303] [188252] (1 PDB entry)

    21. Species Streptomyces coelicolor [TaxId:1902] [189970] (2 PDB entries)

    22. Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [187183] (5 PDB entries)

    23. Species Thermus thermophilus [TaxId:274] [187600] (1 PDB entry)

    24. Species Thermus thermophilus [TaxId:300852] [187188] (4 PDB entries)

    25. Species Toxoplasma gondii [TaxId:383379] [187942] (2 PDB entries)

    26. Species Trypanosoma brucei [TaxId:5702] [187520] (4 PDB entries)

    27. Species Trypanosome (Trypanosoma brucei) [TaxId:5691] [187036] (1 PDB entry)

    28. Species Vibrio cholerae [TaxId:243277] [189479] (4 PDB entries)

    29. Species Vibrio cholerae [TaxId:593588] [189768] (3 PDB entries)

More info for Family c.2.1.2: Tyrosine-dependent oxidoreductases

Timeline for Family c.2.1.2: Tyrosine-dependent oxidoreductases:

• Family c.2.1.2: Tyrosine-dependent oxidoreductases first appeared (with stable ids) in SCOP 1.55
  
• Family c.2.1.2: Tyrosine-dependent oxidoreductases appears in SCOP 1.75
  
• Family c.2.1.2: Tyrosine-dependent oxidoreductases appears in SCOPe 2.02
  
• Family c.2.1.2: Tyrosine-dependent oxidoreductases appears in the current release, SCOPe 2.08