Structural Classification of Proteins




Fold: NAD(P)-binding Rossmann-fold domains
- 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
Lineage:
- Root: scop
- Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
- Fold: NAD(P)-binding Rossmann-fold domains [51734]
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
Superfamilies:
- NAD(P)-binding Rossmann-fold domains [51735] (12)
- Alcohol dehydrogenase-like, C-terminal domain [51736] (28)
N-terminal all-beta domain defines family
- Alcohol dehydrogenase [51737]
- Horse (Equus caballus) [TaxId: 9796] [51738] (38)

- Human (Homo sapiens), different isozymes [TaxId: 9606] [51739] (26)

- Mouse (Mus musculus), class II [TaxId: 10090] [51740] (3)

- Frog (Rana perezi) [TaxId: 8403] [89511] (2)

- Cod (Gadus callarias) [TaxId: 8053] [51741] (1)

- Archaeon Sulfolobus solfataricus [TaxId: 2287] [82286] (4)

- Archaeon Aeropyrum pernix [TaxId: 56636] [102121] (1)

- Pseudomonas aeruginosa [TaxId: 287] [102122] (1)

- Bacillus stearothermophilus [TaxId: 1422] [102123] (1)

- Hypothetical protein TM0436 [102124]
- Thermotoga maritima [TaxId: 2336] [102125] (1)

- Hypothetical protein YhdH [102126]
- Escherichia coli [TaxId: 562] [102127] (2)

- Hypothetical protein YahK [102128]
- Escherichia coli [TaxId: 562] [102129] (1)

- Benzyl alcohol dehydrogenase [89512]
- Acinetobacter calcoaceticus [TaxId: 471] [89513] (1)

- Bacterial secondary alcohol dehydrogenase [51742]
- Clostridium beijerinckii [TaxId: 1520] [51743] (3)

- Thermoanaerobacter brockii [TaxId: 29323] [51744] (6)

- Ketose reductase (sorbitol dehydrogenase) [51745]
- Silverleaf whitefly (Bemisia argentifolii) [TaxId: 77855] [51746] (1)

- Human (Homo sapiens) [TaxId: 9606] [102130] (3)

- Formaldehyde dehydrogenase [82287]
- Pseudomonas putida [TaxId: 303] [82288] (1)

- Quinone oxidoreductase [51747]
- Escherichia coli [TaxId: 562] [51748] (1)

- Thermus thermophilus [TaxId: 274] [89514] (2)

- Human (Homo sapiens) [TaxId: 9606] [117402] (1)

- Putative enoyl reductase domain of polyketide synthase [89515]
- Mycobacterium tuberculosis [TaxId: 1773] [89516] (1)

- 2,4-dienoyl-CoA reductase [89517]
- Yeast (Candida tropicalis) [TaxId: 5482] [89518] (5)

- Putative zinc-binding alcohol dehydrogenase [102131]
- Mouse (Mus musculus) [TaxId: 10090] [102132] (1)

- Cinnamyl alcohol dehydrogenase, ADH6 [110403]
- Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [110404] (3)

- Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase [110405]
- Guinea pig (Cavia porcellus) [TaxId: 10141] [110406] (5)

- B. subtilis YhfP homologue [117403]
- Bacillus stearothermophilus [TaxId: 1422] [117404] (1)

- Hypothetical protein YhfP [117405]
- Bacillus subtilis [TaxId: 1423] [117406] (2)

- Tyrosine-dependent oxidoreductases [51751] (108)
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
- Uridine diphosphogalactose-4-epimerase (UDP-galactose 4-epimerase) [51752]
- Escherichia coli [TaxId: 562] [51753] (17)

- Human (Homo sapiens) [TaxId: 9606] [51754] (7)

- Trypanosoma brucei [TaxId: 5691] [89519] (5)

- Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [141872] (1)

N-terminal domain of bifunctional Gal10 protein
- dTDP-glucose 4,6-dehydratase (RmlB) [51755]
- Escherichia coli [TaxId: 562] [51756] (1)

- Salmonella enterica [TaxId: 28901] [63925] (1)

- Streptococcus suis, serotype 2 [TaxId: 1307] [69406] (6)

- Streptomyces venezuelae [TaxId: 54571] [102133] (2)

- dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) [75102]
- Salmonella enterica serovar typhimurium [TaxId: 90371] [75103] (4)

- GDP-4-keto-6-deoxy-d-mannose epimerase/reductase (GDP-fucose synthetase) [51757]
- Escherichia coli [TaxId: 562] [51758] (8)

- GDP-mannose 4,6-dehydratase [51759]
- Escherichia coli [TaxId: 562] [51760] (1)

- Pseudomonas aeruginosa [TaxId: 287] [102134] (1)

- Human (Homo sapiens) [TaxId: 9606] [102135] (1)

- Thale-cress (Arabidopsis thaliana) [TaxId: 3702] [82289] (2)

- ADP-L-glycero-D-mannoheptose 6-epimerase [51761]
- Escherichia coli [TaxId: 562] [51762] (1)

- CDP-glucose-4,6-dehydratase [102136]
- Yersinia pseudotuberculosis [TaxId: 633] [102137] (1)

- Salmonella typhimurium [TaxId: 602] [141873] (2)

- CDP-tyvelose-2-epimerase [102138]
- Salmonella typhi [TaxId: 601] [102139] (1)

- Phenylcoumaran benzylic ether reductase [102140]
- Loblolly pine (Pinus taeda) [TaxId: 3352] [102141] (1)

- Pinoresinol-lariciresinol reductase [102142]
- Giant arborvitae (Thuja plicata) [TaxId: 3316] [102143] (1)

- Sulfolipid biosynthesis protein SQD1 [51763]
- Thale cress (Arabidopsis thaliana) [TaxId: 3702] [51764] (4)

- Negative transcriptional regulator NmrA [69407]
has an UDP-galactose 4-epimerase-like structure but evolved a different function
- Aspergillus nidulans [TaxId: 162425] [69408] (5)

- Carbonyl reductase [51765]
- Mouse (Mus musculus) [TaxId: 10090] [51766] (1)

- Human (Homo sapiens) [TaxId: 9606] [102144] (5)

dicarbonyl/L-xylulose reductase
- Sepiapterin reductase [51767]
- Mouse (Mus musculus) [TaxId: 10090] [51768] (3)

- Human (Homo sapiens) [TaxId: 9606] [141874] (6)

- Dihydropteridin reductase (pteridine reductase) [51769]
- Rat (Rattus norvegicus) [TaxId: 10116] [51770] (2)

- Human (Homo sapiens) [TaxId: 9606] [51771] (1)

- Leishmania major [TaxId: 5664] [63926] (23)

- Leishmania tarentolae [TaxId: 5689] [102145] (1)

- Trypanosoma cruzi [TaxId: 5693] [102146] (2)

- Nematode (Caenorhabditis elegans) [TaxId: 6239] [89520] (1)

- Human estrogenic 17beta-hydroxysteroid dehydrogenase [51772]
- Human (Homo sapiens) [TaxId: 9606] [51773] (16)

- 7-alpha-hydroxysteroid dehydrogenase [51774]
- Escherichia coli [TaxId: 562] [51775] (3)

- 3-alpha,20-beta-hydroxysteroid dehydrogenase [51776]
- Streptomyces hydrogenans [TaxId: 1905] [51777] (2)

- 3-alpha-hydroxysteroid dehydrogenase [51778]
- Comamonas testosteroni [TaxId: 285] [51779] (2)

- 3beta/17beta hydroxysteroid dehydrogenase [82290]
- Comamonas testosteroni [TaxId: 285] [82291] (1)

- Putative oxidoreductase Rv2002 [82292]
- Mycobacterium tuberculosis [TaxId: 1773] [82293] (3)

- R-specific alcohol dehydrogenase [89521]
- Lactobacillus brevis [TaxId: 1580] [89522] (15)

- Cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase [51780]
- Pseudomonas sp., lb400 [TaxId: 306] [51781] (1)

- Drosophila alcohol dehydrogenase [51782]
- Fruit fly (Drosophila melanogaster) [TaxId: 7227] [102147] (1)

- Fly (Drosophila lebanonensis) [TaxId: 7225] [51783] (7)

- Glucose dehydrogenase [51784]
- Bacillus megaterium [TaxId: 1404] [51785] (4)

- Sorbitol dehydrogenase [102148]
- Rhodobacter sphaeroides [TaxId: 1063] [102149] (1)

- meso-2,3-butanediol dehydrogenase [51786]
- Klebsiella pneumoniae [TaxId: 573] [51787] (1)

- Levodione reductase [89523]
- Corynebacterium aquaticum [TaxId: 144185] [89524] (1)

- Mannitol dehydrogenase [63927]
- Mushroom (Agaricus bisporus) [TaxId: 5341] [63928] (1)

- (3R)-hydroxyacyl-CoA dehydrogenase domain of estradiol 17 beta-Dehydrogenase 4 [82294]
peroxisomal multifunctional enzyme type 2
segment swapping involving a C-terminal extension to the family fold
- Rat (Rattus norvegicus) [TaxId: 10116] [82295] (1)

- beta-keto acyl carrier protein reductase [51788]
- Oil seed rape (Brassica napus) [TaxId: 3708] [51789] (7)

- Escherichia coli [TaxId: 562] [51790] (3)

- Thermotoga maritima [TaxId: 2336] [102150] (1)

TM1169
- Thermus thermophilus [TaxId: 274] [117407] (1)

- Streptomyces coelicolor [TaxId: 1902] [117408] (5)

- Mycobacterium tuberculosis [TaxId: 1773] [141875] (6)

- Thermus thermophilus, TTHB020 [TaxId: 274] [141876] (2)

- Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141877] (1)

- Enoyl-ACP reductase [51791]
- Oil seed rape (Brassica napus) [TaxId: 3708] [51792] (4)

- Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [82296] (19)

- Mycobacterium tuberculosis, TB, gene InhA [TaxId: 1773] [51793] (35)

- Escherichia coli [TaxId: 562] [51794] (14)

- Helicobacter pylori [TaxId: 210] [102151] (8)

- Thermus thermophilus [TaxId: 274] [117409] (9)

- Tropinone reductase [51795]
- Jimsonweed (Datura stramonium), I [TaxId: 4076] [51796] (1)

- Jimsonweed (Datura stramonium), II [TaxId: 4076] [51797] (4)

- Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117410] (2)

- 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase) [51798]
- Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [51799] (4)

- 1,3,6,8-tetrahydroxynaphthalene reductase [63929]
- Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [63930] (1)

- Biliverdin IX beta reductase [63931]
Histidine in the active site instead of the Tyr-Lys dyad
- Human (Homo sapiens) [TaxId: 9606] [63932] (5)

- Type II 3-hydroxyacyl-CoA dehydrogenase [63933]
- Rat (Rattus norvegicus) [TaxId: 10116] [63934] (3)

- Human (Homo sapiens) [TaxId: 9606] [102152] (4)

- Thermus thermophilus [TaxId: 274] [89525] (1)

- Carbonyl reductase/20beta-hydroxysteroid dehydrogenase [63935]
- Pig (Sus scrofa) [TaxId: 9823] [63936] (1)

- Human (Homo sapiens) [TaxId: 9606] [141878] (1)

- Halohydrin dehalogenase HheC [102153]
haloalcohol dehalogenase: evolved a new activity; lost the NAD-binding site
- Agrobacterium tumefaciens [TaxId: 358] [102154] (23)

- Glucose dehydrogenase (5l265) [102155]
- Nematode (Caenorhabditis elegans) [TaxId: 6239] [102156] (1)

- UDP-N-acetylglucosamine 4-epimerase WbpP [110407]
- Pseudomonas aeruginosa [TaxId: 287] [110408] (2)

- DTDP-4-dehydrorhamnose reductase RfbD [110409]
- Clostridium acetobutylicum [TaxId: 1488] [110410] (1)

- Gluconate 5-dehydrogenase [110411]
- Thermotoga maritima [TaxId: 2336] [110412] (1)

- Carbonyl reductase sniffer [110413]
- Fruit fly (Drosophila melanogaster) [TaxId: 7227] [110414] (1)

- Hypothetical protein F25D1.5 [110415]
- Caenorhabditis elegans [TaxId: 6239] [110416] (1)

- Putative dehydrogenase ARPG836 (MGC4172) [117411]
- Human (Homo sapiens) [TaxId: 9606] [117412] (1)

- Aldehyde reductase II [117413]
- Sporobolomyces salmonicolor [TaxId: 5005] [117414] (5)

- Hypothetical protein R05D8.7 [117415]
- Caenorhabditis elegans [TaxId: 6239] [117416] (1)

- Hypothetical protein At5g02240 (T7H20_290) [117417]
- Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117418] (7)

- Polymyxin resistance protein ArnA (PrmI) [117419]
evolved new activities: UDP-glucuronic acid decarboxylase, UDP-4-amino-4-deoxy-L-arabinose formyltransferase
- Escherichia coli [TaxId: 562] [117420] (12)

- 2,4-dienoyl-CoA reductase, mitochondrial (DECR) [117421]
- Human (Homo sapiens), [TaxId: 9606] [117422] (3)

- 11-beta-hydroxysteroid dehydrogenase 1 [117423]
- Human (Homo sapiens) [TaxId: 9606] [117424] (11)

- Guinea pig (Cavia porcellus) [TaxId: 10141] [117425] (1)

- Mouse (Mus musculus) [TaxId: 10090] [141879] (4)

- 17-beta-hydroxysteroid dehydrogenase type XI [117426]
- Human (Homo sapiens) [TaxId: 9606] [117427] (1)

- UDP-glucuronate decarboxylase 1 [141880]
- Human (Homo sapiens) [TaxId: 9606] [141881] (1)

- Xylitol dehydrogenase [141882]
- Gluconobacter oxydans [TaxId: 442] [141883] (8)

- Peroxisomal trans 2-enoyl CoA reductase [141884]
- Human (Homo sapiens) [TaxId: 9606] [141885] (4)

- D(-)-3-hydroxybutyrate dehydrogenase [141886]
- Pseudomonas fragi [TaxId: 296] [141887] (3)

- 15-hydroxyprostaglandin dehydrogenase, PGDH [141888]
- Human (Homo sapiens) [TaxId: 9606] [141889] (1)

- GDP-mannose-3', 5'-epimerase [141890]
- Thale cress (Arabidopsis thaliana) [TaxId: 3702] [141891] (8)

- Bacterial sepiapterin reductase [141892]
- Chlorobium tepidum [TaxId: 1097] [141893] (4)

CT0609
- Dehydrogenase/reductase SDR family member 6, DHRS6 [141894]
Oxidoreductase UCPA
- Human (Homo sapiens) [TaxId: 9606] [141895] (4)

- Hypothetical protein TTHA0369 [141896]
TT0321
- Thermus thermophilus [TaxId: 274] [141897] (4)

- Rhizome secoisolariciresinol dehydrogenase [141898]
- Mayapple (Podophyllum peltatum) [TaxId: 35933] [141899] (4)

- Peroxisomal multifunctional enzyme type 2 [141900]
17-beta-hydroxysteroid dehydrogenase 4
- Human (Homo sapiens) [TaxId: 9606] [141901] (6)

the structure of C-terminal domain is also known, PDB entry 1S9C
- (s)-1-phenylethanol dehydrogenase [141902]
- Azoarcus sp. ebn1 [TaxId: 76114] [141903] (6)

- TAT-interacting protein TIP30 [141904]
- Human (Homo sapiens) [TaxId: 9606] [141905] (1)

- Mouse (Mus musculus) [TaxId: 10090] [141906] (1)

- Retinal dehydrogenase/reductase 3 [141907]
- Human (Homo sapiens) [TaxId: 9606] [141908] (16)

- Erythromycin synthase, eryAI, 1st ketoreductase module [141909]
tandem repeat of two SDR-like modules resembling a dimer commonly founf in the family; only the second module retains the coenzyme-binding site
- Saccharopolyspora erythraea [TaxId: 1836] [141910] (4)

- Hypothetical protein PA4017 [141911]
unknown function; the active site region is blocked by a loop; strong sequence similarity to mammalian TAT-interacting protein TIP30
- Pseudomonas aeruginosa [TaxId: 287] [141912] (2)

- Putative carbonyl reductase sniffer [141913]
- Caenorhabditis elegans [TaxId: 6239] [141914] (6)

- Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain [51800] (51)
family members also share a common alpha+beta fold in C-terminal domain
- Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) [51801]
- Escherichia coli [TaxId: 562] [51802] (7)

- Bacillus stearothermophilus, nca 1503 [TaxId: 1422] [51803] (10)

- Achromobacter xylosoxidans [TaxId: 85698] [89526] (1)

formerly Alcaligenes xylosoxidans
- Thermus aquaticus [TaxId: 271] [51804] (13)

- Thermus thermophilus [TaxId: 274] [102157] (1)

- Thermotoga maritima [TaxId: 2336] [51805] (1)

- Archaeon Sulfolobus solfataricus [TaxId: 2287] [51806] (1)

- Archaeon Methanothermus fervidus [TaxId: 2180] [51807] (1)

- Trypanosoma brucei brucei, glycosome [TaxId: 5702] [51808] (1)

- Trypanosoma cruzi [TaxId: 5693] [75104] (3)

- Leishmania mexicana [TaxId: 5665] [51809] (5)

- American lobster (Homarus americanus) [TaxId: 6706] [51810] (2)

- South China Sea lobster (Palinurus versicolor) [TaxId: 82835] [51811] (5)

- Human (Homo sapiens) [TaxId: 9606] [51812] (1)

- Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [102158] (1)

- Spinach (Spinacia oleracea) [TaxId: 3562] [69409] (21)

- Human(Homo sapiens), liver isoform [TaxId: 9606] [141915] (8)

- Malaria parasite (Plasmodium falciparum) [TaxId: 5833] [141916] (12)

- Aspartate beta-semialdehyde dehydrogenase [51813]
- Escherichia coli [TaxId: 562] [51814] (4)

- Vibrio cholerae [TaxId: 666] [82297] (2)

- Haemophilus influenzae [TaxId: 727] [102159] (12)

- Streptococcus pneumoniae [TaxId: 1313] [141917] (11)

- Acetaldehyde dehydrogenase (acylating) [89527]
- Pseudomonas sp. [TaxId: 306] [89528] (1)

- Homoserine dehydrogenase [51815]
- Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [51816] (4)

- Saccharopine reductase [51817]
- Rice blast fungus (Magnaporthe grisea) [TaxId: 148305] [51818] (3)

- Diaminopimelic acid dehydrogenase (DAPDH) [51819]
- Corynebacterium glutamicum [TaxId: 1718] [51820] (4)

- Dihydrodipicolinate reductase [51821]
- Escherichia coli [TaxId: 562] [51822] (5)

- Mycobacterium tuberculosis [TaxId: 1773] [102160] (14)

- Thermotoga maritima [TaxId: 2336] [110417] (1)

- Myo-inositol 1-phosphate synthase [75105]
- Mycobacterium tuberculosis [TaxId: 1773] [75106] (1)

- Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [75107] (9)

- Archaeoglobus fulgidus [TaxId: 2234] [110418] (1)

- Caenorhabditis elegans [TaxId: 6239] [110419] (1)

- Hypothetical protein TM1419 [102161]
myo-inositol 1-phosphate synthase-related protein
- Thermotoga maritima [TaxId: 2336] [102162] (1)

- Hypothetical protein TM1643 [75108]
- Thermotoga maritima [TaxId: 2336] [75109] (2)

- 1-deoxy-D-xylulose-5-phosphate reductoisomerase [69410]
- Escherichia coli [TaxId: 562] [69411] (12)

- Zymomonas mobilis [TaxId: 542] [110420] (2)

- Biliverdin reductase [51823]
- Rat (Rattus norvegicus) [TaxId: 10116] [51824] (3)

- Glucose-fructose oxidoreductase, N-terminal domain [51825]
- Zymomonas mobilis [TaxId: 542] [51826] (12)

- Glucose 6-phosphate dehydrogenase, N-terminal domain [51827]
- Leuconostoc mesenteroides [TaxId: 1245] [51828] (9)

- Human (Homo sapiens) [TaxId: 9606] [51829] (1)

- Virulence factor MviM [110421]
- Escherichia coli [TaxId: 562] [110422] (1)

- N-acetyl-gamma-glutamyl-phosphate reductase ArgC [110423]
- Thermotoga maritima [TaxId: 2336] [110424] (1)

- Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117428] (5)

- Salmonella typhimurium [TaxId: 602] [141918] (1)

- Putative oxidoreductase VCA1048 [110425]
- Vibrio cholerae [TaxId: 666] [110426] (1)

- Probable oxidoreductase At4g09670 [117429]
- Thale cress (Arabidopsis thaliana) [TaxId: 3702] [117430] (1)

- Putative semialdehyde dehydrogenase [141919]
- Rice (Oryza sativa) [TaxId: 4530] [141920] (4)

- Galactose/lactose metabolism regulatory protein GAL80 [141921]
- Yeast (Kluyveromyces lactis) [TaxId: 28985] [141922] (1)

- Usg-1 protein homolog PA3116 [141923]
- Pseudomonas aeruginosa [TaxId: 287] [141924] (1)

- Hypothetical protein TM0312 [141925]
- Thermotoga maritima [TaxId: 2336] [141926] (2)

- Formate/glycerate dehydrogenases, NAD-domain [51830] (14)
this domain interrupts the other domain which defines family
- Formate dehydrogenase [51831]
- Pseudomonas sp., strain 101 [TaxId: 306] [51832] (2)

- Putative formate dehydrogenase [51833]
- Archaeon Pyrobaculum aerophilum [TaxId: 13773] [51834] (1)

- Transcription corepressor CtbP [82298]
C-terminal binding protein 1; a dehydrogenase
- Human (Homo sapiens), Ctbp1 [TaxId: 9606] [82299] (1)

- Rat (Rattus norvegicus), Ctbp3 [TaxId: 10116] [89529] (2)

- D-2-hydroxyisocaproate dehydrogenase [51835]
- Lactobacillus casei [TaxId: 1582] [51836] (1)

- D-glycerate dehydrogenase [51837]
- Hyphomicrobium methylovorum [TaxId: 84] [51838] (1)

- Phosphoglycerate dehydrogenase [51839]
has additional C-terminal domain of the ferredoxin fold
- Escherichia coli [TaxId: 562] [51840] (18)

- Mycobacterium tuberculosis [TaxId: 1773] [141927] (2)

- D-lactate dehydrogenase [51841]
- Lactobacillus helveticus [TaxId: 1587] [51842] (3)

- L-alanine dehydrogenase [51843]
- Phormidium lapideum [TaxId: 32060] [51844] (3)

- Nicotinamide nucleotide transhydrogenase dI component [63937]
L-alanine dehydrogenase homologue
- Rhodospirillum rubrum [TaxId: 1085] [63938] (28)

- S-adenosylhomocystein hydrolase [51845]
- Human (Homo sapiens) [TaxId: 9606] [51846] (2)

- Rat (Rattus norvegicus) [TaxId: 10116]