Structural Classification of Proteins

Fold: Reductase/isomerase/elongation factor common domain

: barrel, closed; n=6, S=10; greek-key

Lineage:

Root: scop
Class: All beta proteins [48724]
Fold: Reductase/isomerase/elongation factor common domain [50412]
barrel, closed; n=6, S=10; greek-key

Superfamilies:

Riboflavin synthase domain-like [63380] (3)
uperfamily
1. Riboflavin synthase [63783] (2)
  duplication: consists of two homologous domains
  1. Riboflavin synthase [63784]
    trimerizes via the additional C-terminal helix
    1. Escherichia coli [TaxId: 562] [63785] (4)
      SQ P29015 1-87
    2. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82113] (1)
2. Ferredoxin reductase FAD-binding domain-like [63381] (19)
  coupled with a NADP-binding domain of alpha/beta class
  1. Ferredoxin reductase (flavodoxin reductase) N-terminal domain [50415]
    1. Spinach (Spinacia oleracea) [TaxId: 3562] [50416] (7)
    2. Garden pea (Pisum sativum) [TaxId: 3888] [50417] (4)
    3. Paprika (Capsicum annuum) [TaxId: 4072] [50418] (1)
    4. Maize (Zea mays), leaf isoform [TaxId: 4577] [50419] (2)
    5. Maize (Zea mays), root isoform [TaxId: 4577] [63786] (1)
    6. Cyanobacterium (Anabaena sp.), pcc 7119 [TaxId: 1167] [50420] (25)
    7. Escherichia coli [TaxId: 562] [50421] (1)
    8. Azotobacter vinelandii [TaxId: 354] [50422] (1)
  2. NAD(P)H:flavin oxidoreductase [50423]
    1. Escherichia coli [TaxId: 562] [50424] (1)
  3. Nitrate reductase core domain [50425]
    1. Corn (Zea mays) [TaxId: 4577] [50426] (3)
  4. cytochrome b5 reductase [50427]
    1. Pig (Sus scrofa), liver [TaxId: 9823] [50428] (1)
    2. Rat (Rattus norvegicus) [TaxId: 10116] [69273] (3)
      SQ P20070 33-300
    3. Human (Homo sapiens) [TaxId: 9606] [117215] (1)
      SQ P00387 30-300
  5. Phthalate dioxygenase reductase [50430]
    contains additional 2Fe-2S ferredoxin domain
    1. Pseudomonas cepacia, db01 [TaxId: 292] [50431] (1)
  6. Benzoate dioxygenase reductase [74959]
    1. Acinetobacter sp. [TaxId: 472] [74960] (1)
  7. Dihydroorotate dehydrogenase B, PyrK subunit [50433]
    1. Lactococcus lactis, isozyme B [TaxId: 1358] [50434] (3)
  8. Flavohemoglobin, central domain [50436]
    contains additional globin domain
    1. Alcaligenes eutrophus [TaxId: 106590] [50437] (1)
    2. Escherichia coli [TaxId: 562] [74961] (1)
  9. Methane monooxygenase component C, MmoC [117216]
    1. Methylococcus capsulatus [TaxId: 414] [117217] (1)
      SQ P22868 99-348 # structure of the N-terminal, 2Fe-2S ferredoxin domain is also known (1JQ4; scop_sp 69669)
3. NADPH-cytochrome p450 reductase FAD-binding domain-like [50438] (3)
  there is an alpha-helical subdomain inserted in this domain
  1. NADPH-cytochrome p450 reductase [50439]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [50440] (4)
  2. Sulfite reductase flavoprotein [50441]
    1. Escherichia coli [TaxId: 562] [50442] (2)
  3. Neuronal nitric-oxide synthase FAD/NADP+ domain [69274]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [69275] (2)
      SQ P29476 750-1413
Riboflavin kinase-like [82114] (2)
uperfamily
1. ATP-dependent riboflavin kinase-like [82115] (3)
  1. Riboflavin kinase [82116]
    1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [82117] (4)
    2. Human (Homo sapiens) [TaxId: 9606] [89338] (4)
      encoded by FLJ11149
  2. Riboflavin kinase domain of bifunctional FAD synthetase [101786]
    1. Thermotoga maritima [TaxId: 2336] [101787] (7)
      SQ Q9WZW1
      TM0379
2. CTP-dependent riboflavin kinase-like [159154] (2)
  Pfam 01982; newly characterized archaeal family (formerly DUF120)
  1. CTP-dependent riboflavin kinase, Rfk [159155]
    1. Thermoplasma acidophilum [TaxId: 2303] [159156] (1)
      SQ Q9HJA6 90-220
    2. Methanococcus jannaschii [TaxId: 2190] [159157] (7)
      SQ Q60365 1-136
FucI/AraA C-terminal domain-like [50443] (2)
uperfamily
1. L-fucose isomerase, C-terminal domain [50444] (1)
  1. L-fucose isomerase, C-terminal domain [50445]
    1. Escherichia coli [TaxId: 562] [50446] (1)
2. AraA C-terminal domain-like [141331] (1)
  C-terminal part of Pfam 02610
  1. L-arabinose isomerase AraA [141332]
    1. Escherichia coli [TaxId: 562] [141333] (6)
      SQ P08202 329-498
Translation proteins [50447] (6)
uperfamily
1. Elongation factors [50448] (18)
  1. Elongation factor Tu (EF-Tu), domain 2 [50449]
    N-terminal domain is related to G proteins; C-terminal domain is (6,10) barrel of circularly permuted topology
    1. Escherichia coli [TaxId: 562] [50450] (8)
      SQ P02990
    2. Thermus aquaticus [TaxId: 271] [50451] (4)
    3. Thermus thermophilus [TaxId: 274] [50452] (9)
    4. Cow (Bos taurus), mitochondrial [TaxId: 9913] [50453] (2)
      SQ P49410 56-452
  2. Elongation factor eEF-1alpha, domain 2 [50454]
    eukaryotic and archaeal homologue of EF-Tu
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [50455] (6)
    2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69276] (2)
      SQ P35021
  3. Elongation factor G (EF-G), domain II [50456]
    1. Thermus thermophilus [TaxId: 274] [50457] (9)
    2. Thermus thermophilus, EF-G-2 [TaxId: 274] [141334] (2)
      SQ Q5SI76 268-370
      TTHA1498
  4. Elongation factor 2 (eEF-2), domain II [82118]
    1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [82119] (22)
      SQ P32324
  5. Initiation factor eIF2 gamma subunit, domain II [74962]
    1. Archaeon Pyrococcus abyssi [TaxId: 29292] [74963] (5)
    2. Archaeon Methanococcus jannaschii [TaxId: 2190] [101788] (1)
    3. Sulfolobus solfataricus [TaxId: 2287] [141335] (6)
      SQ Q980A5 207-320
  6. Initiation factor IF2/eIF5b, domains 2 and 4 [50458]
    the C-terminal domain 4 has the same fold as domain 2; it probably binds fMet-tRNAfmet
    1. Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262] [50459] (3)
    2. Bacillus stearothermophilus [TaxId: 1422] [50460] (1)
  7. Eukaryotic peptide chain release factor ERF2, post-G domain [110225]
    1. Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] [110226] (3)
      SQ O74718
  8. Hypothetical protein PF0907 [110227]
    stand-alone protein related to this domain
    1. Pyrococcus furiosus [TaxId: 2261] [110228] (1)
      SQ Q8U2D2 18-108
  9. Elongation factor SelB, domains 2 and 4 [117218]
    EF-Tu homologue, contains extra C-terminal domain (domain 4) of the same fold as the postG domain 2
    1. Methanococcus maripaludis [TaxId: 39152] [117219] (3)
      SQ Q8J307
  10. Sulfate adenylate transferase subunit cysN/C, EF-Tu domain 2-like domain [141336]
    1. Pseudomonas syringae pv. tomato [TaxId: 323] [141337] (1)
      SQ Q87WW1 238-329
2. Ribosomal protein L3 [50461] (4)
  1. Ribosomal protein L3 [50462]
    superfamily fold is elaborated with additional structures
    1. Archaeon Haloarcula marismortui [TaxId: 2238] [50463] (58)
      SQ P20279
    2. Thermus thermophilus [TaxId: 274] [159158] (11)
      SQ Q72I04 1-205
    3. Escherichia coli [TaxId: 562] [159159] (29)
      SQ P60438 1-209
    4. Deinococcus radiodurans [TaxId: 1299] [159160] (9)
      SQ Q9RXK2 1-205
3. Ribosomal protein L35ae [117220] (1)
  Pfam 01247
  1. Ribosomal protein L35ae [117221]
    1. Pyrococcus furiosus [TaxId: 2261] [117222] (1)
      SQ Q8TZV6
4. RimM N-terminal domain-like [141338] (1)
  Pfam 01782
  1. 16S rRNA processing protein RimM, N-terminal domain [141339]
    1. Pseudomonas aeruginosa [TaxId: 287] [141340] (1)
      SQ Q9HXQ0 7-95
5. Gar1-like SnoRNP [141341] (1)
  stand alone proteins, which are similar structurally but not sequentially to the elongation factor domains, unlike PF0907
  1. Gar1 homolog PF1791 [141342]
    1. Archaeon Pyrococcus furiosus [TaxId: 2261] [141343] (4)
      SQ Q8U029 1-73
6. AlaX-M N-terminal domain-like [159161] (1)
  Does NOT belong to Pfam 01411
  1. AlaX-M trans-editing enzyme, N-terminal domain [159162]
    1. Pyrococcus horikoshii [TaxId: 53953] [159163] (1)
      SQ O57848 1-87