Structural Classification of Proteins

Fold: Periplasmic binding protein-like II

: consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
Fold: Periplasmic binding protein-like II [53849]
consists of two similar intertwined domain with 3 layers (a/b/a) each: duplication
mixed beta-sheet of 5 strands, order 21354; strand 5 is antiparallel to the rest

Superfamilies:

Periplasmic binding protein-like II [53850] (3)
Similar in architecture to the superfamily I but partly differs in topology
uperfamily
1. Phosphate binding protein-like [53851] (65)
  1. Oligo-peptide binding protein (OPPA) [53852]
    contains an additional alpha+beta domain inserted in the N-terminal domain
    1. Salmonella typhimurium [TaxId: 90371] [53853] (32)
    2. Bacillus subtilis [TaxId: 1423] [142799] (1)
      SQ P42061 40-543
    3. Thermotoga maritima [TaxId: 2336] [142800] (2)
      SQ Q9X0V0 23-557
      TM1223
  2. Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain [53854]
    1. Escherichia coli [TaxId: 562] [53855] (5)
  3. Lysine-,arginine-,ornithine-binding (LAO) protein [53856]
    1. Salmonella typhimurium [TaxId: 90371] [53857] (5)
  4. Sulphate-binding protein [53858]
    1. Salmonella typhimurium [TaxId: 90371] [53859] (1)
  5. Phosphate-binding protein [53860]
    1. Escherichia coli [TaxId: 562] [53861] (13)
    2. Mycobacterium tuberculosis [TaxId: 1773] [110747] (1)
      SQ P15712
  6. D-maltodextrin-binding protein, MBP [53862]
    contains a few additional helices in the C-terminal extension; homologous to thiaminase I
    1. Escherichia coli [TaxId: 562] [53863] (47)
      SQ P02928
    2. Alicyclobacillus acidocaldarius [TaxId: 405212] [102690] (3)
    3. Archaeon Pyrococcus furiosus [TaxId: 2261] [53864] (1)
    4. Archaeon Thermococcus litoralis [TaxId: 2265] [64191] (1)
      trehalose maltose-binding protein
    5. Escherichia coli K12 (Escherichia coli K-12) [TaxId: 83333] [159806] (1)
  7. Thiaminase I [53865]
    contains a few additional helices in the C-terminal extension; homologous to MBP
    1. Paenibacillus thiaminolyticus [TaxId: 49283] [53866] (3)
  8. Ferric-binding protein FbpA [53867]
    1. Haemophilus influenzae [TaxId: 727] [53868] (5)
    2. Mannheimia haemolytica [TaxId: 75985] [102691] (3)
      SQ Q9Z4N6
    3. Neisseria gonorrhoeae [TaxId: 485] [53869] (4)
      SQ Q50964 23-331
    4. Yersinia enterocolitica, YfuA [TaxId: 630] [117742] (1)
      SQ Q56925 28-338
    5. Serratia marcescens, SfuA [TaxId: 615] [117743] (1)
      SQ P21408 32-338
    6. Campylobacter jejuni [TaxId: 197] [117744] (1)
      SQ Q9PIV4 17-334
    7. Bordetella pertussis [TaxId: 520] [117745] (3)
      SQ Q7VXW9 31-349
  9. Dipeptide-binding protein [53870]
    similar domain organization to oligopeptide-binding protein, OPPA
    1. Escherichia coli [TaxId: 562] [53871] (2)
  10. Hypothetical protein YliB [102692]
    similar domain organization to oligo- and dipeptide-binding protein
    1. Escherichia coli [TaxId: 562] [102693] (1)
  11. Nickel-binding periplasmic protein NikA [102694]
    similar domain organization to oligo- and dipeptide-binding protein
    1. Escherichia coli [TaxId: 562] [102695] (10)
  12. Histidine-binding protein [53872]
    1. Escherichia coli [TaxId: 562] [53873] (1)
    2. Salmonella typhimurium [TaxId: 90371] [53874] (1)
  13. Spermidine/putrescine-binding protein PotD [53875]
    1. Escherichia coli [TaxId: 562] [53876] (2)
  14. Putrescine receptor (PotF) [53877]
    1. Escherichia coli [TaxId: 562] [53878] (1)
  15. Glutamine-binding protein [53879]
    1. Escherichia coli [TaxId: 562] [53880] (2)
  16. Glutamate receptor ligand binding core [53881]
    1. Rat (Rattus norvegicus), GluR2 [TaxId: 10116] [53882] (80)
    2. Synechocystis sp., GluR0 [TaxId: 1143] [64192] (3)
    3. Rat (Rattus norvegicus), GluR6 [TaxId: 10116] [142801] (14)
      SQ P42260 421-544,668-804! SQ P42260 429-544,667-806
    4. Rat (Rattus norvegicus), GluR5 [TaxId: 10116] [142802] (13)
      SQ P22756 429-546,667-799! SQ P22756 433-544,682-815
  17. Putative GluR0 ligand binding core [102696]
    1. Thermus thermophilus [TaxId: 274] [102697] (2)
  18. N-methyl-D-aspartate receptor subunit 1 [89787]
    1. Rat (Rattus norvegicus) [TaxId: 10116] [89788] (9)
    2. Rat (Rattus norvegicus), subtype 2A [TaxId: 10116] [142803] (2)
      SQ Q00959 404-539,661-801
  19. ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain [82559]
    there is an additional C-terminal allosteric domain in some species
    1. Mycobacterium tuberculosis [TaxId: 1773] [82560] (2)
    2. Escherichia coli [TaxId: 562] [102698] (2)
    3. Thermotoga maritima [TaxId: 2336] [102699] (3)
      SQ Q9X0D2
    4. Lactococcus lactis [TaxId: 1358] [142804] (8)
      SQ Q02129 1-204
    5. Thermus thermophilus [TaxId: 274] [142805] (1)
      SQ Q5SM15 1-206
  20. Molybdate-binding protein, ModA [53883]
    1. Escherichia coli [TaxId: 562] [53884] (2)
    2. Azotobacter vinelandii [TaxId: 354] [53885] (1)
    3. Archaeoglobus fulgidus [TaxId: 2234] [159807] (4)
      SQ O30142 32-342
  21. Cofactor-binding fragment of LysR-type protein CysB [53886]
    1. Klebsiella aerogenes [TaxId: 28451] [53887] (1)
  22. Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain [64193]
    1. Escherichia coli [TaxId: 562] [64194] (2)
  23. LysR-type regulatory protein CbnR [89789]
    1. Ralstonia eutropha [TaxId: 106590] [89790] (2)
  24. Alginate-binding periplasmic protein AlgQ2 [69624]
    1. Sphingomonas sp. [TaxId: 28214] [69625] (2)
  25. Putative lipoprotein (NlpA family) [102700]
    aka PG110, TpN32
    1. Staphylococcus aureus [TaxId: 1280] [102701] (1)
    2. Treponema pallidum [TaxId: 160] [117746] (1)
      SQ O07950 28-267
  26. Glycine betaine-binding periplasmic protein ProX [102702]
    1. Escherichia coli [TaxId: 562] [102703] (2)
  27. LysR-type regulatory protein DntR [110748]
    1. Burkholderia sp. [TaxId: 36773] [110749] (2)
      SQ Q7WT50 75-301
  28. Osmoprotection protein ProX [110750]
    functionally related to the bacterial ProX
    1. Archaeoglobus fulgidus [TaxId: 2234] [110751] (4)
      SQ O29280 # AF0982
  29. ABC transporter, periplasmic substrate-binding protein VCA0807 [117747]
    1. Vibrio cholerae [TaxId: 666] [117748] (1)
      SQ Q9KLD9 26-274
  30. Hypothetical protein TTHA1568 [142806]
    member of Pfam 02642 (DUF191)
    1. Thermus thermophilus [TaxId: 274] [142807] (2)
      SQ Q5SI12 3-272
  31. Alginate-binding periplasmic protein AlgQ1 [142808]
    1. Sphingomonas sp. [TaxId: 28214] [142809] (3)
      SQ Q9KWT6 25-514
  32. Hypothetical protein AF1704 [142810]
    member of Pfam 02642 (DUF191)
    1. Archaeoglobus fulgidus [TaxId: 2234] [142811] (1)
      SQ O28569 2-261
  33. Probable LysR-type transcriptional regulator PA0477 [142812]
    1. Pseudomonas aeruginosa [TaxId: 287] [142813] (4)
      SQ Q9I641 92-303
  34. Putative amino-acid transporter CjaA [142814]
    1. Campylobacter jejuni [TaxId: 197] [142815] (2)
      SQ Q0P9S0 29-276
  35. LysR-type regulatory protein Cbl [142816]
    1. Escherichia coli [TaxId: 562] [142817] (4)
      SQ Q47083 88-307
  36. Prephenate dehydratase [159808]
    1. Staphylococcus aureus [TaxId: 1280] [159809] (2)
      SQ Q99SX2 1-184
  37. Hypothetical protein SCo4506 [159810]
    1. Streptomyces coelicolor [TaxId: 1902] [159811] (4)
      SQ Q9L0T8 6-282
  38. Hypothetical protein YhfZ [159812]
    1. Shigella flexneri [TaxId: 623] [159813] (1)
      SQ Q83JA6 1-228
  39. Hypothetical protein DR0370 [159814]
    1. Deinococcus radiodurans [TaxId: 1299] [159815] (8)
      SQ Q9RXE3 14-285
  40. PstS-like phosphate-binding protein [159816]
    1. Human (Homo sapiens) [TaxId: 9606] [159817] (1)
      SQ P85173 1-376
2. Transferrin [53888] (11)
  further duplication: composed of two two-domain lobes
  1. Lactoferrin [53889]
    1. Human (Homo sapiens) [TaxId: 9606] [53890] (23)
    2. Cow (Bos taurus) [TaxId: 9913] [53891] (44)
    3. Domestic water buffalo (Bubalus arnee bubalis) [TaxId: 89462] [53892] (2)
    4. Goat (Capra hircus) [TaxId: 9925] [89791] (1)
    5. Horse (Equus caballus) [TaxId: 9796] [53893] (8)
    6. Arabian camel (Camelus dromedarius) [TaxId: 9838] [64195] (2)
  2. Ovotransferrin [53894]
    1. Duck (Anas platyrhynchos) [TaxId: 8839] [53895] (5)
    2. Chicken (Gallus gallus) [TaxId: 9031] [53896] (11)
      SQ P02789
  3. Transferrin [53897]
    1. Rabbit (Oryctolagus cuniculus) [TaxId: 9986] [53898] (6)
    2. Human (Homo sapiens) [TaxId: 9606] [53899] (17)
    3. Pig (Sus scrofa) [TaxId: 9823] [69626] (1)
3. PG0945 N-terminal domain-like [159818] (1)
  truncated to one domain; extra C-terminal region provides dimerisation interface
  1. Uncharacterized protein PG0945 [159819]
    putative ABC transporter, permease
    1. Porphyromonas gingivalis [TaxId: 837] [159820] (1)
      SQ Q7MVU4 48-183