Structural Classification of Proteins
home mail help root up expand collapse

Superfamily: Periplasmic binding protein-like II

Similar in architecture to the superfamily I but partly differs in topology
link to SUPERFAMILY database - Superfamily

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. 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
  4. Superfamily: Periplasmic binding protein-like II [53850]
    Similar in architecture to the superfamily I but partly differs in topology
    link to SUPERFAMILY database - Superfamily

Families:

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

Enter search key:

MRC
site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
Copyright © 1994-2009 The scop authors / scop@mrc-lmb.cam.ac.uk