SCOPe 2.04: Family c.94.1.1: Phosphate binding protein-like

Lineage for Family c.94.1.1: Phosphate binding protein-like

1. Root: SCOPe 2.04

2. Class c: Alpha and beta proteins (a/b) [51349] (148 folds)

3. Fold c.94: Periplasmic binding protein-like II [53849] (1 superfamily)
   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 c.94.1: Periplasmic binding protein-like II [53850] (4 families)
   Similar in architecture to the superfamily I but partly differs in topology

5. Family c.94.1.1: Phosphate binding protein-like [53851] (42 proteins)

Proteins:

1. ABC transporter, periplasmic substrate-binding protein VCA0807 [117747] (1 species)

   • Species Vibrio cholerae [TaxId:666] [117748] (1 PDB entry)
     Uniprot Q9KLD9 26-274

2. Alginate-binding periplasmic protein AlgQ1 [142808] (1 species)

   • Species Sphingomonas sp. [TaxId:28214] [142809] (1 PDB entry)
     Uniprot Q9KWT6 25-514

3. Alginate-binding periplasmic protein AlgQ2 [69624] (1 species)

   • Species Sphingomonas sp. [TaxId:28214] [69625] (2 PDB entries)

4. ATP phosphoribosyltransferase (ATP-PRTase, HisG), catalytic domain [82559] (5 species)
   there is an additional C-terminal allosteric domain in some species

   1. Species Escherichia coli [TaxId:562] [102698] (2 PDB entries)

   2. Species Lactococcus lactis [TaxId:1358] [142804] (2 PDB entries)
      Uniprot Q02129 1-204

   3. Species Mycobacterium tuberculosis [TaxId:1773] [82560] (2 PDB entries)

   4. Species Thermotoga maritima [TaxId:2336] [102699] (3 PDB entries)
      Uniprot Q9X0D2

   5. Species Thermus thermophilus [TaxId:274] [142805] (1 PDB entry)
      Uniprot Q5SM15 1-206

5. Cofactor-binding fragment of LysR-type protein CysB [53886] (1 species)

   • Species Klebsiella aerogenes [TaxId:28451] [53887] (1 PDB entry)

6. D-maltodextrin-binding protein, MBP [53862] (5 species)
   contains a few additional helices in the C-terminal extension; homologous to thiaminase I

   1. Species Alicyclobacillus acidocaldarius [TaxId:405212] [102690] (3 PDB entries)

   2. Species Escherichia coli K-12 [TaxId:83333] [159806] (5 PDB entries)

   3. Species Escherichia coli [TaxId:562] [53863] (62 PDB entries)
      Uniprot P02928

   4. Species Pyrococcus furiosus [TaxId:2261] [53864] (1 PDB entry)

   5. Species Thermococcus litoralis [TaxId:2265] [64191] (1 PDB entry)
      trehalose maltose-binding protein

7. Dipeptide-binding protein [53870] (1 species)
   similar domain organization to oligopeptide-binding protein, OPPA

   • Species Escherichia coli [TaxId:562] [53871] (2 PDB entries)

8. Ferric-binding protein FbpA [53867] (7 species)

   1. Species Bordetella pertussis [TaxId:520] [117745] (1 PDB entry)
      Uniprot Q7VXW9 31-349

   2. Species Campylobacter jejuni [TaxId:197] [117744] (2 PDB entries)
      Uniprot Q9PIV4 17-334

   3. Species Haemophilus influenzae [TaxId:727] [53868] (12 PDB entries)

   4. Species Mannheimia haemolytica [TaxId:75985] [102691] (3 PDB entries)
      Uniprot Q9Z4N6

   5. Species Neisseria gonorrhoeae [TaxId:485] [53869] (5 PDB entries)
      Uniprot Q50964 23-331

   6. Species Serratia marcescens, SfuA [TaxId:615] [117743] (1 PDB entry)
      Uniprot P21408 32-338

   7. Species Yersinia enterocolitica, YfuA [TaxId:630] [117742] (1 PDB entry)
      Uniprot Q56925 28-338

9. Glutamate receptor ligand binding core [53881] (5 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [189807] (3 PDB entries)

   2. Species Norway rat (Rattus norvegicus), GluR2 [TaxId:10116] [53882] (124 PDB entries)

   3. Species Norway rat (Rattus norvegicus), GluR5 [TaxId:10116] [142802] (3 PDB entries)
      Uniprot P22756 429-546,667-799! Uniprot P22756 433-544,682-815

   4. Species Norway rat (Rattus norvegicus), GluR6 [TaxId:10116] [142801] (3 PDB entries)
      Uniprot P42260 421-544,668-804! Uniprot P42260 429-544,667-806

   5. Species Synechocystis sp., GluR0 [TaxId:1143] [64192] (3 PDB entries)

10. Glutamine-binding protein [53879] (1 species)

    • Species Escherichia coli [TaxId:562] [53880] (2 PDB entries)

11. Glycine betaine-binding periplasmic protein ProX [102702] (1 species)

    • Species Escherichia coli [TaxId:562] [102703] (2 PDB entries)

12. Histidine-binding protein [53872] (2 species)

    1. Species Escherichia coli [TaxId:562] [53873] (1 PDB entry)

    2. Species Salmonella typhimurium [TaxId:90371] [53874] (1 PDB entry)

13. Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain [64193] (1 species)

    • Species Escherichia coli [TaxId:562] [64194] (2 PDB entries)

14. Hypothetical protein AF1704 [142810] (1 species)
    member of Pfam PF02642 (DUF191)

    • Species Archaeoglobus fulgidus [TaxId:2234] [142811] (1 PDB entry)
      Uniprot O28569 2-261

15. Hypothetical protein DR0370 [159814] (1 species)

    • Species Deinococcus radiodurans [TaxId:1299] [159815] (1 PDB entry)
      Uniprot Q9RXE3 14-285

16. Hypothetical protein SCo4506 [159810] (1 species)

    • Species Streptomyces coelicolor [TaxId:1902] [159811] (1 PDB entry)
      Uniprot Q9L0T8 6-282

17. Hypothetical protein TTHA1568 [142806] (1 species)
    member of Pfam PF02642 (DUF191)

    • Species Thermus thermophilus [TaxId:274] [142807] (2 PDB entries)
      Uniprot Q5SI12 3-272

18. Hypothetical protein YhfZ [159812] (1 species)

    • Species Shigella flexneri [TaxId:623] [159813] (1 PDB entry)
      Uniprot Q83JA6 1-228

19. Hypothetical protein YliB [102692] (1 species)
    similar domain organization to oligo- and dipeptide-binding protein

    • Species Escherichia coli [TaxId:562] [102693] (1 PDB entry)

20. Lysine-,arginine-,ornithine-binding (LAO) protein [53856] (1 species)

    • Species Salmonella typhimurium [TaxId:90371] [53857] (5 PDB entries)

21. LysR-type regulatory protein Cbl [142816] (1 species)

    • Species Escherichia coli [TaxId:562] [142817] (1 PDB entry)
      Uniprot Q47083 88-307

22. LysR-type regulatory protein CbnR [89789] (1 species)

    • Species Ralstonia eutropha [TaxId:106590] [89790] (2 PDB entries)

23. LysR-type regulatory protein DntR [110748] (1 species)

    • Species Burkholderia sp. [TaxId:36773] [110749] (2 PDB entries)
      Uniprot Q7WT50 75-301

24. Molybdate-binding protein, ModA [53883] (3 species)

    1. Species Archaeoglobus fulgidus [TaxId:2234] [159807] (3 PDB entries)
       Uniprot O30142 32-342

    2. Species Azotobacter vinelandii [TaxId:354] [53885] (1 PDB entry)

    3. Species Escherichia coli [TaxId:562] [53884] (2 PDB entries)

25. N-methyl-D-aspartate receptor subunit 1 [89787] (2 species)

    1. Species Norway rat (Rattus norvegicus) [TaxId:10116] [89788] (14 PDB entries)

    2. Species Norway rat (Rattus norvegicus), subtype 2A [TaxId:10116] [142803] (1 PDB entry)
       Uniprot Q00959 404-539,661-801

26. Nickel-binding periplasmic protein NikA [102694] (2 species)
    similar domain organization to oligo- and dipeptide-binding protein

    1. Species Brucella suis [TaxId:29461] [259856] (1 PDB entry)

    2. Species Escherichia coli [TaxId:562] [102695] (18 PDB entries)

27. Oligo-peptide binding protein (OPPA) [53852] (3 species)
    contains an additional alpha+beta domain inserted in the N-terminal domain

    1. Species Bacillus subtilis [TaxId:1423] [142799] (1 PDB entry)
       Uniprot P42061 40-543

    2. Species Salmonella typhimurium [TaxId:90371] [53853] (32 PDB entries)

    3. Species Thermotoga maritima [TaxId:2336] [142800] (3 PDB entries)
       Uniprot Q9X0V0 23-557
       TM1223

28. Osmoprotection protein ProX [110750] (1 species)
    functionally related to the bacterial ProX

    • Species Archaeoglobus fulgidus [TaxId:2234] [110751] (5 PDB entries)
      Uniprot O29280 # AF0982

29. Phosphate-binding protein [53860] (4 species)

    1. Species Escherichia coli [TaxId:562] [53861] (13 PDB entries)

    2. Species Mycobacterium tuberculosis [TaxId:1773] [110747] (1 PDB entry)
       Uniprot P15712

    3. Species Pseudomonas fluorescens [TaxId:216595] [189064] (1 PDB entry)

    4. Species Pseudomonas fluorescens [TaxId:294] [189065] (4 PDB entries)

30. Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain [53854] (1 species)

    • Species Escherichia coli [TaxId:562] [53855] (5 PDB entries)

31. Prephenate dehydratase [159808] (1 species)

    • Species Staphylococcus aureus [TaxId:1280] [159809] (1 PDB entry)
      Uniprot Q99SX2 1-184

32. Probable LysR-type transcriptional regulator PA0477 [142812] (1 species)

    • Species Pseudomonas aeruginosa [TaxId:287] [142813] (1 PDB entry)
      Uniprot Q9I641 92-303

33. PstS-like phosphate-binding protein [159816] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [159817] (1 PDB entry)
      Uniprot P85173 1-376

34. Putative amino-acid transporter CjaA [142814] (1 species)

    • Species Campylobacter jejuni [TaxId:197] [142815] (1 PDB entry)
      Uniprot Q0P9S0 29-276

35. Putative GluR0 ligand binding core [102696] (1 species)

    • Species Thermus thermophilus [TaxId:274] [102697] (2 PDB entries)

36. Putative lipoprotein (NlpA family) [102700] (2 species)
    aka PG110, TpN32

    1. Species Staphylococcus aureus [TaxId:1280] [102701] (1 PDB entry)

    2. Species Treponema pallidum [TaxId:160] [117746] (1 PDB entry)
       Uniprot O07950 28-267

37. Putrescine receptor (PotF) [53877] (1 species)

    • Species Escherichia coli [TaxId:562] [53878] (1 PDB entry)

38. Sialic acid-binding protein SiaP [254345] (1 species)
    Pfam PF03480; TRAP transporter; homology to other Type II ESRs (Extracytoplasmic solute receptors) discussed in PubMed 16702222

    • Species Haemophilus influenzae [TaxId:727] [254778] (6 PDB entries)

39. Spermidine/putrescine-binding protein PotD [53875] (1 species)

    • Species Escherichia coli [TaxId:562] [53876] (2 PDB entries)

40. Sulphate-binding protein [53858] (1 species)

    • Species Salmonella typhimurium [TaxId:90371] [53859] (1 PDB entry)

41. Thiaminase I [53865] (1 species)
    contains a few additional helices in the C-terminal extension; homologous to MBP

    • Species Paenibacillus thiaminolyticus [TaxId:49283] [53866] (3 PDB entries)

42. automated matches [190140] (17 species)
    not a true protein

    1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:559292] [226716] (1 PDB entry)

    2. Species Bordetella pertussis [TaxId:257313] [187275] (2 PDB entries)

    3. Species Burkholderia cepacia [TaxId:292] [255595] (2 PDB entries)

    4. Species Burkholderia sp. [TaxId:233098] [190010] (5 PDB entries)

    5. Species Escherichia coli K-12 [TaxId:83333] [189211] (13 PDB entries)

    6. Species Escherichia coli [TaxId:536056] [255489] (2 PDB entries)

    7. Species Escherichia coli [TaxId:562] [189978] (6 PDB entries)

    8. Species Haemophilus influenzae [TaxId:727] [255670] (6 PDB entries)

    9. Species Human (Homo sapiens) [TaxId:9606] [189406] (2 PDB entries)

    10. Species Norway rat (Rattus norvegicus) [TaxId:10116] [189278] (25 PDB entries)

    11. Species Pasteurella multocida [TaxId:1169409] [257948] (1 PDB entry)

    12. Species Pseudomonas aeruginosa [TaxId:287] [195694] (2 PDB entries)

    13. Species Salmonella enterica [TaxId:99287] [227690] (6 PDB entries)

    14. Species Sphingomonas sp. [TaxId:90322] [186866] (5 PDB entries)

    15. Species Thermotoga maritima [TaxId:243274] [259690] (2 PDB entries)

    16. Species Unidentified prokaryotic [TaxId:2725] [228734] (3 PDB entries)

    17. Species Yersinia pestis [TaxId:214092] [188272] (2 PDB entries)

More info for Family c.94.1.1: Phosphate binding protein-like

Timeline for Family c.94.1.1: Phosphate binding protein-like:

• Family c.94.1.1: Phosphate binding protein-like first appeared (with stable ids) in SCOP 1.55
  
• Family c.94.1.1: Phosphate binding protein-like appears in SCOPe 2.03
  
• Family c.94.1.1: Phosphate binding protein-like appears in SCOPe 2.05
  
• Family c.94.1.1: Phosphate binding protein-like appears in the current release, SCOPe 2.08