Structural Classification of Proteins
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Fold: Phosphorylase/hydrolase-like

core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops

Lineage:

  1. Root: scop
  2. Class: Alpha and beta proteins (a/b) [51349]
    Mainly parallel beta sheets (beta-alpha-beta units)
  3. Fold: Phosphorylase/hydrolase-like [53162]
    core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops

Superfamilies:

  1. HybD-like [53163] (2)
    the HybD fold coincides with the consensus core structure
    link to SUPERFAMILY database - Superfamily
    1. Hydrogenase maturating endopeptidase HybD [53164] (1)
      1. Hydrogenase maturating endopeptidase HybD [53165]
        1. Escherichia coli [TaxId: 562] [53166] (1) picpic
    2. Germination protease [64095] (1)
      elaborated with the N-terminal alpha+beta subdomain and the insertion all-alpha dimerisation subdomain
      1. Germination protease [64096]
        1. Bacillus megaterium [TaxId: 1404] [64097] (1) picpic
  2. Purine and uridine phosphorylases [53167] (1)
    complex architecture; contains mixed beta-sheet of 8 strands, order 23415867, strands 3, 6 & 7 are antiparallel to the rest; and barrel, closed; n=5, S=8
    link to SUPERFAMILY database - Superfamily
    1. Purine and uridine phosphorylases [53168] (18)
      1. Purine nucleoside phosphorylase, PNP [53169]
        1. Human (Homo sapiens) [TaxId: 9606] [53170] (17) picpic
          SQ P00491
        2. Cow (Bos taurus) [TaxId: 9913] [53171] (20) picpic
          SQ P55859
        3. Escherichia coli [TaxId: 562] [53172] (19) picpic
        4. Vibrio cholerae [TaxId: 666] [102499] (2) picpic
        5. Cellulomonas sp. [TaxId: 40001] [53173] (2) picpic
        6. Mycobacterium tuberculosis [TaxId: 1773] [64098] (3) picpic
        7. Thermus thermophilus [TaxId: 274] [89721] (4) picpic
        8. Thermotoga maritima [TaxId: 2336] [117654] (1) picpic
          SQ Q9X1T2
        9. Bacillus anthracis [TaxId: 1392] [117655] (3) picpic
          SQ Q81T09
      2. Uridine phosphorylase [53176]
        1. Escherichia coli [TaxId: 562] [53177] (40) picpic
          also includes the PDB entry (1rxs) where protein chains are designated by both upper case and lower case letters creating problems with its processing and presentation in SCOP
        2. Salmonella typhimurium [TaxId: 90371] [117656] (1) picpic
          SQ P0A1F6
      3. Putative uridine phosphorylase [102500]
        1. Plasmodium falciparum [TaxId: 5833] [102501] (4) picpic
      4. 5'-deoxy-5'-methylthioadenosine phosphorylase [53174]
        1. Human (Homo sapiens) [TaxId: 9606] [53175] (5) picpic
          SQ Q13126
        2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [69536] (9) picpic
        3. Sulfolobus tokodaii [TaxId: 111955] [117657] (1) picpic
          SQ Q975C3
      5. 5'-Methylthioadenosine/S-Adenosylhomocysteine nucleosidase [82448]
        1. Escherichia coli [TaxId: 562] [82449] (8) picpic
      6. AMP nucleosidase [110645]
        contains extra N-terminal oligomerisation (sub)domain (8-153)
        1. Escherichia coli [TaxId: 562] [110646] (4) picpic
          SQ P15272
        2. Bacteroides thetaiotaomicron [TaxId: 818] [117658] (1) picpic
          SQ Q7MVU1
  3. Peptidyl-tRNA hydrolase-like [53178] (1)
    link to SUPERFAMILY database - Superfamily
    1. Peptidyl-tRNA hydrolase-like [53179] (2)
      1. Peptidyl-tRNA hydrolase [53180]
        1. Escherichia coli [TaxId: 562] [53181] (1) picpic
      2. Chloroplast group II intron splicing factor Crs2 [102502]
        1. Maize (Zea mays) [TaxId: 4577] [102503] (3) picpic
  4. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53182] (1)
    link to SUPERFAMILY database - Superfamily
    1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53183] (4)
      1. Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) [53184]
        1. Archaeon Thermococcus litoralis [TaxId: 2265] [53185] (1) picpic
        2. Bacillus amyloliquefaciens [TaxId: 1390] [53186] (1) picpic
        3. Archaeon Pyrococcus furiosus [TaxId: 2261] [64099] (2) picpic
        4. Archaeon Pyrococcus horikoshii [TaxId: 53953] [75246] (1) picpic
  5. Zn-dependent exopeptidases [53187] (9)
    core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest
    link to SUPERFAMILY database - Superfamily
    1. Pancreatic carboxypeptidases [53188] (10)
      1. Carboxypeptidase A [53189]
        1. Cow (Bos taurus) [TaxId: 9913] [53190] (30) picpic
        2. Pig (Sus scrofa) [TaxId: 9823] [53191] (1) picpic
        3. Human (Homo sapiens) [TaxId: 9606] [53192] (7) picpic
        4. Cotton bollworm (Helicoverpa armigera) [TaxId: 29058] [75247] (1) picpic
      2. Carboxypeptidase B [53193]
        1. Pig (Sus scrofa) [TaxId: 9823] [53194] (54) picpic
        2. Human (Homo sapiens) [TaxId: 9606] [75248] (2) picpic
        3. Cow (Bos taurus) [TaxId: 9913] [53195] (1) picpic
        4. Corn earworm (Helicoverpa zea) [TaxId: 7113] [142511] (2) picpic
          SQ Q3T905 117-428
      3. Carboxypeptidase D, catalytic domain [53196]
        1. Crested duck (Lophonetta specularioides) [TaxId: 8836] [53197] (2) picpic
      4. Carboxypeptidase M, catalytic domain [102504]
        1. Human (Homo sapiens) [TaxId: 9606] [102505] (1) picpic
    2. Carboxypeptidase T [53198] (1)
      1. Carboxypeptidase T [53199]
        1. Thermoactinomyces vulgaris [TaxId: 2026] [53200] (1) picpic
    3. Leucine aminopeptidase, C-terminal domain [53201] (2)
      1. Leucine aminopeptidase, C-terminal domain [53202]
        1. Cow (Bos taurus) [TaxId: 9913] [53203] (9) picpic
        2. Escherichia coli, PepA [TaxId: 562] [75249] (1) picpic
    4. Bacterial dinuclear zinc exopeptidases [53204] (19)
      1. Aminopeptidase [53205]
        1. Aeromonas proteolytica [TaxId: 671] [53206] (13) picpic
          SQ Q01693
          synonym: Vibrio proteolyticus
        2. Streptomyces griseus [TaxId: 1911] [53207] (11) picpic
      2. Aminopeptidase PepV [82450]
        unspecific amino dipeptidase
        1. Lactobacillus delbrueckii [TaxId: 1584] [82451] (1) picpic
      3. Carboxypeptidase G2, catalytic domain [53208]
        1. Pseudomonas sp., strain rs-16 [TaxId: 306] [53209] (1) picpic
      4. Peptidase T (tripeptidase), catalytic domain [75250]
        1. Salmonella typhimurium [TaxId: 90371] [75251] (1) picpic
        2. Escherichia coli [TaxId: 562] [102506] (1) picpic
      5. Peptidase-like beta-alanine synthase, catalytic domain [102507]
        1. Yeast (Saccharomyces kluyveri) [TaxId: 4934] [102508] (2) picpic
      6. Succinyl-diaminopimelate desuccinylase, catalytic domain [102509]
        1. Neisseria meningitidis [TaxId: 487] [102510] (1) picpic
      7. Aminoacylase-1, catalytic domain [102511]
        1. Human (Homo sapiens) [TaxId: 9606] [102512] (1) picpic
      8. Hypothetical protein YsdC, catalytic domain [102513]
        contains insert beta-barrel domain
        1. Bacillus subtilis [TaxId: 1423] [102514] (1) picpic
      9. Putative endoglucanase TM1048, catalytic domain [102515]
        contains insert beta-barrel domain
        1. Thermotoga maritima [TaxId: 2336] [102516] (1) picpic
      10. Frv operon protein FrvX, catalytic domain [117659]
        1. Pyrococcus horikoshii [TaxId: 53953] [117660] (3) picpic
          SQ O59196 # PH1527
      11. Probable aminopeptidase ApeA [117661]
        contains insert beta-barrel domain
        1. Borrelia burgdorferi [TaxId: 139] [117662] (1) picpic
          SQ Q45055
      12. IAA-amino acid hydrolase, catalytic domain [117663]
        1. Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702] [117664] (2) picpic
          SQ P54970 37-428
      13. Deblocking aminopeptidase YhfE [142512]
        contains insert beta-barrel domain
        1. Bacillus cereus [TaxId: 1396] [142513] (16) picpic
          SQ Q81HB5 3-73,187-348
          BC0901
      14. Allantoate amidohydrolase AllC catalytic domain [142514]
        1. Escherichia coli [TaxId: 562] [142515] (4) picpic
          SQ P77425 2-210,328-411
      15. Endoglucanase TM1049 [142516]
        1. Thermotoga maritima [TaxId: 2336] [142517] (1) picpic
          SQ Q9X0D9 1-64,149-339
      16. Protein YxeP [142518]
        1. Bacillus subtilis [TaxId: 1423] [142519] (2) picpic
          SQ P54955 4-177,293-379
      17. Aminopeptidase YpdE [142520]
        1. Shigella flexneri [TaxId: 623] [142521] (6) picpic
          SQ Q83K87 1-66,148-345
          hypothetical protein SF2450 (PDB)/SF2449.1 (UniProt)
    5. FolH catalytic domain-like [53210] (2)
      1. Transferrin receptor ectodomain, protease-like domain [53211]
        1. Human (Homo sapiens) [TaxId: 9606] [53212] (4) picpic
      2. Glutamate carboxypeptidase II FOLH1 [142522]
        Folate hydrolase 1, FolH homologue
        1. Human (Homo sapiens) [TaxId: 9606] [142523] (17) picpic
          SQ Q04609 57-117,351-593
    6. N-acetylmuramoyl-L-alanine amidase-like [102517] (2)
      1. N-acetylmuramoyl-L-alanine amidase CwlV [102518]
        1. Paenibacillus polymyxa [TaxId: 1406] [102519] (1) picpic
      2. Endolysin Ply, catalytic domain [142524]
        1. Bacteriophage Psa [TaxId: 171618] [142525] (1) picpic
          SQ Q8W5Y8 1-180
    7. AstE/AspA-like [142526] (6)
      Pfam 04952; Succinylglutamate desuccinylase / Aspartoacylase family; contains extra C-terminal domain, new variant of the Barrel-sandwich hybrid fold (scop_cf 51229)
      1. Succinylglutamate desuccinylase AstE [142527]
        1. Vibrio cholerae [TaxId: 666] [142528] (1) picpic
          SQ Q9KSL4 3-342
        2. Vibrio parahaemolyticus [TaxId: 670] [142529] (2) picpic
          SQ Q87Q40 4-342
        3. Escherichia coli [TaxId: 562] [142530] (2) picpic
          SQ P76215 1-322
        4. Chromobacterium violaceum [TaxId: 536] [142531] (1) picpic
          SQ Q7NU26 2-332
      2. Aspartoacylase AspA [159649]
        1. Rat (Rattus norvegicus) [TaxId: 10116] [159650] (1) picpic
          SQ Q6AZ03 4-310
        2. Human (Homo sapiens) [TaxId: 9606] [159651] (1) picpic
          SQ P45381 9-310
    8. Glutaminyl-peptide cyclotransferase-like [142532] (1)
      part of Pfam 04389
      1. Glutaminyl-peptide cyclotransferase, QPCT [142533]
        Glutaminyl cyclase
        1. Human (Homo sapiens) [TaxId: 9606] [142534] (16) picpic
          SQ Q16769 33-361
    9. FGase-like [159652] (2)
      Pfam 05013; N-formylglutamate amidohydrolase
      1. N-formylglutamate amidohydrolase [159653]
        1. Ralstonia eutropha [TaxId: 106590] [159654] (2) picpic
          SQ Q46VW8 10-289
      2. Hypothetical protein Atu2144 [159655]
        1. Agrobacterium tumefaciens [TaxId: 358] [159656] (8) picpic
          SQ Q8UDI1 6-257
  6. LigB-like [53213] (1)
    circular permutation of the common fold, most similar to the PNP fold
    link to SUPERFAMILY database - Superfamily
    1. LigB-like [53214] (2)
      1. LigB subunit of an aromatic-ring-opening dioxygenase LigAB [53215]
        1. Pseudomonas paucimobilis [TaxId: 13689] [53216] (2) picpic
      2. Uncharacterized protein YgiD [159657]
        1. Escherichia coli [TaxId: 562] [159658] (1) picpic
          SQ P24197 14-271
  7. AF0625-like [142535] (1)
    contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134
    link to SUPERFAMILY database - Superfamily
    1. AF0625-like [142536] (2)
      Pfam 04414; DUF516, binds magnesium ion and pyrophosphate in the putative active site
      1. Hypothetical protein PH0006 [142537]
        1. Pyrococcus horikoshii [TaxId: 53953] [142538] (3) picpic
          SQ O57774 1-274
      2. Hypothetical protein AF0625 [142539]
        1. Archaeoglobus fulgidus [TaxId: 2234] [142540] (1) picpic
          SQ O29630 1-278
  8. Cgl1923-like [159659] (1)
    1. Cgl1923-like [159660] (1)
      Pfam 01908; DUF75
      1. Hypothetical protein Cgl1923 [159661]
        1. Corynebacterium glutamicum [TaxId: 1718] [159662] (3) picpic
          SQ Q8NP93 6-274
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MRC site Generated from scop database 1.75 with scopm 1.101 on Wed Jun 3 10:42:06 2009
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