Structural Classification of Proteins

Fold: Ntn hydrolase-like

: 4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing

Lineage:

Root: scop
Class: Alpha and beta proteins (a+b) [53931]
Mainly antiparallel beta sheets (segregated alpha and beta regions)
Fold: Ntn hydrolase-like [56234]
4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing

Superfamilies:

N-terminal nucleophile aminohydrolases (Ntn hydrolases) [56235] (7)
N-terminal residue provides two catalytic groups, nucleophile and proton donor
uperfamily
1. Class II glutamine amidotransferases [56236] (9)
  has slightly different topology than other families do
  1. Glucosamine 6-phosphate synthase, N-terminal domain [56237]
    1. Escherichia coli [TaxId: 562] [56238] (8)
      SQ P17169 1-238
  2. Glutamine PRPP amidotransferase, N-terminal domain [56239]
    1. Bacillus subtilis [TaxId: 1423] [56240] (2)
    2. Escherichia coli [TaxId: 562] [56241] (5)
  3. Asparagine synthetase B, N-terminal domain [56242]
    1. Escherichia coli [TaxId: 562] [56243] (1)
  4. beta-Lactam synthetase [69831]
    Asparagine synthetase B homologue
    1. Streptomyces clavuligerus [TaxId: 1901] [69832] (5)
    2. Pectobacterium carotovorum [TaxId: 554] [103312] (2)
      carbapenam synthetase CarA
  5. Alpha subunit of glutamate synthase, N-terminal domain [69833]
    1. Azospirillum brasilense [TaxId: 192] [69834] (7)
    2. Synechocystis sp. [TaxId: 1143] [75566] (5)
  6. Hypothetical protein YafJ (PA1307) [111217]
    1. Pseudomonas aeruginosa [TaxId: 287] [111218] (1)
      SQ Q9I437
2. Penicillin acylase, catalytic domain [56244] (4)
  1. Penicillin acylase [56245]
    also contains 2 all-alpha and a beta-barrel domains
    will be divided into domains in future release
    1. Escherichia coli [TaxId: 562] [56246] (24)
    2. Providencia rettgeri [TaxId: 587] [56247] (1)
  2. Cephalosporin acylase [64425]
    1. Brevundimonas diminuta [TaxId: 293] [64426] (4)
    2. Pseudomonas sp., glutarylamidase [TaxId: 306] [69835] (5)
3. Penicillin V acylase [56248] (1)
  1. Penicillin V acylase [56249]
    1. Bacillus sphaericus [TaxId: 1421] [56250] (2)
4. Proteasome subunits [56251] (14)
  1. Proteasome beta subunit (catalytic) [56252]
    1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [56253] (50)
    2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90043] (1)
    3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56254] (112)
      The structure of yeast proteasome complexed with the proteasome activator pa26 is available from PDB (1fnt). The 1FNT entry designates protein chains by both upper case and lower case letters creating problems with its processing and presentation in SCOP; the proteasome activator pa26 structure is classified elsewhere in SCOP (a.24.8)
    4. Cow (Bos taurus) [TaxId: 9913] [75567] (1)
    5. Rhodococcus erythropolis [TaxId: 1833] [103313] (9)
  2. Proteasome alpha subunit (non-catalytic) [56255]
    contains an extension to the common fold at the N-terminus
    1. Archaeon Thermoplasma acidophilum [TaxId: 2303] [56256] (50)
    2. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [90044] (2)
    3. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [56257] (108)
      The structure of yeast proteasome complexed with the proteasome activator pa26 is available from PDB (1fnt). The 1FNT entry designates protein chains by both upper case and lower case letters creating problems with its processing and presentation in SCOP; the proteasome activator pa26 structure is classified elsewhere in SCOP (a.24.8)
    4. Cow (Bos taurus) [TaxId: 9913] [75568] (1)
    5. Rhodococcus erythropolis [TaxId: 1833] [103314] (9)
  3. HslV (ClpQ) protease [56258]
    dodecameric prokaryotic homologue of proteasome
    1. Escherichia coli [TaxId: 562] [56259] (7)
    2. Haemophilus influenzae [TaxId: 727] [56260] (6)
    3. Thermotoga maritima [TaxId: 2336] [90045] (1)
    4. Bacillus subtilis [TaxId: 1423] [160845] (26)
      SQ P39070 2-181
5. (Glycosyl)asparaginase [56261] (3)
  1. Glycosylasparaginase (aspartylglucosaminidase, AGA) [56262]
    the precursor chain is cleaved onto 2 fragments by autoproteolysis
    1. Human (Homo sapiens) [TaxId: 9606] [56263] (2)
    2. Flavobacterium meningosepticum [TaxId: 238] [56264] (8)
    3. Escherichia coli [TaxId: 562] [103315] (3)
      SQ P37595
      isoaspartyl peptidase with L-asparaginase activity
      putative L-asparaginase YbiK
6. Gamma-glutamyltranspeptidase-like [143906] (4)
  Pfam 01019
  1. Hypothetical protein Ta0994 [143907]
    1. Thermoplasma acidophilum [TaxId: 2303] [143908] (4)
      SQ Q9HJH4 1-516
  2. Cephalosporin acylase [143909]
    1. Bacillus halodurans [TaxId: 86665] [143910] (4)
      SQ Q9KEI5 3-539
  3. Gamma-glutamyltranspeptidase, GGT [143911]
    1. Helicobacter pylori [TaxId: 210] [143912] (1)
      SQ O25743 29-375,380-565
    2. Escherichia coli [TaxId: 562] [143913] (14)
      SQ P18956 29-387,391-580! SQ P18956 29-580
7. SPO2555-like [160846] (1)
  Pfam 06267; DUF1028
  1. Hypothetical protein SPO2555 [160847]
    1. Silicibacter pomeroyi [TaxId: 89184] [160848] (1)
      SQ Q5LQD5 1-229
Archaeal IMP cyclohydrolase PurO [75569] (1)
has a putative active site in the same topological location as the Ntn hydrolase but lacks the N-terminal nucleophile
uperfamily
1. Archaeal IMP cyclohydrolase PurO [75570] (1)
  Pfam 07826
  1. Hypothetical protein MTH1020 [75571]
    1. Archaeon Methanothermobacter thermautotrophicus [TaxId: 145262] [75572] (13)