Structural Classification of Proteins

Superfamily: Phospholipase D/nuclease

: uperfamily

Lineage:

Root: scop
Class: Alpha and beta proteins (a+b) [53931]
Mainly antiparallel beta sheets (segregated alpha and beta regions)
Fold: Phospholipase D/nuclease [56023]
beta-alpha-beta-alpha-beta-alpha-beta(4)-alpha; mixed sheet: order 1765234
Superfamily: Phospholipase D/nuclease [56024]
uperfamily

Families:

Nuclease [56025] (1)
1. Nuclease Nuc [56026]
  1. Salmonella typhimurium [TaxId: 90371] [56027] (2)
    1. 1byr
      1. chain a [41450]
    2. 1bys
      complexed with wo4
      1. chain a [41451]
Phospholipase D [64391] (1)
duplication: contains two domains of this fold arranged as in the Nuc dimer
1. Phospholipase D [64392]
  1. Streptomyces sp. [TaxId: 1931] [64393] (8)
    SQ P84147
    1. 1v0w
      complexed with po3
      1. region a:6-263 [108220]
      2. region a:264-514 [108221]
    2. 1f0i
      complexed with po4
      1. region a:6-263 [59566]
      2. region a:264-514 [59567]
    3. 1v0u
      complexed with po3
      1. region a:6-263 [108216]
      2. region a:264-513 [108217]
    4. 1v0t
      complexed with po3
      1. region a:6-263 [108214]
      2. region a:264-513 [108215]
    5. 1v0r
      complexed with wo5
      1. region a:6-263 [108210]
      2. region a:264-514 [108211]
    6. 1v0y
      complexed with hi5
      1. region a:6-263 [108222]
      2. region a:264-514 [108223]
    7. 1v0v
      complexed with po3
      1. region a:6-263 [108218]
      2. region a:264-513 [108219]
    8. 1v0s
      1. region a:6-263 [108212]
      2. region a:264-514 [108213]
Tyrosyl-DNA phosphodiesterase TDP1 [69815] (2)
1. Tyrosyl-DNA phosphodiesterase TDP1 [69816]
  1. Human (Homo sapiens) [TaxId: 9606] [69817] (12)
    1. 1jy1
      1. region a:145-350 [67438]
      2. region a:351-608 [67439]
    2. 1rff
      complexed with spm, vo4; mutant
      1. region a:162-350 [97376]
      2. region a:351-608 [97377]
      3. region b:162-350 [97378]
      4. region b:351-607 [97379]
    3. 1mu7
      complexed with gol, wo4; mutant
      1. region a:162-350 [79475]
      2. region a:351-608 [79476]
      3. region b:158-350 [79477]
      4. region b:351-608 [79478]
    4. 1rgt
      complexed with otr, ots, spm, vo4; mutant
      1. region a:162-350 [97446]
      2. region a:351-608 [97447]
      3. region b:162-350 [97448]
      4. region b:351-607 [97449]
    5. 1mu9
      complexed with gol, vo4; mutant
      1. region a:162-350 [79479]
      2. region a:351-608 [79480]
      3. region b:159-350 [79481]
      4. region b:351-608 [79482]
    6. 1rg1
      complexed with ots, spm, vo4; mutant
      1. region a:162-350 [97415]
      2. region a:351-608 [97416]
      3. region b:162-350 [97417]
      4. region b:351-607 [97418]
    7. 1rg2
      complexed with otr, ots, spm, vo4; mutant
      1. region a:162-350 [97419]
      2. region a:351-608 [97420]
      3. region b:159-350 [97421]
      4. region b:351-608 [97422]
    8. 1qzq
      1. region a:161-350 [96655]
      2. region a:351-608 [96656]
      3. region b:161-350 [96657]
      4. region b:351-608 [96658]
    9. 1rfi
      complexed with spm, vo4; mutant
      1. region a:162-350 [97380]
      2. region a:351-608 [97381]
      3. region b:162-350 [97382]
      4. region b:351-607 [97383]
    10. 1rgu
      complexed with ots, spm, vo4; mutant
      1. region a:162-350 [97450]
      2. region a:351-608 [97451]
      3. region b:162-350 [97452]
      4. region b:351-607 [97453]
    11. 1rh0
      complexed with ots, spm, vo4; mutant
      1. region a:162-350 [97458]
      2. region a:351-608 [97459]
      3. region b:162-350 [97460]
      4. region b:351-607 [97461]
    12. 1nop
      complexed with a topoisomerase I-derived peptide, chain C
      complexed with vo4; mutant
      1. region a:162-350 [85928]
      2. region a:351-608 [85929]
      3. region b:159-350 [85930]
      4. region b:351-607 [85931]
  2. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [111180] (1)
    SQ P38319 79-538
    1. 1q32
      1. region a:79-293 [104507]
      2. region a:302-538 [104508]
      3. region b:79-293 [104509]
      4. region b:302-538 [104510]
      5. region c:79-293 [104511]
      6. region c:302-538 [104512]
      7. region d:79-293 [104513]
      8. region d:302-538 [104514]
Polyphosphate kinase C-terminal domain [143860] (2)
C-terminal part of Pfam 02503; similar to PLD; contains two domains of this fold arranged as in the Nuc dimer
1. Polyphosphate kinase, PPK [143861]
  1. Porphyromonas gingivalis [TaxId: 837] [143862] (4)
    SQ Q7MTR1 318-505! SQ Q7MTR1 506-691
    1. 2o8r
      complexed with so4; mutant
      1. region a:318-505 [138935]
    2. 2o8r
      complexed with so4; mutant
      1. region a:506-691 [138936]
    3. 2o8r
      automatically matched to 2O8R A:318-505
      complexed with so4; mutant
      1. region b:318-505 [138939]
    4. 2o8r
      automatically matched to 2O8R A:506-691
      complexed with so4; mutant
      1. region b:506-690 [138940]
  2. Escherichia coli [TaxId: 562] [143863] (8)
    SQ P0A7B1 315-501! SQ P0A7B1 502-688
    1. 1xdp
      automatically matched to 1XDO A:315-501
      complexed with atp, mg
      1. region a:315-501 [121898]
    2. 1xdp
      automatically matched to 1XDO A:502-688
      complexed with atp, mg
      1. region a:502-688 [121899]
    3. 1xdp
      automatically matched to 1XDO A:315-501
      complexed with atp, mg
      1. region b:315-501 [121902]
    4. 1xdp
      automatically matched to 1XDO A:502-688
      complexed with atp, mg
      1. region b:502-688 [121903]
    5. 1xdo
      1. region a:315-501 [121890]
    6. 1xdo
      1. region a:502-688 [121891]
    7. 1xdo
      automatically matched to 1XDO A:315-501
      1. region b:315-501 [121894]
    8. 1xdo
      automatically matched to 1XDO A:502-688
      1. region b:502-688 [121895]
TrmB middle domain-like [160780] (1)
N-terminal part of PfamB 004822
1. Transcriptional regulator TrmB [160781]
  1. Thermococcus litoralis [TaxId: 2265] [160782] (1)
    SQ Q7LYW4 110-246
    1. 2f5t
      complexed with imd, mal
      1. region x:110-246 [146997]