Structural Classification of Proteins
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Superfamily: Restriction endonuclease-like

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: Restriction endonuclease-like [52979]
    core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
  4. Superfamily: Restriction endonuclease-like [52980]
    link to SUPERFAMILY database - Superfamily

Families:

  1. Restriction endonuclease EcoRI [52981] (1)
    1. Restriction endonuclease EcoRI [52982]
      1. Escherichia coli [TaxId: 562] [52983] (7) picpic
  2. Restriction endonuclease EcoRV [52984] (1)
    1. Restriction endonuclease EcoRV [52985]
      1. Escherichia coli [TaxId: 562] [52986] (31) picpic
  3. Restriction endonuclease BamHI [52987] (1)
    1. Restriction endonuclease BamHI [52988]
      1. Bacillus amyloliquefaciens [TaxId: 1390] [52989] (5) picpic
  4. Restriction endonuclease BglI [52990] (1)
    1. Restriction endonuclease BglI [52991]
      1. Bacillus subtilis [TaxId: 1423] [52992] (1) picpic
  5. Restriction endonuclease BglII [52993] (1)
    1. Restriction endonuclease BglII [52994]
      1. Bacillus subtilis [TaxId: 1423] [52995] (3) picpic
  6. Restriction endonuclease BstyI [102471] (1)
    1. Restriction endonuclease BstyI [102472]
      local sequence similarity to BglII
      1. Geobacillus stearothermophilus [TaxId: 1422] [102473] (5) picpic
  7. Restriction endonuclease PvuII [52996] (1)
    1. Restriction endonuclease PvuII [52997]
      1. Proteus vulgaris [TaxId: 585] [52998] (9) picpic
  8. Cfr10I/Bse634I [52999] (2)
    1. Restriction endonuclease Cfr10I [53000]
      1. Citrobacter freundii [TaxId: 546] [53001] (1) picpic
    2. Restriction endonuclease Bse634I [69523]
      1. Bacillus stearothermophilus [TaxId: 1422] [69524] (1) picpic
  9. Restriction endonuclease MunI [53002] (1)
    1. Restriction endonuclease MunI [53003]
      1. Mycoplasma, unidentified species [TaxId: 2093] [53004] (1) picpic
  10. Restriction endonuclease NaeI [53005] (1)
    1. Restriction endonuclease NaeI [53006]
      1. Nocardia aerocolonigenes [TaxId: 68170] [53007] (2) picpic
  11. Restriction endonuclease NgoIV [53008] (1)
    1. Restriction endonuclease NgoIV [53009]
      1. Neisseria gonorrhoeae [TaxId: 485] [53010] (1) picpic
  12. Restriction endonuclease BsobI [53011] (1)
    1. Restriction endonuclease BsobI [53012]
      1. Bacillus stearothermophilus [TaxId: 1422] [53013] (1) picpic
  13. Restriction endonuclease HincII [69525] (1)
    1. Restriction endonuclease HincII [69526]
      1. Haemophilus influenzae [TaxId: 727] [69527] (12) picpic
        SQ P17743 ! SQ P44413
  14. Restriction endonuclease FokI, C-terminal (catalytic) domain [53014] (1)
    1. Restriction endonuclease FokI, C-terminal (catalytic) domain [53015]
      1. Flavobacterium okeanokoites [TaxId: 244] [53016] (2) picpic
  15. Type II restriction endonuclease catalytic domain [102474] (1)
    1. Restriction endonuclease EcoRII, C-terminal domain [102475]
      1. Escherichia coli [TaxId: 562] [102476] (1) picpic
  16. lambda exonuclease [53017] (1)
    1. lambda exonuclease [53018]
      1. Bacteriophage lambda [TaxId: 10710] [53019] (1) picpic
  17. DNA mismatch repair protein MutH from [53020] (1)
    1. DNA mismatch repair protein MutH from [53021]
      1. Escherichia coli [TaxId: 562] [53022] (2) picpic
  18. Very short patch repair (VSR) endonuclease [53023] (1)
    1. Very short patch repair (VSR) endonuclease [53024]
      1. Escherichia coli [TaxId: 562] [53025] (3) picpic
  19. TnsA endonuclease, N-terminal domain [53026] (1)
    1. TnsA endonuclease, N-terminal domain [53027]
      a catalytic component of the tn7 transposition system
      1. Escherichia coli [TaxId: 562] [53028] (2) picpic
        SQ P13988
  20. Endonuclease I (Holliday junction resolvase) [53029] (1)
    1. Endonuclease I (Holliday junction resolvase) [53030]
      forms dimer by swapping the common core elements
      1. Bacteriophage T7 [TaxId: 10760] [53031] (3) picpic
  21. Hjc-like [64080] (3)
    Pfam 01870
    1. Archaeal Holliday junction resolvase Hjc [64081]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64082] (2) picpic
      2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [64083] (1) picpic
    2. Holliday-junction resolvase SSO1176 [117617]
      1. Sulfolobus solfataricus [TaxId: 2287] [117618] (2) picpic
        SQ Q97YX6
  22. XPF/Rad1/Mus81 nuclease [89716] (3)
    1. Putative ATP-dependent RNA helicase Hef, nuclease domain [89717]
      1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89718] (4) picpic
    2. DNA excision repair protein ERCC-1 [142445]
      1. Human (Homo sapiens) [TaxId: 9606] [142446] (3) picpic
        SQ P07992 99-227
    3. XPF endonuclease [142447]
      1. Aeropyrum pernix [TaxId: 56636] [142448] (6) picpic
        SQ Q9YC15 16-148
  23. Restriction endonuclease MspI [110624] (1)
    1. Restriction endonuclease MspI [110625]
      1. Moraxella sp. [TaxId: 479] [110626] (3) picpic
        SQ P11405
  24. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117619] (1)
    related to the RecC domain
    1. Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [117620]
      1. Escherichia coli [TaxId: 562] [117621] (1) picpic
        SQ P08394
  25. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117622] (1)
    related to the RecB domain
    1. Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [117623]
      1. Escherichia coli [TaxId: 562] [117624] (1) picpic
        SQ P07648
  26. Hypothetical protein VC1899 [117625] (1)
    contains 2 extra N-terminal domains; d1: [alpha/beta; 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest; topological similarity to the Formyltransferase fold (scop_cf 53327)]; d2: [distorted "winged helix" fold (scop_sf 46785)]
    1. Hypothetical protein VC1899 [117626]
      1. Vibrio cholerae [TaxId: 666] [117627] (1) picpic
        SQ Q9KQU9 # d1 (1-156); d2 (161-249); putative catalytic domain d3 (250-383)
  27. Hypothetical protein TT1808 (TTHA1514) [117628] (1)
    Pfam 05685; DUF820
    1. Hypothetical protein TT1808 (TTHA1514) [117629]
      1. Thermus thermophilus [TaxId: 274] [117630] (1) picpic
        SQ Q5SI60
  28. RecU-like [117631] (2)
    Pfam 03838
    1. Recombination protein U (RecU)/PBP related factor A (PrfA) [117632]
      1. Bacillus subtilis [TaxId: 1423] [117633] (1) picpic
        SQ P39792 34-196
      2. Bacillus stearothermophilus [TaxId: 1422] [117634] (1) picpic
        SQ Q5KXY4 31-198 # 99% sequence identity; Geobacillus kaustophilus TaxID: 1462
  29. Restriction endonuclease EcoO109IR [117635] (1)
    1. Restriction endonuclease EcoO109IR [117636]
      1. Escherichia coli [TaxId: 562] [117637] (2) picpic
        SQ Q9RPJ3
  30. MRR-like [117638] (1)
    Pfam 04471
    1. Hypothetical protein AF1548, N-terminal domain [117639]
      1. Archaeoglobus fulgidus [TaxId: 2234] [117640] (1) picpic
        SQ 28724
  31. PA4535-like [142449] (1)
    contains the PD motif at the beginning of strand 2 and putative catalytic glutamate in strand 3, whereas the putative catalytic lysine is migrated to an alpha-helix
    1. Hypothetical protein PA4535 [142450]
      1. Pseudomonas aeruginosa [TaxId: 287] [142451] (1) picpic
        SQ Q9HVP2 1-209
  32. XisH-like [159601] (2)
    Pfam 08814
    1. FdxN element excision controlling factor protein [159602]
      1. Nostoc punctiforme [TaxId: 272131] [159603] (1) picpic
      2. Anabaena variabilis [TaxId: 1172] [159604] (2) picpic
        SQ Q3M7W6 4-139
  33. YaeQ-like [159605] (2)
    Pfam 07152; contains extra N- and C-terminal beta-structures forming additional five-stranded beta-sheet; retains the PD motif in the putative active site
    1. Hypothetical protein XAC2396 [159606]
      1. Xanthomonas axonopodis pv. citri [TaxId: 92829] [159607] (2) picpic
        SQ Q8PJY1 4-182
    2. Hypothetical protein PSPTO1487 [159608]
      1. Pseudomonas syringae pv. tomato [TaxId: 323] [159609] (1) picpic
        SQ Q886T9 2-180
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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