Structural Classification of Proteins
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Fold: Restriction endonuclease-like

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

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

Superfamilies:

  1. Restriction endonuclease-like [52980] (33)
    link to SUPERFAMILY database - Superfamily
    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
  2. tRNA-intron endonuclease catalytic domain-like [53032] (1)
    link to SUPERFAMILY database - Superfamily
    1. tRNA-intron endonuclease catalytic domain-like [53033] (3)
      1. Tetrameric tRNA splicing endonuclease, C-terminal domain [53034]
        1. Archaeon Methanococcus jannaschii [TaxId: 2190] [53035] (1) picpic
      2. Dimeric tRNA splicing endonuclease, domains 2 and 4 [102477]
        duplication: one subunit consists of two tetrameric tRNA splicing endonuclease subunit-like repeats
        1. Archaeon Archaeoglobus fulgidus [TaxId: 2234] [102478] (11) picpic
      3. tRNA-splicing endonuclease subunit Sen15 [159610]
        1. Human (Homo sapiens) [TaxId: 9606] [159611] (2) picpic
          SQ Q8WW01 36-157
  3. Eukaryotic RPB5 N-terminal domain [53036] (1)
    link to SUPERFAMILY database - Superfamily
    1. Eukaryotic RPB5 N-terminal domain [53037] (1)
      1. Eukaryotic RPB5 N-terminal domain [53038]
        1. Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] [53039] (26) picpic
          SQ P20434; part of multichain biological unit
  4. TBP-interacting protein-like [159612] (1)
    contains extra C-terminal alpha+beta domain of complex fold with an embeded C2H2 zinc-finger
    1. TBP-interacting protein-like [159613] (1)
      PfamB 059845 (N-terminal domain) and Pfam B059846 (C-terminal region)
      1. TBP-interacting protein [159614]
        1. Thermococcus kodakaraensis [TaxId: 311400] [159615] (1) picpic
          SQ Q9V2W6 1-218
          TK1172
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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