Structural Classification of Proteins

Superfamily: Restriction endonuclease-like

: uperfamily

Lineage:

Root: scop
Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
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
Superfamily: Restriction endonuclease-like [52980]
uperfamily

Families:

Restriction endonuclease EcoRI [52981] (1)
1. Restriction endonuclease EcoRI [52982]
  1. Escherichia coli [TaxId: 562] [52983] (7)
    1. 1ckq
      protein/DNA complex
      1. chain a [33229]
    2. 1cl8
      complexed with prn
      1. chain a [33230]
    3. 1qrh
      protein/DNA complex; mutant
      1. chain a [33232]
    4. 1qri
      protein/DNA complex; mutant
      1. chain a [33233]
    5. 1eri
      protein/DNA complex
      1. chain a [33231]
    6. 1qps
      complexed with mn
      1. chain a [33234]
    7. 1qc9
      1. chain a [33235]
      2. chain b [33236]
      3. chain c [33237]
Restriction endonuclease EcoRV [52984] (1)
1. Restriction endonuclease EcoRV [52985]
  1. Escherichia coli [TaxId: 562] [52986] (31)
    1. 1sx5
      complexed with mn; mutant
      1. chain a [99023]
      2. chain b [99024]
    2. 1eon
      complexed with acy, cl, tsp
      1. chain a [33238]
      2. chain b [33239]
    3. 1rva
      protein/DNA complex
      1. chain a [33240]
      2. chain b [33241]
    4. 1suz
      complexed with mg, na; mutant
      1. chain a [99013]
      2. chain b [99014]
    5. 1rvc
      protein/DNA complex; complexed with mg
      1. chain a [33242]
      2. chain b [33243]
    6. 1rvb
      protein/DNA complex; complexed with mg
      1. chain a [33244]
      2. chain b [33245]
    7. 1az0
      protein/DNA complex; complexed with ca
      1. chain a [33248]
      2. chain b [33249]
    8. 1eo4
      protein/DNA complex; complexed with acy, mn, tsp
      1. chain a [33246]
      2. chain b [33247]
    9. 1b94
      complexed with ca
      1. chain a [33250]
      2. chain b [33251]
    10. 1b97
      mutant
      1. chain a [33252]
      2. chain b [33253]
    11. 1bsu
      protein/DNA complex; complexed with 5cm, ca, imp
      1. chain a [33258]
      2. chain b [33259]
    12. 1bgb
      protein/DNA complex
      1. chain a [33254]
      2. chain b [33255]
    13. 1eo3
      protein/DNA complex; complexed with acy, mg, tsp
      1. chain a [33260]
      2. chain b [33261]
    14. 2b0d
      automatically matched to d1az0a_
      complexed with ca
      1. region a:2-245 [127634]
    15. 2b0d
      automatically matched to d1az0a_
      complexed with ca
      1. region b:2-245 [127635]
    16. 2b0e
      automatically matched to d1az0a_
      complexed with ca, du
      1. region a:2-245 [127636]
    17. 2b0e
      automatically matched to d1az0a_
      complexed with ca, du
      1. region b:2-245 [127637]
    18. 1bua
      protein/DNA complex; complexed with imp
      1. chain a [33266]
      2. chain b [33267]
    19. 1b95
      mutant
      1. chain a [33264]
      2. chain b [33265]
    20. 1stx
      complexed with mn; mutant
      1. chain a [98989]
      2. chain b [98990]
    21. 1rv5
      protein/DNA complex
      1. chain a [33262]
      2. chain b [33263]
    22. 1bss
      protein/DNA complex; complexed with cl; mutant
      1. chain a [33256]
      2. chain b [33257]
    23. 1sx8
      complexed with mn; mutant
      1. chain a [99025]
      2. chain b [99026]
    24. 1b96
      mutant
      1. chain a [33268]
      2. chain b [33269]
    25. 1eoo
      1. chain a [33270]
      2. chain b [33271]
    26. 1eop
      1. chain a [33272]
      2. chain b [33273]
    27. 1az3
      1. chain a [33276]
      2. chain b [33277]
    28. 1az4
      mutant
      1. chain a [33278]
      2. chain b [33279]
    29. 1rve
      1. chain a [33274]
      2. chain b [33275]
    30. 2rve
      protein/DNA complex
      1. chain a [33283]
      2. chain b [33284]
    31. 4rve
      protein/DNA complex
      1. chain a [33280]
      2. chain b [33281]
      3. chain c [33282]
Restriction endonuclease BamHI [52987] (1)
1. Restriction endonuclease BamHI [52988]
  1. Bacillus amyloliquefaciens [TaxId: 1390] [52989] (5)
    1. 1bam
      1. chain a [33285]
    2. 1esg
      protein/DNA complex
      1. chain a [33286]
      2. chain b [33287]
    3. 3bam
      protein/DNA complex; complexed with mn
      1. chain a [33288]
      2. chain b [33289]
    4. 2bam
      protein/DNA complex; complexed with ca
      1. chain a [33292]
      2. chain b [33293]
    5. 1bhm
      protein/DNA complex
      1. chain a [33290]
      2. chain b [33291]
Restriction endonuclease BglI [52990] (1)
1. Restriction endonuclease BglI [52991]
  1. Bacillus subtilis [TaxId: 1423] [52992] (1)
    1. 1dmu
      1. chain a [33294]
Restriction endonuclease BglII [52993] (1)
1. Restriction endonuclease BglII [52994]
  1. Bacillus subtilis [TaxId: 1423] [52995] (3)
    1. 1dfm
      1. chain a [33295]
      2. chain b [33296]
    2. 1d2i
      1. chain a [33297]
      2. chain b [33298]
    3. 1es8
      free enzyme
      complexed with acy
      1. chain a [33299]
Restriction endonuclease BstyI [102471] (1)
1. Restriction endonuclease BstyI [102472]
  local sequence similarity to BglII
  1. Geobacillus stearothermophilus [TaxId: 1422] [102473] (5)
    1. 1sdo
      1. chain a [98809]
    2. 2p0j
      automatically matched to d1sdoa_
      1. region a:1-203 [139454]
    3. 2p0j
      automatically matched to d1sdoa_
      1. region b:1-203 [139455]
    4. 1vrr
      automatically matched to d1sdoa_
      1. region a:1-203 [120477]
    5. 1vrr
      automatically matched to d1sdoa_
      1. region b:1-203 [120478]
Restriction endonuclease PvuII [52996] (1)
1. Restriction endonuclease PvuII [52997]
  1. Proteus vulgaris [TaxId: 585] [52998] (9)
    1. 3pvi
      protein/DNA complex; mutant
      1. chain a [33300]
      2. chain b [33301]
    2. 2pvi
      protein/DNA complex; complexed with cyi
      1. chain a [33302]
      2. chain b [33303]
    3. 1eyu
      protein/DNA complex
      1. chain a [33304]
      2. chain b [33305]
    4. 1k0z
      complexed with pr, so4
      1. chain a [84273]
      2. chain b [84274]
    5. 1pvu
      1. chain a [33306]
      2. chain b [33307]
    6. 1f0o
      protein/DNA complex; complexed with ca
      1. chain a [33308]
      2. chain b [33309]
    7. 1h56
      complexed with mg
      1. chain a [90620]
      2. chain b [90621]
    8. 1pvi
      protein/DNA complex
      1. chain a [33310]
      2. chain b [33311]
    9. 1ni0
      mutant
      1. chain a [80522]
      2. chain b [80523]
      3. chain c [80524]
Cfr10I/Bse634I [52999] (2)
1. Restriction endonuclease Cfr10I [53000]
  1. Citrobacter freundii [TaxId: 546] [53001] (1)
    1. 1cfr
      1. chain a [33312]
2. Restriction endonuclease Bse634I [69523]
  1. Bacillus stearothermophilus [TaxId: 1422] [69524] (1)
    1. 1knv
      complexed with act, cl
      1. chain a [68707]
      2. chain b [68708]
Restriction endonuclease MunI [53002] (1)
1. Restriction endonuclease MunI [53003]
  1. Mycoplasma, unidentified species [TaxId: 2093] [53004] (1)
    1. 1d02
      protein/DNA complex; mutant
      1. chain a [33313]
      2. chain b [33314]
Restriction endonuclease NaeI [53005] (1)
1. Restriction endonuclease NaeI [53006]
  1. Nocardia aerocolonigenes [TaxId: 68170] [53007] (2)
    1. 1ev7
      1. chain a [33315]
      2. chain b [33316]
    2. 1iaw
      complexed with 17mer DNA
      1. chain a [62126]
      2. chain b [62127]
Restriction endonuclease NgoIV [53008] (1)
1. Restriction endonuclease NgoIV [53009]
  1. Neisseria gonorrhoeae [TaxId: 485] [53010] (1)
    1. 1fiu
      protein/DNA complex; complexed with acy, mg
      1. chain a [33317]
      2. chain b [33318]
      3. chain c [33319]
      4. chain d [33320]
Restriction endonuclease BsobI [53011] (1)
1. Restriction endonuclease BsobI [53012]
  1. Bacillus stearothermophilus [TaxId: 1422] [53013] (1)
    1. 1dc1
      protein/DNA complex; complexed with dio
      1. chain a [33321]
      2. chain b [33322]
Restriction endonuclease HincII [69525] (1)
1. Restriction endonuclease HincII [69526]
  1. Haemophilus influenzae [TaxId: 727] [69527] (12)
    SQ P17743 ! SQ P44413
    1. 1xhv
      complexed with mn
      1. chain a [109597]
      2. chain b [109598]
      3. chain c [109599]
      4. chain d [109600]
    2. 1tx3
      automatically matched to d1kc6a_
      complexed with na
      1. region a:2-258 [119371]
    3. 1tx3
      automatically matched to d1kc6a_
      complexed with na
      1. region b:2-257 [119372]
    4. 1tx3
      automatically matched to d1kc6a_
      complexed with na
      1. region c:2-257 [119373]
    5. 1tx3
      automatically matched to d1kc6a_
      complexed with na
      1. region d:2-257 [119374]
    6. 1kc6
      complexed with na
      1. chain a [68419]
      2. chain b [68420]
      3. chain c [68421]
      4. chain d [68422]
    7. 1tw8
      complexed with ca, na
      1. chain a [107377]
      2. chain b [107378]
      3. chain c [107379]
      4. chain d [107380]
    8. 2gie
      automatically matched to d1kc6a_
      complexed with na
      1. region a:2-258 [135240]
    9. 2gie
      automatically matched to d1kc6a_
      complexed with na
      1. region b:2-257 [135241]
    10. 2gie
      automatically matched to d1kc6a_
      complexed with na
      1. region c:2-258 [135242]
    11. 2gie
      automatically matched to d1kc6a_
      complexed with na
      1. region d:2-257 [135243]
    12. 1xhu
      1. chain a [109593]
      2. chain b [109594]
      3. chain c [109595]
      4. chain d [109596]
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)
    1. 2fok
      1. region a:387-579 [33323]
      2. region b:387-579 [33324]
    2. 1fok
      protein/DNA complex
      1. region a:387-579 [33325]
Type II restriction endonuclease catalytic domain [102474] (1)
1. Restriction endonuclease EcoRII, C-terminal domain [102475]
  1. Escherichia coli [TaxId: 562] [102476] (1)
    1. 1na6
      mutant
      1. region a:179-398 [91749]
      2. region b:183-402 [91751]
lambda exonuclease [53017] (1)
1. lambda exonuclease [53018]
  1. Bacteriophage lambda [TaxId: 10710] [53019] (1)
    1. 1avq
      complexed with act, po4; mutant
      1. chain a [33326]
      2. chain b [33327]
      3. chain c [33328]
DNA mismatch repair protein MutH from [53020] (1)
1. DNA mismatch repair protein MutH from [53021]
  1. Escherichia coli [TaxId: 562] [53022] (2)
    1. 1azo
      complexed with edo
      1. chain a [33329]
    2. 2azo
      1. chain a [33330]
      2. chain b [33331]
Very short patch repair (VSR) endonuclease [53023] (1)
1. Very short patch repair (VSR) endonuclease [53024]
  1. Escherichia coli [TaxId: 562] [53025] (3)
    1. 1vsr
      complexed with zn
      1. chain a [33332]
    2. 1cw0
      1. chain a [33333]
    3. 1odg
      bound to the reaction product site
      complexed with 5cm, zn
      1. chain a [86849]
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)
    SQ P13988
    1. 1t0f
      complexed with the transposition protein TnsC peptide (SQ P05846 505-553), chains C and D
      complexed with mg, mla, mpd
      1. region a:7-168 [112196]
      2. region b:7-168 [112198]
    2. 1f1z
      complexed with cl, mg
      1. region a:8-168 [33334]
      2. region b:8-168 [33335]
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)
    1. 1m0d
      complexed with mn, so4
      1. chain a [74354]
      2. chain b [74355]
      3. chain c [74356]
      4. chain d [74357]
    2. 1fzr
      CASP4
      mutant
      1. chain a [33336]
      2. chain b [33337]
      3. chain c [33338]
      4. chain d [33339]
    3. 1m0i
      complexed with so4
      1. chain a [78340]
      2. chain b [78341]
      3. chain c [78342]
      4. chain d [78343]
Hjc-like [64080] (3)
Pfam 01870
1. Archaeal Holliday junction resolvase Hjc [64081]
  1. Archaeon Pyrococcus furiosus [TaxId: 2261] [64082] (2)
    1. 1gef
      complexed with so4
      1. chain a [60465]
      2. chain b [60466]
      3. chain d [60467]
      4. chain e [60468]
    2. 1ipi
      1. chain a [66255]
      2. chain b [66256]
  2. Archaeon Sulfolobus solfataricus [TaxId: 2287] [64083] (1)
    1. 1hh1
      1. chain a [61036]
2. Holliday-junction resolvase SSO1176 [117617]
  1. Sulfolobus solfataricus [TaxId: 2287] [117618] (2)
    SQ Q97YX6
    1. 1ob8
      complexed with edo, so4
      1. chain a [111627]
      2. chain b [111628]
    2. 1ob9
      complexed with edo, fmt
      1. chain a [111629]
XPF/Rad1/Mus81 nuclease [89716] (3)
1. Putative ATP-dependent RNA helicase Hef, nuclease domain [89717]
  1. Archaeon Pyrococcus furiosus [TaxId: 2261] [89718] (4)
    1. 1j23
      mutant
      1. chain a [84007]
    2. 1j24
      complexed with ca; mutant
      1. chain a [84008]
    3. 1j22
      mutant
      1. chain a [84006]
    4. 1j25
      complexed with mn; mutant
      1. chain a [84009]
2. DNA excision repair protein ERCC-1 [142445]
  1. Human (Homo sapiens) [TaxId: 9606] [142446] (3)
    SQ P07992 99-227
    1. 2a1i
      complexed with hg
      1. region a:99-227 [125999]
    2. 2jpd
      automatically matched to d2a1ia1
      1. region a:99-219 [148165]
    3. 2jnw
      automatically matched to d2a1ia1
      1. region a:99-214 [148152]
3. XPF endonuclease [142447]
  1. Aeropyrum pernix [TaxId: 56636] [142448] (6)
    SQ Q9YC15 16-148
    1. 2bgw
      complexed with mg, so4
      1. region a:16-148 [128501]
    2. 2bgw
      automatically matched to 2BGW A:16-148
      complexed with mg, so4
      1. region b:18-148 [128503]
    3. 2bhn
      automatically matched to 2BGW A:16-148
      1. region a:19-148 [128535]
    4. 2bhn
      automatically matched to 2BGW A:16-148
      1. region b:19-148 [128537]
    5. 2bhn
      automatically matched to 2BGW A:16-148
      1. region c:20-147 [128539]
    6. 2bhn
      automatically matched to 2BGW A:16-148
      1. region d:19-148 [128541]
Restriction endonuclease MspI [110624] (1)
1. Restriction endonuclease MspI [110625]
  1. Moraxella sp. [TaxId: 479] [110626] (3)
    SQ P11405
    1. 1sa3
      complexed with na
      1. chain a [105400]
      2. chain b [105401]
    2. 1yfi
      automatically matched to d1sa3a_
      1. region a:1-262 [123068]
    3. 1yfi
      automatically matched to d1sa3a_
      1. region b:1-262 [123069]
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)
    SQ P08394
    1. 1w36
      complexed with ca
      1. region b:899-1174 [114124]
      2. region e:899-1174 [114132]
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)
    SQ P07648
    1. 1w36
      complexed with ca
      1. region c:818-1121 [114127]
      2. region f:818-1121 [114135]
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)
    SQ Q9KQU9 # d1 (1-156); d2 (161-249); putative catalytic domain d3 (250-383)
    1. 1xmx
      Structural genomics target
      complexed with fmt, gol, mg
      1. chain a [115568]
Hypothetical protein TT1808 (TTHA1514) [117628] (1)
Pfam 05685; DUF820
1. Hypothetical protein TT1808 (TTHA1514) [117629]
  1. Thermus thermophilus [TaxId: 274] [117630] (1)
    SQ Q5SI60
    1. 1wdj
      Structural genomics target
      1. chain a [114536]
      2. chain b [114537]
      3. chain c [114538]
RecU-like [117631] (2)
Pfam 03838
1. Recombination protein U (RecU)/PBP related factor A (PrfA) [117632]
  1. Bacillus subtilis [TaxId: 1423] [117633] (1)
    SQ P39792 34-196
    1. 1rzn
      1. chain a [111981]
      2. chain b [111982]
  2. Bacillus stearothermophilus [TaxId: 1422] [117634] (1)
    SQ Q5KXY4 31-198 # 99% sequence identity; Geobacillus kaustophilus TaxID: 1462
    1. 1y1o
      Structural genomics target
      complexed with ni, so4
      1. chain a [116345]
      2. chain b [116346]
      3. chain c [116347]
      4. chain d [116348]
Restriction endonuclease EcoO109IR [117635] (1)
1. Restriction endonuclease EcoO109IR [117636]
  1. Escherichia coli [TaxId: 562] [117637] (2)
    SQ Q9RPJ3
    1. 1wte
      complexed with na
      1. chain a [114876]
      2. chain b [114877]
    2. 1wtd
      complexed with gol
      1. chain a [114874]
      2. chain b [114875]
MRR-like [117638] (1)
Pfam 04471
1. Hypothetical protein AF1548, N-terminal domain [117639]
  1. Archaeoglobus fulgidus [TaxId: 2234] [117640] (1)
    SQ 28724
    1. 1y88
      Structural genomics target
      complexed with cl, so4
      1. region a:3-127 [116561]
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)
    SQ Q9HVP2 1-209
    1. 1y0k
      1. region a:1-209 [122485]
XisH-like [159601] (2)
Pfam 08814
1. FdxN element excision controlling factor protein [159602]
  1. Nostoc punctiforme [TaxId: 272131] [159603] (1)
    1. 2inb
      complexed with cl, gol
      1. region a:5-139 [147738]
  2. Anabaena variabilis [TaxId: 1172] [159604] (2)
    SQ Q3M7W6 4-139
    1. 2okf
      complexed with act, cl, edo
      1. region a:4-139 [148803]
    2. 2okf
      automatically matched to 2OKF A:4-139
      complexed with act, cl, edo
      1. region b:4-139 [148804]
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)
    SQ Q8PJY1 4-182
    1. 2g3w
      complexed with act
      1. region a:4-182 [147077]
    2. 2g3w
      automatically matched to 2G3W A:4-182
      complexed with act
      1. region b:4-180 [147078]
2. Hypothetical protein PSPTO1487 [159608]
  1. Pseudomonas syringae pv. tomato [TaxId: 323] [159609] (1)
    SQ Q886T9 2-180
    1. 2ot9
      complexed with na, srt
      1. region a:2-180 [149009]