List of restriction enzyme cutting sites: Bd–Bp
This article contains a list of the most studied restriction enzymes whose names start with Bd to Bp inclusive. It contains approximately 100 enzymes.
Legend of nucleobases | |
---|---|
Code | Nucleotide represented |
A | Adenine (A) |
C | Cytosine (C) |
G | Guanine (G) |
T | Thymine (T) |
N | A, C, G or T |
M | A or C |
R | A or G |
W | A or T |
Y | C or T |
S | C or G |
K | G or T |
H | A, C or T |
B | C, G or T |
V | A, C or G |
D | A, G or T |
The following information is given:
- Enzyme: Accepted name of the molecule, according to the internationally adopted nomenclature[1][2], and bibliographical references. (Further reading: see the section "Nomenclature" in the article "Restriction enzyme".)
- PDB code: Code used to identify the structure of a protein in the PDB database of protein structures. The 3D atomic structure of a protein provides highly valuable information to understand the intimate details of its mechanism of action[3][4].
- Source: Organism that naturally produces the enzyme.
- Recognition sequence: Sequence of DNA recognized by the enzyme and to which it specifically binds.
- Cut: Cutting site and DNA products of the cut. The recognition sequence and the cutting site usually match, but sometimes the cutting site can be dozens of nucleotides away from the recognition site[5][6].
- Isoschizomers and neoschizomers: An isoschizomer is an enzyme that recognizes the same sequence as another. A neoschizomer is a special type of isoschizomer that recognizes the same sequence as another, but cuts in a different manner. A maximum number of 8-10 most common isoschizomers are indicated for every enzyme but there may be many more. Neoschizomers are shown in bold and green color font (e.g.: BamHI). When "None on date" is indicated, that means that there were no registered isoschizomers in the databases on that date with a clearly defined cutting site. Isoschizomers indicated in white font and grey background correspond to enzymes not listed in the current lists:
as in this not listed enzyme: EcoR70I
Whole list navigation
Restriction enzymes
Bd - Bp
Enzyme | PDB code | Source | Recognition sequence | Cut | Isoschizomers | ||||||
BdiI | Brevibacterium divaricatum | 5' ATCGAT 3' TAGCTA |
5' ---AT CGAT--- 3' 3' ---TAGC TA--- 5' |
BavCI, Bci29I, Bli41I, Bli86I, BseCI, BsuTUI, Rme21I, SpmI | |||||||
BdiSI | Bacteroides distasonis | 5' CTRYAG 3' GAYRTC |
5' ---C TRYAG--- 3' 3' ---GAYRT C--- 5' |
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BecAII | Brevibacterium sp. A | 5' GGCC 3' CCGG |
5' ---GG CC--- 3' 3' ---CC GG--- 5' |
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BepI | Brevibacterium epidermidis | 5' CGCG 3' GCGC |
5' ---CG CG--- 3' 3' ---GC GC--- 5' |
AccII, BepI, BspFNI, BstUI, Bsu1532I, BtkI, FalII, FauBII, ThaI | |||||||
BetI | Brevibacterium acetyliticum | 5' WCCGGW 3' WGGCCW |
5' ---W CCGGW--- 3' 3' ---WGGCC W--- 5' |
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BfaI [7] | Bacteroides fragilis | 5' CTAG 3' GATC |
5' ---C TAG--- 3' 3' ---GAT C--- 5' |
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BfiI | 2C1L | Bacillus firmus S8120 | 5' ACTGGG 3' TGACCC |
5' ---ACTGGGNNNNN --- 3' 3' ---TGACCCNNNN N--- 5' |
BmrI | ||||||
Bfi57I | Butyrivibrio fibrisolvens OB157 | 5' GATC 3' CTAG |
5' --- GATC--- 3' 3' ---CTAG --- 5' |
Bsp105I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NdeII, SsiBI | |||||||
Bfi89I | Butyrivibrio fibrisolvens OB189 | 5' YGGCCR 3' RCCGGY |
5' ---Y GGCCR--- 3' 3' ---RCCGG Y--- 5' |
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BflI | Bacillus flavothermus | 5' CCN7GG 3' GGN7CC |
5' ---CCNNNNN NNGG--- 3' 3' ---GGNN NNNNNCC--- 5' |
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BfmI | Bacillus firmus S8-336 | 5' CTRYAG 3' GAYRTC |
5' ---C TRYAG--- 3' 3' ---GAYRT C--- 5' |
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BfrI | Bacteroides fragilis | 5' CTTAAG 3' GAATTC |
5' ---C TTAAG--- 3' 3' ---GAATT C--- 5' |
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BfrBI [8] | Bacteroides fragilis BE3 | 5' ATGCAT 3' TACGTA |
5' ---ATGCA T--- 3' 3' ---T ACGTA--- 5' |
Csp68KIII, EcoT22I, Mph1103I, PinBI, Ppu10I, SepI, SspD5II, Zsp2I | |||||||
BfuI | Bacillus firmus Auk 22-m21 | 5' GTATCC 3' CATAGG |
5' ---GTATCCN4NN --- 3' 3' ---CATAGGN4N N--- 5' |
BciVI | |||||||
BfuAI | Bacillus fusiformis | 5' ACCTGC 3' TGGACG |
5' ---ACCTGCNNNN NNNN--- 3' 3' ---TGGACGNNNNNNNN --- 5' |
Acc36I, BspMI, BveI | |||||||
BfuCI | Bacillus fusiformis 1226 | 5' GATC 3' CTAG |
5' --- GATC--- 3' 3' ---CTAG --- 5' |
Bce243I, Bsp105I, BspFI, BstKTI, CpfI, HacI, MkrAI, Sth368I | |||||||
BglI | 1DMU | Bacillus globigii | 5' GCCN5GGC 3' CGGN5CCG |
5' ---GCCNNNN NGGC--- 3' 3' ---CGGN NNNNCCG--- 5' |
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BglII | 1ES8 | Bacillus globigii | 5' AGATCT 3' TCTAGA |
5' ---A GATCT--- 3' 3' ---TCTAG A--- 5' |
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BimI | Brevibacterium immotum | 5' TTCGAA 3' AAGCTT |
5' ---TT CGAA--- 3' 3' ---AAGC TT--- 5' |
AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | |||||||
Bim19I | Brevibacterium immotum 19 | 5' TTCGAA 3' AAGCTT |
5' ---TT CGAA--- 3' 3' ---AAGC TT--- 5' |
AcpI, AsuII, Bpu14I, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | |||||||
Bim19II | Brevibacterium immotum 19 | 5' GGCC 3' CCGG |
5' ---GG CC--- 3' 3' ---CC GG--- 5' |
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BinI | Bifidobacterium infantis 659 | 5' GGATC 3' CCTAG |
5' ---GGATCNNNN N--- 3' 3' ---CCTAGNNNNN --- 5' |
| |||||||
BlfI | Bacillus licheniformis | 5' TCCGGA 3' AGGCCT |
5' ---T CCGGA--- 3' 3' ---AGGCC T--- 5' |
AccIII, Aor13HI, BseAI, BsiMI, BspMII, Bsu23I, Kpn2I, PinBII | |||||||
Bli41I | Bacillus licheniformis 41 | 5' ATCGAT 3' TAGCTA |
5' ---AT CGAT--- 3' 3' ---TAGC TA--- 5' |
Bci29I, Bli86I, BseCI, BsiXI, BsuTUI, Rme21I, SpmI, Ssp27144I | |||||||
Bli86I | Bacillus licheniformis 86 | 5' ATCGAT 3' TAGCTA |
5' ---AT CGAT--- 3' 3' ---TAGC TA--- 5' |
BliAI, Bli41I, BseDI, BsiXI, Rme21I, SpmI, Ssp27144I, ZhoI | |||||||
Bli736I | Bacillus licheniformis 736 | 5' GGTCTC 3' CCAGAG |
5' ---GGTCTCN NNNN--- 3' 3' ---CCAGAGNNNNN --- 5' |
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BliAI | Bacillus licheniformis | 5' ATCGAT 3' TAGCTA |
5' ---AT CGAT--- 3' 3' ---TAGC TA--- 5' |
BliRI, Bli41I, BsiXI, BspDI, Rme21I, SpmI, Ssp27144I, ZhoI | |||||||
BliHKI | Bacillus licheniformis HK | 5' CCTNAGG 3' GGANTCC |
5' ---CC TNAGG--- 3' 3' ---GGANT CC--- 5' |
AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI | |||||||
BliRI | Bacillus licheniformis | 5' ATCGAT 3' TAGCTA |
5' ---AT CGAT--- 3' 3' ---TAGC TA--- 5' |
BciBI, BdiI, Bli41I, BsiXI, BspDI, BspXI, LplI, SpmI, ZhoI | |||||||
BlnI | Brevibacterium linens | 5' CCTAGG 3' GGATCC |
5' ---C CTAGG--- 3' 3' ---GGATC C--- 5' |
AspA2I, AvrII, AvrBII, BspA2I, XmaJI | |||||||
BloHI | Bifidobacterium longum E194b | 5' RGATCY 3' YCTAGR |
5' ---R GATCY--- 3' 3' ---YCTAG R--- 5' |
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BloHII | Bifidobacterium longum E194b | 5' CTGCAG 3' GACGTC |
5' ---CTGCA G--- 3' 3' ---G ACGTC--- 5' |
AjoI, Asp713I, BsuBI, CflI, CfuII, HalII, PstI, SalPI, SflI, Sst12I | |||||||
BlpI | Bacillus lentus | 5' GCTNAGC 3' CGANTCG |
5' ---GC TNAGC--- 3' 3' ---CGANT CG--- 5' |
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BluI | Brevibacterium luteum | 5' CTCGAG 3' GAGCTC |
5' ---C TCGAG--- 3' 3' ---GAGCT C--- 5' |
AbrI, BssHI, BstVI, PanI, Sau3239I, Sfr274I, TliI, XhoI | |||||||
Bme12I | Bacillus megaterium 12 | 5' GATC 3' CTAG |
5' --- GATC--- 3' 3' ---CTAG --- 5' |
Bfi57I, Bsp143I, BspJI, BstMBI, CviAI, Kzo9I, NlaII, SsiBI | |||||||
Bme18I | Bacillus megaterium 18 | 5' GGWCC 3' CCWGG |
5' ---G GWCC--- 3' 3' ---CCWG G--- 5' |
BamNxI, BcuAI, Csp68KI, EagMI, FssI, HgiCII, HgiJI, SinI | |||||||
Bme142I | Bacillus megaterium 142 | 5' RGCGCY 3' YCGCGR |
5' ---RGC GCY--- 3' 3' ---YCG CGR--- 5' |
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Bme216I | Bacillus megaterium 216 | 5' GGWCC 3' CCWGG |
5' ---G GWCC--- 3' 3' ---CCWG G--- 5' |
BamNxI, BcuAI, Csp68KI, Eco47I, FssI, HgiCII, HgiJI, SinI | |||||||
Bme361I | Bacillus megaterium 361 | 5' GGCC 3' CCGG |
5' ---GG CC--- 3' 3' ---CC GG--- 5' |
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Bme585I | Bacillus mesentericus 585 | 5' CCCGC 3' GGGCG |
5' ---CCCGCNNNN NN--- 3' 3' ---GGGCGNNNNNN --- 5' |
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Bme1390I | Bacillus megaterium RFL1390 | 5' CCNGG 3' GGNCC |
5' ---CC NGG--- 3' 3' ---GGN CC--- 5' |
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Bme1580I | Bacillus megaterium 1580 | 5' GKGCMC 3' CMCGKG |
5' ---GKGCM C--- 3' 3' ---C MCGKG--- 5' |
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BmgBI | Bacillus megaterium | 5' CACGTC 3' GTGCAG |
5' ---CAC GTC--- 3' 3' ---GTG CAG--- 5' |
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BmrI [9][10] | Bacillus megaterium | 5' ACTGGG 3' TGACCC |
5' ---ACTGGGNNNNN --- 3' 3' ---TGACCCNNNN N--- 5' |
BfiI | |||||||
BmtI | Bacillus megaterium S2 | 5' GCTAGC 3' CGATCG |
5' ---GCTAG C--- 3' 3' ---C GATCG--- 5' |
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BmyI [11] | Bacillus mycoides | 5' GDGCHC 3' CHCGDG |
5' ---GDGCH C--- 3' 3' ---C HCGDG--- 5' |
AocII, BsoCI, Bsp1286I, BspLS2I, MhlI, NspII, SduI | |||||||
BnaI | Bacillus natto B3364 | 5' GGATCC 3' CCTAGG |
5' ---G GATCC--- 3' 3' ---CCTAG G--- 5' |
AccEBI, BamHI, Bce751I, BstI, CelI, OkrAI, Nsp29132II, Pfl8I, SolI | |||||||
BoxI | Brevibacterium oxydans Iti 12-025 | 5' GACN4GTC 3' CTGN4CAG |
5' ---GACNN NNGTC--- 3' 3' ---CTGNN NNCAG--- 5' |
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BpcI | Bacillus sphaericus | 5' CTRYAG 3' GAYRTC |
5' ---C TRYAG--- 3' 3' ---GAYRT C--- 5' |
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BpiI | Bacillus pumilus sw 4-3 | 5' GAAGAC 3' CTTCTG |
5' ---GAAGACNN NNNN--- 3' 3' ---CTTCTGNNNNNN --- 5' |
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BplI | Bacillus pumilus | 5' GAGN5CTC 3' CTCN5GAG |
5' ---GAGN5CTCN7NNNNNN --- 3' 3' ---CTCN5GAGN7N NNNNN--- 5' |
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BpmI | Bacillus pumilus | 5' CTGGAG 3' GACCTC |
5' ---CTGGAGN13NNN --- 3' 3' ---GACCTCN13N NN--- 5' |
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BpoAI | Bacillus polymyxa | 5' ATTAAT 3' TAATTA |
5' ---AT TAAT--- 3' 3' ---TAAT TA--- 5' |
AseI, AsnI, PshBI, Sru4DI, VspI | |||||||
BptI | Bacillus pantothenticus | 5' CCWGG 3' GGWCC |
5' ---CC WGG--- 3' 3' ---GGW CC--- 5' |
AjnI, BseBI, Bse16I, BstNI, BstOI, BstM6I, Bst2UI, EcoRII, MvaI | |||||||
BpuI | Bacillus pumilus AHU1387A | 5' GRGCYC 3' CYCGRG |
5' ---GRGCY C--- 3' 3' ---C YCGRG--- 5' |
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Bpu10I | Bacillus pumilus 10 | 5' CCTNAGC 3' GGANTCG |
5' ---CC TNAGC--- 3' 3' ---GGANT CG--- 5' |
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Bpu14I | Bacillus pumilus 14 | 5' TTCGAA 3' AAGCTT |
5' ---TT CGAA--- 3' 3' ---AAGC TT--- 5' |
AcpI, AsuII, BsiCI, BspT104I, CbiI, FspII, MlaI, PpaAI, SfuI | |||||||
Bpu95I | Bacillus pumilus 95 | 5' CGCG 3' GCGC |
5' ---CG CG--- 3' 3' ---GC GC--- 5' |
AccII, BepI, BspFNI, BstUI, Bsu1532I, FalII, FnuDII, MvnI, ThaI | |||||||
Bpu1102I | Bacillus pumilus RFL1102 | 5' GCTNAGC 3' CGANTCG |
5' ---GC TNAGC--- 3' 3' ---CGANT CG--- 5' |
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BpuAI [12] | Bacillus pumilus | 5' GAAGAC 3' CTTCTG |
5' ---GAAGACNN NNNN--- 3' 3' ---CTTCTGNNNNNN --- 5' |
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BpuAmI | Bacillus pumilus | 5' GAGCTC 3' CTCGAG |
5' ---GAG CTC--- 3' 3' ---CTC GAG--- 5' |
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BpuB5I | Bacillus pumilus | 5' CGTACG 3' GCATGC |
5' ---C GTACG--- 3' 3' ---GCATG C--- 5' |
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BpuDI | Bacillus pumilus 1117 | 5' CCTNAGC 3' GGANTCG |
5' ---CC TNAGC--- 3' 3' ---GGANT CG--- 5' |
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BpuEI | Bacillus pumilus 2187a | 5' CTTGAG 3' GAACTC |
5' ---CTTGAGN13NNN --- 3' 3' ---GAACTCN13N NN--- 5' |
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BpuJI [13][14] | 2VLA | Bacillus pumilus RFL1458 | 5' CCCGT 3' GGGCA |
5' ---CCCGTN10N NNNNNNNN--- 3' 3' ---GGGCAN10NNNNNNNNN --- 5' |
— None on May 2010 — | ||||||
BpuSI | Bacillus pumilus | 5' GGGAC 3' CCCTG |
5' ---GGGACN9N NNNN--- 3' 3' ---CCCTGN9NNNNN --- 5' |
Notes
- Smith HO, Nathans D (December 1973). "Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes". J. Mol. Biol. 81 (3): 419–23. doi:10.1016/0022-2836(73)90152-6. PMID 4588280.
- Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SK, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Krüger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY (April 2003). "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes". Nucleic Acids Res. 31 (7): 1805–12. doi:10.1093/nar/gkg274. PMC 152790. PMID 12654995.
- Jeremy MB, John LT, Lubert S (2002). "3. Protein Structure and Function". Biochemistry. San Francisco: W. H. Freeman. ISBN 0-7167-4684-0.
- Anfinsen C.B. (1973). "Principles that Govern the Folding of Protein Chains". Science. 181 (4096): 223–30. doi:10.1126/science.181.4096.223. PMID 4124164.
- Kessler C, Manta V (August 1990). "Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3)". Gene. 92 (1–2): 1–248. doi:10.1016/0378-1119(90)90486-B. PMID 2172084.
- Pingoud A, Jeltsch A (September 2001). "Structure and function of type II restriction endonucleases". Nucleic Acids Res. 29 (18): 3705–27. doi:10.1093/nar/29.18.3705. PMC 55916. PMID 11557805.
- Reinecke SN, Morgan RD (March 1991). "BfaI, a new MaeI isoschizomer from Bacteroides fragilis, recognizes the sequence 5' C decreases TAG 3'". Nucleic Acids Res. 19 (5): 1152. doi:10.1093/nar/19.5.1152. PMC 333798. PMID 2020550.
- Azeddoug H, Reysset G, Sebald M (August 1992). "Characterization of restriction endonuclease BfrBI from Bacteroides fragilis strains BE3 and AIP 10006". FEMS Microbiol Lett. 74 (2–3): 133–6. doi:10.1111/j.1574-6968.1992.tb05355.x. PMID 1526445.
- Bao Y, Higgins L, Zhang P, Chan SH, Laget S, Sweeney S, Lunnen K, Xu SY (March 2008). "Expression and purification of BmrI restriction endonuclease and its N-terminal cleavage domain variants". Protein Expr Purif. 58 (1): 42–52. doi:10.1016/j.pep.2007.11.002. PMC 2275207. PMID 18164625.
- Chan SH, Bao Y, Ciszak E, Laget S, Xu SY (September 2007). "Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities". Nucleic Acids Res. 35 (18): 6238–48. doi:10.1093/nar/gkm665. PMC 2094064. PMID 17855396.
- Wagner E, Schmitz GG, Kaluza K, Jarsch M, Götz F, Kessler C (May 1990). "BmyI, a novel SduI isoschizomer from Bacillus mycoides recognizing 5'-GDGCH/C-3'". Nucleic Acids Res. 18 (10): 3088. doi:10.1093/nar/18.10.3088. PMC 330873. PMID 2161522.
- Pogge von Strandmann R, Städtler P, Walter T, Frey B, Kaluza K, Hengstenberg W, Schmitz G (September 1992). "BpuAI, a novel BbsI and BbvII isoschizomer from Bacillus pumilus recognizing 5'-GAAGAC-3'". Nucleic Acids Res. 20 (17): 4664. doi:10.1093/nar/20.17.4664. PMC 334204. PMID 1408773.
- Sukackaite R, Lagunavicius A, Stankevicius K, Urbanke C, Venclovas C, Siksnys V (March 2007). "Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family". Nucleic Acids Res. 35 (7): 2377–89. doi:10.1093/nar/gkm164. PMC 1874659. PMID 17392342.
- Sukackaite R, Grazulis S, Bochtler M, Siksnys V (March 2008). "The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution". J Mol Biol. 378 (5): 1084–93. doi:10.1016/j.jmb.2008.03.041. PMID 18433771.
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