List of restriction enzyme cutting sites: Bd–Bp

Main articles: List of restriction enzyme cutting sites and Restriction enzyme

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

This article contains a list of the most studied restriction enzymes whose names start with Bd to Bp inclusive. It contains approximately 100 enzymes.

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'

BecAII Brevibacterium sp. A 5' GGCC
3' CCGG 5' ---GG CC--- 3'
3' ---CC GG--- 5'

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'

BfaI ^[7] Bacteroides fragilis 5' CTAG
3' GATC 5' ---C TAG--- 3'
3' ---GAT C--- 5'

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'

BflI Bacillus flavothermus 5' CCN₇GG
3' GGN₇CC 5' ---CCNNNNN NNGG--- 3'
3' ---GGNN NNNNNCC--- 5'

BfmI Bacillus firmus S8-336 5' CTRYAG
3' GAYRTC 5' ---C TRYAG--- 3'
3' ---GAYRT C--- 5'

BfrI Bacteroides fragilis 5' CTTAAG
3' GAATTC 5' ---C TTAAG--- 3'
3' ---GAATT C--- 5'

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'

BglII 1ES8 Bacillus globigii 5' AGATCT
3' TCTAGA 5' ---A GATCT--- 3'
3' ---TCTAG A--- 5'

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'

BinI

Bifidobacterium infantis 659

5' GGATC
3' CCTAG

5' ---GGATCNNNN N--- 3'
3' ---CCTAGNNNNN --- 5'

AclWI, AlwI,

BsrWI,

BspPI,

BstH9I,

Bth617I,

EacI

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'

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'

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'

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'

AccB2I,	BfoI,	Bsp143II,
BstH2I, HaeII, LpnI

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'

Bme585I Bacillus mesentericus 585 5' CCCGC
3' GGGCG 5' ---CCCGCNNNN NN--- 3'
3' ---GGGCGNNNNNN --- 5'

Bme1390I Bacillus megaterium RFL1390 5' CCNGG
3' GGNCC 5' ---CC NGG--- 3'
3' ---GGN CC--- 5'

Bme1580I Bacillus megaterium 1580 5' GKGCMC
3' CMCGKG 5' ---GKGCM C--- 3'
3' ---C MCGKG--- 5'

BmgBI Bacillus megaterium 5' CACGTC
3' GTGCAG 5' ---CAC GTC--- 3'
3' ---GTG CAG--- 5'

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'

AceII, AsuNHI,	BspOI,	NheI,
LlaG2I, PstNHI

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'

BpcI Bacillus sphaericus 5' CTRYAG
3' GAYRTC 5' ---C TRYAG--- 3'
3' ---GAYRT C--- 5'

BpiI Bacillus pumilus sw 4-3 5' GAAGAC
3' CTTCTG 5' ---GAAGACNN NNNN--- 3'
3' ---CTTCTGNNNNNN --- 5'

BplI Bacillus pumilus 5' GAGN₅CTC
3' CTCN₅GAG 5' ---GAGN₅CTCN₇NNNNNN --- 3'
3' ---CTCN₅GAGN₇N NNNNN--- 5'

BpmI Bacillus pumilus 5' CTGGAG
3' GACCTC 5' ---CTGGAGN₁₃NNN --- 3'
3' ---GACCTCN₁₃N NN--- 5'

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'

Bpu10I Bacillus pumilus 10 5' CCTNAGC
3' GGANTCG 5' ---CC TNAGC--- 3'
3' ---GGANT CG--- 5'

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'

BpuAI ^[12] Bacillus pumilus 5' GAAGAC
3' CTTCTG 5' ---GAAGACNN NNNN--- 3'
3' ---CTTCTGNNNNNN --- 5'

BpuAmI Bacillus pumilus 5' GAGCTC
3' CTCGAG 5' ---GAG CTC--- 3'
3' ---CTC GAG--- 5'

BpuB5I Bacillus pumilus 5' CGTACG
3' GCATGC 5' ---C GTACG--- 3'
3' ---GCATG C--- 5'

BpuDI Bacillus pumilus 1117 5' CCTNAGC
3' GGANTCG 5' ---CC TNAGC--- 3'
3' ---GGANT CG--- 5'

BpuEI Bacillus pumilus 2187a 5' CTTGAG
3' GAACTC 5' ---CTTGAGN₁₃NNN --- 3'
3' ---GAACTCN₁₃N NN--- 5'

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'

This list is incomplete; you can help by expanding it.

Current list/Article:

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. 25 (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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