List of restriction enzyme cutting sites: Bd–Bp

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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[edit]

Restriction enzymes[edit]

Bd - Bp[edit]

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'

Notes[edit]

  1. ^ 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.
  2. ^ 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.
  3. ^ Jeremy MB, John LT, Lubert S (2002). "3. Protein Structure and Function". Biochemistry. San Francisco: W. H. Freeman. ISBN 0-7167-4684-0.
  4. ^ 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.
  5. ^ 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.
  6. ^ 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.
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
  10. ^ 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.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.