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3.1.21.4: type II site-specific deoxyribonuclease

This is an abbreviated version!
For detailed information about type II site-specific deoxyribonuclease, go to the full flat file.

Word Map on EC 3.1.21.4

Reaction

endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates =

Synonyms

AatII, AcuI, acuIRM, AfeI, AflII, AflIII, aflIIR, AgeI, AhaIII, AlfI, AloI, AluI, AlwNI, Apa BI, Apa CI, Apa DI, ApaI, ApaLI, apaLIR, AsuI, AsuII, AvaI, AvaII, AvaIII, AvrII, BaeI, BamHI, bamHIR, BbeI, BbvCI, BbvI, BbvII, bbvIR, BcefI, BcgI, BclI, Bfi2411I, BgII, BglI, BglII, bglIIR, BinI, BmrI, BplI, BpmI, bpmIR, BpuEI, BpuIOI, BsaAI, BsaBI, BsaWI, BsaXI, Bse634I, BsePI, BseRI, BseRI endonuclease, BsgI, BsmAI, BsmBI, BsmI, BsoBI, Bsp CI, BspD6I, BspGI, BspHI, BspI, BspMI, BSPMII, BspRI, BsrI, BssSI, BstEII, BstF5I, BstII, BstXI, BstYI, Bsu2413I, BtsI, CauII, Cfr101, Cfr10I, CfrBI, CfrI, CjeI, ClaI, CspCI, CstMI, CviAI, CviJI, DdeI, DNA restriction endonuclease, DNA restriction enzyme, DpnI, DpnII, DraII, DraIII, DrdI, DrdII, DsaI, EC 3.1.23, EC 3.1.24, EciI, Eco1524I, Eco311, Eco31I, Eco47III, Eco571, Eco57I, eco57IR, EcoO109I, EcoP15I, ecoP15Ires, EcoRI, EcoRII, ecoRIR, EcoRV, EcoVIII, EgeI, EheI, Endonuclease AbrI, Endonuclease AccI, Endonuclease AgeI, Endonuclease ApaLI, Endonuclease AvaI, Endonuclease BamHI, Endonuclease BanI, Endonuclease BglI, Endonuclease BglII, Endonuclease BsoBI, Endonuclease Bsp6I, Endonuclease BstVI, Endonuclease BsuBI, Endonuclease BsuFI, Endonuclease BsuRI, Endonuclease CeqI, Endonuclease Cfr10I, Endonuclease Cfr9I, Endonuclease CfrBI, Endonuclease CviAII, Endonuclease CviJI, Endonuclease DdeI, Endonuclease DpnI, Endonuclease DpnII, Endonuclease Eco47I, Endonuclease Eco47II, Endonuclease EcoRI, Endonuclease EcoRII, Endonuclease EcoRV, Endonuclease FokI, Endonuclease HaeII, Endonuclease HaeIII, Endonuclease HgAI, Endonuclease HgiBI, Endonuclease HgiCI, Endonuclease HgiCII, Endonuclease HgiDI, Endonuclease HgiEI, Endonuclease HgiGI, Endonuclease HhaII, Endonuclease HincII, Endonuclease HindII, Endonuclease HindIII, Endonuclease HindVP, Endonuclease HinfI, Endonuclease HpaI, Endonuclease HpaII, Endonuclease HphI, Endonuclease KpnI, Endonuclease LlaDCHI, Endonuclease MamI, Endonuclease MboI, Endonuclease MboII, Endonuclease MjaI, Endonuclease MjaII, Endonuclease MjaIII, Endonuclease MjaIV, Endonuclease MjaV, Endonuclease MjaVIP, Endonuclease MspI, Endonuclease MthTI, Endonuclease MthZI, Endonuclease MunI, Endonuclease MwoI, Endonuclease NaeI, Endonuclease NgoBI, Endonuclease NgoBV, Endonuclease NgoFVII, Endonuclease NgoMIV, Endonuclease NgoPII, Endonuclease NlaIII, Endonuclease NlaIV, Endonuclease NmeDIP, Endonuclease NspV, Endonuclease PaeR7I, Endonuclease PstI, Endonuclease PvuI, Endonuclease PvuII, Endonuclease RsrI, Endonuclease SacI, Endonuclease SalI, Endonuclease Sau3AI, Endonuclease Sau96I, Endonuclease ScaI, Endonuclease ScrFI, Endonuclease SfiI, Endonuclease SinI, Endonuclease SmaI, Endonuclease SsoII, Endonuclease StsI, Endonuclease TaqI, Endonuclease TthHB8I, Endonuclease XamI, Endonuclease XcyI, endoR*Bsp, Esp3I, EspI, FauI, FinI, Fnu4HI, FnuSII, FokI, fokIR, FseI, GdiII, GGCC-specific restriction endonuclease, GsuI, HaeI, HaeII, HaeIII, HaeVI, HgaI, HgiAI, HgiCI, HgiEI, HgiEII, HgiJII, HhaI, HhaII, HincII, HindII, HindIII, hindIIIR, HinfI, HinP1I, HpaI, HpaII, HphI, Hpy188I, Hpy8I, Hpy99II, Hpy99IV, Hpy99VIIIP, HpyAXII, HpyF17I, KasI, KpnI, KpnIR, Ksp6321, LlaDI, LlaII, LmoJ2, LmoJ3, MaeI, MaeII, MaeIII, MboI, MboII, McaTI, McrI, MfeI, MjaIV, MjaV, MluI, Mly113I, MlyI, MmeI, mmeIRM, MmoSTI, MnlI, More, MseI, MspA1I, MspI, MstI, MunI, Mva1269I, Mva1269I restriction endonuclease, MvaI, MwoI, NaeI, NarI, NcoI, ncoIR, NdeI, NgoMIV, NheI, NlaIII, NlaIV, NmeDI, NmeDIP, NotI, NruI, NspBII, NspV, Nt.BspD6I, nuclease, deoxyribonucleic restriction endo-, nuclease, restriction endodeoxyribo-, PabI, PflMI, PhoI, PleI, PmaCI, PPII, PpuMI, PsasM2I, PshAI, PspGI, PstI, pstIR, PvuI, PvuII, R.AbrI, R.AccI, R.AgeI, R.ApaLI, R.AvaI, R.BamHI, R.BanI, R.BglI, R.BglII, R.BsoBI, R.Bsp6I, R.BstVI, R.BsuBI, R.BsuFI, R.BsuRI, R.CeqI, R.Cfr10I, R.Cfr9I, R.CfrBI, R.CviAII, R.CviJI, R.DdeI, R.DpnI, R.DpnII, R.Eco47I, R.Eco47II, R.EcoRI, R.EcoRII, R.EcoRV, R.FokI, R.HaeII, R.HaeIII, R.HgAI, R.HgiBI, R.HgiCI, R.HgiCII, R.HgiDI, R.HgiEI, R.HgiGI, R.HhaII, R.HincII, R.HindII, R.HindIII, R.HindVP, R.HinfI, R.HpaI, R.HpaII, R.HphI, R.KpnI, R.LlaDCHI, R.MamI, R.MboI, R.MboII, R.MjaI, R.MjaII, R.MjaIII, R.MjaIV, R.MjaV, R.MjaVIP, R.MspI, R.MthTI, R.MthZI, R.MunI, R.MwoI, R.NaeI, R.NgoBI, R.NgoBV, R.NgoFVII, R.NgoI, R.NgoMIV, R.NgoPII, R.NgoV, R.NgoVII, R.NlaIII, R.NlaIV, R.NmeDIP, R.NspV, R.PaeR7I, R.PstI, R.PvuI, R.PvuII, R.RsrI, R.SacI, R.SalI, R.Sau3AI, R.Sau96I, R.ScaI, R.ScrFI, R.SfiI, R.SinI, R.SmaI, R.SsoII, R.StsI, R.TaqI, R.TthHB8I, R.XamI, R.XcyI, REase, restriction endodeoxyribonuclease, restriction endonuclease, restriction endonuclease EcoRV, restriction endonuclease SuaI, restriction enzyme, RleAI, RsaI, SacI, SacII, SacIR, SalI, Sau3AI, sau96I, SauI, ScaI, ScrFI, SduI, SecI, SfaNI, SfeI, SfiI, SfoI, SgrAI, Sho27844P, site-specific endonuclease BME142I, site-specific endonuclease Bme216I, site-specific endonuclease BmeI, site-specific type II endonuclease, SmaI, SmuI, SnaBI, SnaI, SpeI, SphI, SpiI, ss.BspD6I, Sse9I, SspI, StuI, StyI, SuaI, SuiI, TaqI, TaqII, TfiI, Tsp451, TspEI, TstI, Tth111I, Tth111II, type II ENase, type II REase, type II restriction endonuclease, type II restriction endonuclease EcoO109I, type II restriction enonuclease, type II restriction enzyme, type II restriction-modification protein, type II restriction-modification system, type II RM system, type IIB restriction endonuclease, type IIE restriction endonuclease, type IIF restriction endonuclease, type IIP REase, type IIP restriction endonuclease, Type IIS REase, type IIS restriction endonuclease, type IIS restriction enzyme, type IIT restriction endonuclease BbvCI, typeIIS restriction endonuclease, Uba1105I, Uba1108I, UbaLAI, UpaP162, UPV_230, VspI, XbaI, XcmI, XhoI, XhoII, XmaIII, XmnI

ECTree

     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.21 Endodeoxyribonucleases producing 5'-phosphomonoesters
                3.1.21.4 type II site-specific deoxyribonuclease

Crystallization

Crystallization on EC 3.1.21.4 - type II site-specific deoxyribonuclease

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
small and large subunit of Bsp6I
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crystallization of the R2 subunit at low pH reveals an elongated dimer with the two catalytic sites located on opposite sides. Subsequent crystallization at physiological pH reveals a tetramer comprising two copies of each subunit, with a pair of deep clefts each containing two catalytic sites appropriately positioned and oriented for DNA cleavage
Q5D6Y5; Q5D6Y4
crystal structure of EcoO109I and its complex with DNA
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database information: http://rebase.neb.com
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sitting drop vapor diffusion method at 19°C
structure of BstYI bound to a cognate DNA sequence (AGATCT). The structure reveals the basis for degenerate DNA recognition and offers insight into possibilities and limitations in changing the specificities of closely related restriction enzymes
-
crystal structures of mutant enzyme Q138F bound to GTTAAC, GTCGAC both with and without Ca2+, as well as the structure of the wild-type HincII bound to GTTAAC
hanging-drop method
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three-dimensional model of the enzyme's catalytic domain
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crystal structure of MmeI in complex with its DNA substrate (a 29-mer DNA duplex containing a single MmeI recognition site (TCCGAC)) and an S-adenosylmethionine analog sinefungin. The co-crystals are obtained in the presence of sinefungin and diffracted to 2.6 A resolution with synchrotron radiation. They belong to space group P1 with unit cell dimensions of a = 61.87 A, b = 95.29 A, c = 161.96 A, alpha = 72.84°, beta = 89.15°, and gamma = 71.61°, and contain two MmeI/DNA/sinefungin complexes in the crystallographic asymmetric unit
crystal structures of a specific MspI-DNA complex in a monoclinic space group and an orthorhombic space group, at 1.95 A and 2.7 A resolution, respectively. Native enzyme, Hg(OAc)2 derivatives, CH3HgCl derivatives, Sm(OAc)3 derivative
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single-chain variant scPvuII constructed by tandemly joining the two subunits through the peptide linker Gly-Ser-Gly-Gly. Resolution of 2.35 A, space group P42
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C-terminal 232-419 amino acids fragment, space group P212121, resolution 2.8 A, one molecule per asymmetric unit
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both native enzyme and as selenomethionyl derivative
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sitting drop vapor diffusion method at 19°C. 1.6 A co-crystal structure of UbaLAI N-terminal domain