R.EcoRII

{{short description|Restriction enzyme}} [[Image:Eco RII 1NA6.png|thumb|300px|Eco RII dimer based on PDB ID [http://www.rcsb.org/pdb/explore/explore.do?structureId=1NA6 1NA6] ]] '''EcoRII''' (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the restriction modification system (RM) naturally found in ''Escherichia coli'', a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being composed of 402 amino acids.<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | access-date = 2008-03-23 | author = Richard J. Roberts | work = REBASE - The Restriction Enzyme Database }}</ref>

==Mode of action== EcoRII is a bacterial Type IIE<ref name="pmid12654995">{{cite journal |vauthors=Roberts RJ, Belfort M, Bestor T, etal | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF]{{dead link|date=May 2021|bot=medic}}{{cbignore|bot=medic}}</ref> REase that interacts with two<ref name="pmid10903314">{{cite journal |vauthors=Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 | doi-access = free }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]{{Dead link|date=July 2022 |bot=InternetArchiveBot |fix-attempted=yes }}</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal |vauthors=Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | s2cid = 27800123 | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic DNA recognition sequence 5'-CCWGG-3' (W = A or T), one being the actual target of cleavage, the other(s) serving as the allosteric activator(s). EcoRII cuts the target DNA sequence CCWGG, generating sticky ends.<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | isbn = 978-0-7167-3520-5 }}</ref>

==Cut diagram== {| class="wikitable" | Recognition site | Cut results |- | 5' NN'''CCWGG'''NN 3' NN'''GGWCC'''NN | 5' NN '''CCWGG'''NN 3' NN'''GGWCC''' NN |}

==Structure== {{Infobox protein family | Symbol = EcoRII-N | Name = Restriction endonuclease EcoRII, N-terminal | image = PDB 1na6 EBI.jpg | width = | caption = crystal structure of restriction endonuclease ecorii mutant r88a | Pfam = PF09217 | Pfam_clan = CL0405 | InterPro = IPR015300 | SMART = | PROSITE = | MEROPS = | SCOP = 1na6 | TCDB = | OPM family = | OPM protein = | CAZy = | CDD = }} {{Infobox protein family | Symbol = EcoRII-C | Name = EcoRII C terminal | image = PDB 1na6 EBI.jpg | width = | caption = crystal structure of restriction endonuclease ecorii mutant r88a | Pfam = PF09019 | Pfam_clan = CL0236 | InterPro = IPR015109 | SMART = | PROSITE = | MEROPS = | SCOP = | TCDB = | OPM family = | OPM protein = | CAZy = | CDD = }} The apo crystal structure of EcoRII mutant R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal |vauthors=Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 Å resolution. The EcoRII monomer has two domains, N-terminal and C-terminal, linked through a hinge loop.

===Effector-binding domain=== The N-terminal effector-binding domain has an archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent cleft. Structural superposition showed it is evolutionarily related to: *B3 DNA binding domain ({{SCOP|117343}}) from the transcription factors in higher plants ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal |vauthors=Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 | bibcode = 2004PlanC..16.3448Y }}[https://web.archive.org/web/20110522203235/http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref> *C-terminal domain of restriction endonuclease BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | access-date = 2008-03-23 | author = Richard J. Roberts | work = REBASE - The Restriction Enzyme Database }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | vauthors = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 | bibcode = 2005PNAS..10215797G | url = http://bib-pubdb1.desy.de/record/138680/files/2005_Grazulis_15797.pdf | doi-access = free }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]{{dead link|date=July 2025|bot=medic}}{{cbignore|bot=medic}}</ref>

===Catalytic domain=== The C-terminal catalytic domain has a typical<ref name="pmid17369272">{{cite journal |vauthors=Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = Nucleic Acids Research | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}}</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) restriction endonuclease superfamily ({{SCOP|52980}}).

==Autoinhibition/activation mechanism== Structure-based sequence alignment and site-directed mutagenesis identified the putative PD..D/EXK active sites of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/>

==See also== *EcoRI, another nuclease enzyme from ''Escherichia coli''. *EcoRV, another nuclease enzyme from ''Escherichia coli''. *B3 DNA binding domain from higher plants is evolutionary related to EcoRII  *FokI, another nuclease enzyme from ''Flavobacterium okeanokoites''

==External links== *EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]

==References== {{Reflist|2}}

{{DEFAULTSORT:R.Ecorii}} Category:EC 3.1.21 Category:Bacterial enzymes Category:Restriction enzymes Category:EC 3.1 Category:Nucleases