R.EcoRII

Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an enzyme of restriction modification system (RM) naturally found in "Escherichia coli", a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being comprised of 402 amino acids.cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = ]

Mode of action

EcoRII is a bacterial Type IIEcite journal | author = Roberts RJ, Belfort M, Bestor T, "et al" | 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 | issn = [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] ] REase that interacts with twocite journal | author = 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 | issn = [http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF] ] or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gifthree] cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | 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 | issn = ] 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 cut target DNA sequence CCWGG generating sticky ends.cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = ]

Cut diagram

tructure

The apo crystal structure of EcoRII mutant R88A (PDB|1NA6)cite journal | author = 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 | issn = ] 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 a 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)cite journal | author = 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 | issn = [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF] ]
*C-terminal domain of restriction endonuclease BfiIcite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = ] (PDB|2C1L)cite journal | author = 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 | issn = [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF] ]

Catalytic domain

The C-terminal catalytic domain has a typicalcite journal | author = 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 = NAR | volume = 35 | issue = 7 | pages = 2227-37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF] ] 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.

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