Restriction enzyme
Eco RII dimer based on PDB ID 1NA6 EcoRII (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the restriction modification system (RM) naturally found in Escherichia coli Gram-negative bacteria . Its molecular mass is 45.2 kDa , being composed of 402 amino acids .[ 1]
EcoRII is a bacterial Type IIE[ 2] REase that interacts with two[ 3] three [ 4] DNA recognition sequence 5' -CC WGG -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 .[ 5]
Recognition site
Cut results
5' NNCCWGG NN
3' NNGGWCC NN
5' NN CCWGG NN
3' NNGGWCC NN
Protein family
Protein family
The apo crystal structure of EcoRII mutant R88A (PDB : 1NA6 [ 6] Å resolution . The EcoRII monomer has two domains , N-terminal and C-terminal , linked through a hinge loop .
Effector-binding domain [ edit ] The N-terminal effector -binding domain has an archetypal DNA-binding pseudobarrel fold (SCOP 101936 cleft . Structural superposition showed it is evolutionarily related to:
The C-terminal catalytic domain has a typical[ 10] SCOP 52979 restriction endonuclease superfamily (SCOP 52980
[ edit ] 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.[ 6]
EcoRII in Restriction Enzyme Database REBASE
^ Richard J. Roberts. "EcoRII" . REBASE - The Restriction Enzyme Database . Retrieved 2008-03-23 . ^ Roberts RJ, Belfort M, Bestor T, et al. (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 . PDF [dead link ^ Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M (2000). "Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage" . J. Biol. Chem . 275 (39): 30631– 7. doi :10.1074/jbc.M003904200 PMID 10903314 . PDF [permanent dead link ^ Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL (2007). "Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy". Biochemistry . 46 (39): 11128– 36. doi :10.1021/bi701123u . PMID 17845057 . S2CID 27800123 . ^ Griffiths, Anthony J. F. (1999). An Introduction to genetic analysis . San Francisco: W.H. Freeman. ISBN 978-0-7167-3520-5 ^ a b Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L (2004). "Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold". J. Mol. Biol . 335 (1): 307– 19. doi :10.1016/j.jmb.2003.10.030 . PMID 14659759 . ^ 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 (2004). "Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1" . Plant Cell . 16 (12): 3448– 59. Bibcode :2004PlanC..16.3448Y . doi :10.1105/tpc.104.026112 . PMC 535885 PMID 15548737 . PDF ^ Richard J. Roberts. "BfiI" . REBASE - The Restriction Enzyme Database . Retrieved 2008-03-23 . ^ Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V (2005). "Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease" (PDF) . Proc. Natl. Acad. Sci. U.S.A . 102 (44): 15797– 802. Bibcode :2005PNAS..10215797G . doi :10.1073/pnas.0507949102 PMC 1266039 PMID 16247004 . PDF [dead link ^ Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA (2007). "Topology of Type II REases revisited; structural classes and the common conserved core" . Nucleic Acids Research . 35 (7): 2227– 37. doi :10.1093/nar/gkm045 . PMC 1874628 PMID 17369272 .
Basic Concept Recognition sequence 4bp Recognition sequence 5bp Recognition sequence 6bp Recognition sequence 8bp Lists
