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3'-biotinylated 51 bp dsDNA + H2O
?
-
-
-
?
5'-biotinylated 51 bp ssDNA + H2O
?
-
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + phosphate
-
-
-
?
linear plasmid DNA pDRM-2R + ATP
?
-
-
-
?
plasmid pACYC184 + ATP
?
-
-
-
-
?
plasmid pET20b + ATP
?
-
-
-
-
?
plasmid pTK-neo + ATP
?
-
the enzyme recognises the symmetrical sequence GAAN7TTC at position 2535 bp
-
-
?
plasmid pUC19 + ATP
?
-
the enzyme recognises the symmetrical sequence GAAN7TTC at positions 1126 bp and 2294 bp
-
-
?
supercoiled plasmid DNA pRK + ATP
?
-
-
-
?
synthetic oligonucleotide + ATP
?
additional information
?
-
DNA + H2O
?
-
EcoR124I couples ATP hydrolysis to bidirectional DNA translocation
-
-
?
DNA + H2O
?
-
the enzyme must overcome a similar slow step before translocation reaches a steady state
-
-
?
DNA + H2O
?
-
HsdR subunit can produce only a single cleavage of the phosphodiester backbone of the DNA but can cooperate with another HsdR subunit to produce full DNA cleavage, producing DNA with overhanging ends of single-stranded DNA. On a single-site plasmid, cleavage requires the association of HsdR, from solution, to the cleavage complex in order to produce double-strand cleavage
-
-
?
DNA + H2O
?
-
R.HpyAXII effectively restricts chromosomal DNA during natural transformation
-
-
?
DNA + H2O
?
-
R.HpyAXII effectively restricts chromosomal DNA during natural transformation
-
-
?
DNA + H2O
?
-
the PspGI restriction-modification system recognizes the sequence CCWGG. R.PspGI cuts DNA before the first C in the cognate sequence and M.PspGI methylates N4 of one of the cytosines in the sequence. R.PspGI flips both bases in the central base pair out of the duplex
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
-
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
overview of recognition sequences
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
-
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
overview of recognition sequences
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
the wild type enzyme EcoK cleaves circular DNA. Only one endonuclease molecule is required per cleavage event. Cleavage of linear DNA may require a second endonuclease molecule
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
the enzyme is both a restriction endonuclease and a modification methylase. Hemi-methylated DNA is the preferred substrate for methylation
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
the site of restriction cleavage is random, occuring between 1 and 5 kb from the recognition site. The modification methylase acts directly at the recognition sequence
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
the modification methylase binds sequence specifically to DNA and protects a 25bp fragment containing its cognate recognition sequence from digestion by exonuclease III, specific adenine on each strand of DNA is the site of methylation
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
supercoiled with one or two SR124I recognition sites is cleaved by the same mechanism. Nicked-circle DNA is an intermediate of the cleavage reaction
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
EcoAI preferentially generates 3'-overhangs of 2-3 nt. Displays some preference for the formation of 5'-overhangs of a length of 6-7 and 3-5 nt, respectively. type I restriction enzymes require two restriction subunits to introduce DNA double-stran breaks, each providing one catalytic center for phosphodiester bond hydrolysis
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
EcoKI displays some preference for the formation of 5'-overhangs of a length of 6-7 and 3-5 nt, respectively. Type I restriction enzymes require two restriction subunits to introduce DNA double-stran breaks, each providing one catalytic center for phosphodiester bond hydrolysis
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
EcoR124I displays some preference for the formation of 5'-overhangs of a length of 6-7 and 3-5 nt, respectively. Type I restriction enzymes require two restriction subunits to introduce DNA double-stran breaks, each providing one catalytic center for phosphodiester bond hydrolysis
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
initiation of translocation by type I restriction-modification enzymes is associated with a short DNA extrusion
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
the two motor subunits of Eco124I are independent motors that translocate along the helical pitch of the DNA. Dynamic termination and reinitiation of translocation activity is governed by disassembly and reassembly of the enzyme
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
type I enzymes recognize bipartite DNA sequences comprising two half-sequences separated by a gap, for example, AACNNNNNNGTGC (AAC N6 GTGC) where N=any base
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
-
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
-
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
restricts unmodified phage DNA
-
-
?
duplex DNA + ATP
double-stranded DNA fragments with terminal 5'-phosphate + ADP + inorganic phosphate
-
restricts unmodified phage DNA
-
-
?
plasmid DNA + H2O
?
-
EcoKI prefers to have a partially filled DNA-binding site rather than one fully occupied by non-specific DNA. Dimerization of EcoKI does not occur before DNA binding and takes place on specific sites before any looping. Dimerization occurs before the two specific sites are bought together. Looping initially occurs between a target site and a non-specific region of DNA
-
-
?
plasmid DNA + H2O
?
-
R.HpyAXII effectively restricts unmethylated plasmid during natural transformation
-
-
?
plasmid DNA + H2O
?
-
R.HpyAXII effectively restricts unmethylated plasmid during natural transformation
-
-
?
synthetic oligonucleotide + ATP
?
-
recognition sequence: CA(underlined)C(5N)T(underlined)GGC
-
-
?
synthetic oligonucleotide + ATP
?
-
recognition sequence: GA(underlined)C(5N)RT(underlined)AAY
-
-
?
synthetic oligonucleotide + ATP
?
-
recognition sequence: GCA(underlined)(6N)CT(underlined)GA
-
-
?
synthetic oligonucleotide + ATP
?
-
recognition sequence: GTCA(underlined)(6N)T(underlined)GAY
-
-
?
additional information
?
-
-
-
-
-
?
additional information
?
-
-
the database REBASE contains information about recognition sites and cleavage sites
-
-
?
additional information
?
-
-
a bacterial population may switch the recognition sequence of its type I restriction-modification system by single recombination events and thus is able to maintain a prokaryotic analogue of the immune system of variable specificity
-
-
?
additional information
?
-
-
enzyme restricts the exchange of genetic material between bacteria of different strains or species
-
-
?
additional information
?
-
-
C.PvuII binding to operator left activates transcription. Binding preference for operator left over operator right. All four bases of the inter-operator TGTA spacer are required for C.PvuII-dependent activation
-
-
?
additional information
?
-
-
enzyme restricts the exchange of genetic material between bacteria of different strains or species
-
-
?
additional information
?
-
-
restricts unmodified phage DNA after both infection and transfection
-
-
?
additional information
?
-
-
isoform Sau1 is the major mechanism for blocking transfer of resistance genes and other mobile genetic elements into Staphylococcus aureus isolates from other species, as well as for controlling the spread of resistance genes between isolates of different Staphylococcus aureus lineages
-
-
?
additional information
?
-
-
does not cut pUC19 plasmid
-
-
?
additional information
?
-
-
determination of target sequences recognized by the Sau1 Type I RM systems present in a wide range of the most prevalent Staphylococcus aureus lineages and assigned the sequences recognized to particular target recognition domains within the RM enzymes
-
-
?
additional information
?
-
-
restricts unmodified phage DNA after both infection and transfection
-
-
?
additional information
?
-
-
basal transcription from promoter esp1396ICR results in gradual accumulation of C.Esp1396I, which upon dimerization binds to a single site in promoter esp1396IM, preventing further transcription from this promoter. Further accumulation of C.Esp1396I results in activation and then gradual repression of promoter esp1396ICR
-
-
?
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Janscak, P.; Abadjieva, A.; Firman, K.
The type I restriction endonuclease R.EcoR124I: Over-production and biochemical properties
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Escherichia coli
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Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes
EMBO J.
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Escherichia coli
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A deletion mutant of the type IC restriction endonuclease EcoR124I expressing a novel DNA specificity
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Escherichia coli
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Substrate recognition and selectivity in the type IC DNA modification methylase M.EcoR124I
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Escherichia coli
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On the structure and operation of type I DNA restriction enzymes
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290
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Escherichia coli
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Zinkevich, V.; Heslop, P.; Glover, S.W.; Weiserova, M.; Hubacek, J.; Firman, K.
Mutation in the specificity polypeptide of the type I restriction endonuclease R*EcoK that affects subunit assembly
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227
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Escherichia coli
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Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition
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12
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Escherichia coli
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Analysis of the subunit assembly of the typeIC restriction-modification enzyme EcoR124I
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26
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Escherichia coli
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Type I restriction enzymes
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14
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Escherichia coli, Salmonella enterica subsp. enterica serovar Typhimurium
-
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133
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Citrobacter freundii, Escherichia coli, Staphylococcus aureus, Staphylococcus aureus RN450
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Restriction enzymes and their isoschizomers
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18
2331-2365
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Citrobacter freundii, Escherichia coli, Salmonella enterica subsp. enterica serovar Typhi
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Restriction and modification enzymes and their recognition sequences
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11
r135-r167
1983
Escherichia coli
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Cloning, production and characterisation of wild type and mutant forms of the R*EcoK endonucleases
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21
373-379
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Escherichia coli
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Roberts, R.J.; Macelis, D.
REBASE - restriction enzymes and methylases
Nucleic Acids Res.
29
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Escherichia coli
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Holubova, I.; Vejsadova, S.; Firman, K.; Weiserova, M.
Cellular localization of Type I restriction-modification enzymes is family dependent
Biochem. Biophys. Res. Commun.
319
375-380
2004
Escherichia coli
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Szczelkun, M.D.
Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases
Biochemistry
41
2067-2074
2002
Escherichia coli
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Matsuno, H.; Furusawa, H.; Okahata, Y.
Direct monitoring of DNA cleavages catalyzed by an ATP-dependent deoxyribonuclease on a 27 MHz quartz-crystal microbalance
Chem. Commun. (Camb.)
2002
470-471
2002
Micrococcus luteus
-
brenda
Thomas, A.T.; Brammar, W.J.; Wilkins, B.M.
Plasmid R16 ArdA protein preferentially targets restriction activity of the type I restriction-modification system EcoKI
J. Bacteriol.
185
2022-2025
2003
Escherichia coli
brenda
McClelland, S.E.; Dryden, D.T.F.; Szczelkun, M.D.
Continous asay for DNA translocation using fluorescent triplex dissociation: application to type I restriction endonucleases
J. MOl. Biol.
348
895-915
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Escherichia coli
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Bianco, P.R.; Hurley, E.M.
The type I restriction endonuclease EcoR124I, couples ATP hydrolysis to bidirectional DNA translocation
J. Mol. Biol.
352
837-859
2005
Escherichia coli
brenda
Seidel, R.; van Noort, J.; van der Scheer, C.; Bloom, J.G.; Dekker, N.H.; Dutta, C.F.; Blundell, A.; Robinson, T.; Firman, K.; Dekker, C.
Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I
Nat. Struct. Mol. Biol.
11
838-843
2004
Escherichia coli
brenda
van Noort, J.; van der Heijden, T.; Dutta, C.F.; Firman, K.; Dekker, C.
Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion
Nucleic Acids Res.
32
6540-6547
2004
Escherichia coli
brenda
Chin, V.; Valinluck, V.; Magaki, S.; Ryu, J.
KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system
Nucleic Acids Res.
32
e138
2004
Klebsiella pneumoniae (Q6WN39), Klebsiella pneumoniae, Klebsiella pneumoniae GM236 (Q6WN39)
brenda
Jindrova, E.; Schmid-Nuoffer, S.; Hamburger, F.; Janscak, P.; Bickle, T.A.
On the DNA cleavage mechanism of type I restriction enzymes
Nucleic Acids Res.
33
1760-1766
2005
Escherichia coli
brenda
Kasarjian, J.K.; Kodama, Y.; Iida, M.; Matsuda, K.; Ryu, J.
Four new type I restriction enzymes identified in Escherichia coli clinical isolates
Nucleic Acids Res.
33
e114
2005
Escherichia coli
brenda
Lapkouski, M.; Panjikar, S.; Kuta Smatanova, I.; Csefalvay, E.
Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from Escherichia coli
Acta Crystallogr. Sect. F
63
582-585
2007
Escherichia coli
brenda
Cajthamlova, K.; Sisakova, E.; Weiser, J.; Weiserova, M.
Phosphorylation of Type IA restriction-modification complex enzyme EcoKI on the HsdR subunit
FEMS Microbiol. Lett.
270
171-177
2007
Escherichia coli
brenda
Waleron, K.; Waleron, M.; Osipiuk, J.; Podhajska, A.J.; Lojkowska, E.
Identification of a DNA restriction-modification system in Pectobacterium carotovorum strains isolated from Poland
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100
343-351
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Pectobacterium carotovorum
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Waldron, D.E.; Lindsay, J.A.
Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S. aureus isolates of different lineages
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Staphylococcus aureus
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HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling
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376
438-452
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Escherichia coli (Q304R3)
brenda
Neely, R.K.; Roberts, R.J.
The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs
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9
48
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Geobacillus stearothermophilus (B0LX59), Geobacillus stearothermophilus CPW11 (B0LX59)
brenda
Ohno, S.; Handa, N.; Watanabe-Matsui, M.; Takahashi, N.; Kobayashi, I.
Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity
J. Bacteriol.
190
2039-2049
2008
Escherichia coli
brenda
Carpenter, M.A.; Bhagwat, A.S.
DNA base flipping by both members of the PspGI restriction-modification system
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36
5417-5425
2008
Pyrococcus sp.
brenda
Humbert, O.; Salama, N.R.
The Helicobacter pylori HpyAXII restriction-modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components
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36
6893-6906
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Helicobacter pylori
brenda
Mruk, I.; Blumenthal, R.M.
Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system
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37
983-998
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Escherichia coli K-12
brenda
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Crystallization and preliminary X-ray diffraction analysis of the HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
Acta Crystallogr. Sect. F
64
926-928
2008
Vibrio vulnificus YJ016
brenda
Veiga, H.; Pinho, M.G.
Inactivation of the Sau1 Type I restriction-modification system is not sufficient to generate Staphylococcus aureus strains capable of efficiently accepting foreign DNA
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75
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Staphylococcus aureus
brenda
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Characterization of a restriction modification system from the commensal Escherichia coli strain A0 34/86 (O83:K24:H31)
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8
106
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EcoR124I: from plasmid-encoded restriction-modification system to nanodevice
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72
365-77
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Escherichia coli
brenda
Ryu, J.; Rowsell, E.
Quick identification of type I restriction enzyme isoschizomers using newly developed ptypeI and reference plasmids
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36
e81
2008
Escherichia coli, Salmonella-Escherichia coli hybrid
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Atomic force microscopy of the EcoKI type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping
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37
2053-2063
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Escherichia coli
brenda
Bogdanova, E.; Zakharova, M.; Streeter, S.; Taylor, J.; Heyduk, T.; Kneale, G.; Severinov, K.
Transcription regulation of restriction-modification system Esp1396I
Nucleic Acids Res.
37
:3354-3366
2009
synthetic construct
brenda
Lee, H.J.; Nishi, K.; Song, J.M.; Kim, J.S.
Expression, crystallization and preliminary X-ray diffraction analysis of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
Acta Crystallogr. Sect. F
65
1271-1273
2009
Vibrio vulnificus YJ016
brenda
Lapkouski, M.; Panjikar, S.; Janscak, P.; Smatanova, I.K.; Carey, J.; Ettrich, R.; Csefalvay, E.
Structure of the motor subunit of type I restriction-modification complex EcoR124I
Nat. Struct. Mol. Biol.
16
94-95
2009
Escherichia coli (Q304R3)
brenda
Uyen, N.T.; Park, S.Y.; Choi, J.W.; Lee, H.J.; Nishi, K.; Kim, J.S.
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity
Nucleic Acids Res.
37
6960-6969
2009
Vibrio vulnificus YJ016 (Q7MPU7), Vibrio vulnificus YJ016
brenda
Park, S.Y.; Lee, H.J.; Song, J.M.; Sun, J.; Hwang, H.J.; Nishi, K.; Kim, J.S.
Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
Acta Crystallogr. Sect. D
68
1570-1577
2012
Vibrio vulnificus (Q7MPU6)
brenda
Sinha, D.; Shamayeva, K.; Ramasubramani, V.; Reha, D.; Bialevich, V.; Khabiri, M.; Guzanova, A.; Milbar, N.; Weiserova, M.; Csefalvay, E.; Carey, J.; Ettrich, R.
Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I
J. Mol. Model.
20
2334
2014
Escherichia coli (P10486)
brenda
Roberts, G.A.; Houston, P.J.; White, J.H.; Chen, K.; Stephanou, A.S.; Cooper, L.P.; Dryden, D.T.; Lindsay, J.A.
Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations
Nucleic Acids Res.
41
7472-7484
2013
Staphylococcus aureus
brenda
Loenen, W.A.; Dryden, D.T.; Raleigh, E.A.; Wilson, G.G.
Type I restriction enzymes and their relatives
Nucleic Acids Res.
42
20-44
2014
Escherichia coli
brenda
Taylor, J.E.; Swiderska, A.; Artero, J.B.; Callow, P.; Kneale, G.
Structural and functional analysis of the symmetrical Type I restriction endonuclease R.EcoR124I(NT)
PLoS ONE
7
e35263
2012
Escherichia coli
brenda
Grinkevich, P.; Iermak, I.; Luedtke, N.A.; Mesters, J.R.; Ettrich, R.; Ludwig, J.
pHluorin-assisted expression, purification, crystallization and X-ray diffraction data analysis of the C-terminal domain of the HsdR subunit of the Escherichia coli type I restriction-modification system EcoR124I
Acta Crystallogr. Sect. F
72
672-676
2016
Escherichia coli (Q304R3), Escherichia coli
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Huo, W.; Adams, H.M.; Trejo, C.; Badia, R.; Palmer, K.L.
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