PDBsum entry 4rve

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
Jmol PyMol
Protein chains
240 a.a.
Waters ×23
PDB id:
Name: Hydrolase/DNA
Title: The crystal structure of ecorv endonuclease and of its complexes with cognate and non-cognate DNA segments
Structure: DNA (5'-d( Gp Gp Gp Ap Tp Ap Tp Cp Cp C)-3'). Chain: d, e, f. Engineered: yes. Protein (eco rv . Chain: a, b, c. Engineered: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
3.00Å     R-factor:   0.176    
Authors: F.K.Winkler,D.W.Banner,C.Oefner,D.Tsernoglou,R.S.Brown, S.P.Heathman,R.K.Bryan,P.D.Martin,K.Petratos,K.S.Wilso
Key ref: F.K.Winkler et al. (1993). The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J, 12, 1781-1795. PubMed id: 8491171
18-Feb-93     Release date:   15-Apr-93    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04390  (T2E5_ECOLX) -  Type-2 restriction enzyme EcoRV
245 a.a.
240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   2 terms 
  Biochemical function     hydrolase activity     5 terms  


EMBO J 12:1781-1795 (1993)
PubMed id: 8491171  
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments.
F.K.Winkler, D.W.Banner, C.Oefner, D.Tsernoglou, R.S.Brown, S.P.Heathman, R.K.Bryan, P.D.Martin, K.Petratos, K.S.Wilson.
The crystal structure of EcoRV endonuclease has been determined at 2.5 A resolution and that of its complexes with the cognate DNA decamer GGGATATCCC (recognition sequence underlined) and the non-cognate DNA octamer CGAGCTCG at 3.0 A resolution. Two octamer duplexes of the non-cognate DNA, stacked end-to-end, are bound to the dimeric enzyme in B-DNA-like conformations. The protein--DNA interactions of this complex are prototypic for non-specific DNA binding. In contrast, only one cognate decamer duplex is bound and deviates considerably from canonical B-form DNA. Most notably, a kink of approximately 50 degrees is observed at the central TA step with a concomitant compression of the major groove. Base-specific hydrogen bonds between the enzyme and the recognition base pairs occur exclusively in the major groove. These interactions appear highly co-operative as they are all made through one short surface loop comprising residues 182-186. Numerous contacts with the sugar phosphate backbone extending beyond the recognition sequence are observed in both types of complex. However, the total surface area buried on complex formation is > 1800 A2 larger in the case of cognate DNA binding. Two acidic side chains, Asp74 and Asp90, are close to the reactive phosphodiester group in the cognate complex and most probably provide oxygen ligands for binding the essential cofactor Mg2+. An important role is also indicated for Lys92, which together with the two acidic functions appears to be conserved in the otherwise unrelated structure of EcoRI endonuclease. The structural results give new insight into the physical basis of the remarkable sequence specificity of this enzyme.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB code: 3odh
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
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PDB code: 3ndh
21522129 T.J.Petty, S.Emamzadah, L.Costantino, I.Petkova, E.S.Stavridi, J.G.Saven, E.Vauthey, and T.D.Halazonetis (2011).
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PDB codes: 3q01 3q05 3q06
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Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
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PDB codes: 3fc3 3gox
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Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes.
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18252770 A.Matsugami, T.Ohyama, M.Inada, N.Inoue, N.Minakawa, A.Matsuda, and M.Katahira (2008).
Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.
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PDB code: 2rmq
18477633 D.Svozil, J.Kalina, M.Omelka, and B.Schneider (2008).
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PDB code: 3ebc
18544605 I.Bonnet, A.Biebricher, P.L.Porté, C.Loverdo, O.Bénichou, R.Voituriez, C.Escudé, W.Wende, A.Pingoud, and P.Desbiolles (2008).
Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.
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18456708 J.Orlowski, and J.M.Bujnicki (2008).
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
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17729285 N.Shaw, W.Tempel, J.Chang, H.Yang, C.Cheng, J.Ng, J.Rose, Z.Rao, B.C.Wang, and Z.J.Liu (2008).
Crystal structure solution of a ParB-like nuclease at atomic resolution.
  Proteins, 70, 263-267.
PDB code: 1vk1
18669665 R.H.Porecha, and J.T.Stivers (2008).
Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils.
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18502761 S.R.Coffin, and N.O.Reich (2008).
Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences.
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17089162 A.Myari, N.Hadjiliadis, A.Garoufis, J.Malina, and V.Brabec (2007).
NMR analysis of duplex d(CGCGATCGCG)2 modified by Lambda- and Delta-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study.
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17437711 A.Pingoud, and W.Wende (2007).
A sliding restriction enzyme pauses.
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17307879 B.M.Reinhard, S.Sheikholeslami, A.Mastroianni, A.P.Alivisatos, and J.Liphardt (2007).
Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes.
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Protein interfacial pocket engineering via coupled computational filtering and biological focusing criterion.
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17437717 S.A.Townson, J.C.Samuelson, Y.Bao, S.Y.Xu, and A.K.Aggarwal (2007).
BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning.
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PDB code: 2p0j
17870087 S.R.Bellamy, S.E.Milsom, Y.S.Kovacheva, R.B.Sessions, and S.E.Halford (2007).
A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease.
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17977824 T.P.Jurkowski, N.Anspach, L.Kulishova, W.Nellen, and A.Jeltsch (2007).
The M.EcoRV DNA-(Adenine N6)-methyltransferase Uses DNA Bending for Recognition of an Expanded EcoDam Recognition Site.
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17175542 Y.T.Wang, W.J.Yang, C.L.Li, L.G.Doudeva, and H.S.Yuan (2007).
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.
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PDB codes: 2ivh 2ivk
16497933 A.Banerjee, W.L.Santos, and G.L.Verdine (2006).
Structure of a DNA glycosylase searching for lesions.
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PDB codes: 2f5n 2f5o 2f5p 2f5q 2f5s
16981705 D.A.Hiller, and J.J.Perona (2006).
Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.
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PDB code: 2ge5
16723432 G.J.Gemmen, R.Millin, and D.E.Smith (2006).
DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.
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16868081 G.J.Gemmen, R.Millin, and D.E.Smith (2006).
Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force.
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16963513 G.J.Gemmen, R.Millin, and D.E.Smith (2006).
Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA.
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16962970 G.Tamulaitiene, A.Jakubauskas, C.Urbanke, R.Huber, S.Grazulis, and V.Siksnys (2006).
The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.
  Structure, 14, 1389-1400.
PDB code: 2ixs
17008406 J.Iwahara, M.Zweckstetter, and G.M.Clore (2006).
NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA.
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16895336 J.T.Stivers, and R.Nagarajan (2006).
Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens.
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16498623 K.J.Skowronek, J.Kosinski, and J.M.Bujnicki (2006).
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16893959 M.Carpenter, P.Divvela, V.Pingoud, J.Bujnicki, and A.S.Bhagwat (2006).
Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.
  Nucleic Acids Res, 34, 3762-3770.  
16481311 S.L.Williams, L.K.Parkhurst, and L.J.Parkhurst (2006).
Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer.
  Nucleic Acids Res, 34, 1028-1035.  
17124171 S.V.Kuznetsov, S.Sugimura, P.Vivas, D.M.Crothers, and A.Ansari (2006).
Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF.
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15667656 A.A.Chmiel, J.M.Bujnicki, and K.J.Skowronek (2005).
A homology model of restriction endonuclease SfiI in complex with DNA.
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15869395 A.Sarai, and H.Kono (2005).
Protein-DNA recognition patterns and predictions.
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15886396 B.van den Broek, M.C.Noom, and G.J.Wuite (2005).
DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway.
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16308566 E.S.Vanamee, H.Viadiu, R.Kucera, L.Dorner, S.Picone, I.Schildkraut, and A.K.Aggarwal (2005).
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
  EMBO J, 24, 4198-4208.
PDB codes: 2ezv 2f03
16209953 J.Y.Lee, J.Chang, N.Joseph, R.Ghirlando, D.N.Rao, and W.Yang (2005).
MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
  Mol Cell, 20, 155-166.
PDB codes: 2aoq 2aor
15894630 M.Fuxreiter, M.Mezei, I.Simon, and R.Osman (2005).
Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.
  Biophys J, 89, 903-911.  
16195548 Q.S.Xu, R.J.Roberts, and H.C.Guo (2005).
Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
  Protein Sci, 14, 2590-2600.
PDB code: 1yfi
15893669 S.A.Townson, J.C.Samuelson, S.Y.Xu, and A.K.Aggarwal (2005).
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
  Structure, 13, 791-801.
PDB code: 1vrr
15888729 S.Nikolajewa, A.Beyer, M.Friedel, J.Hollunder, and T.Wilhelm (2005).
Common patterns in type II restriction enzyme binding sites.
  Nucleic Acids Res, 33, 2726-2733.  
15805123 Z.Yang, J.R.Horton, R.Maunus, G.G.Wilson, R.J.Roberts, and X.Cheng (2005).
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
  Nucleic Acids Res, 33, 1892-1901.
PDB code: 1ynm
15210696 B.B.Hopkins, and N.O.Reich (2004).
Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex.
  J Biol Chem, 279, 37049-37060.  
15256668 C.G.Kalodimos, N.Biris, A.M.Bonvin, M.M.Levandoski, M.Guennuegues, R.Boelens, and R.Kaptein (2004).
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.
  Science, 305, 386-389.
PDB code: 1osl
15465864 M.Slutsky, and L.A.Mirny (2004).
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
  Biophys J, 87, 4021-4035.  
15178741 S.E.Halford, and J.F.Marko (2004).
How do site-specific DNA-binding proteins find their targets?
  Nucleic Acids Res, 32, 3040-3052.  
14661948 D.A.Hiller, J.M.Fogg, A.M.Martin, J.M.Beechem, N.O.Reich, and J.J.Perona (2003).
Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence.
  Biochemistry, 42, 14375-14385.  
12628933 D.M.Gowers, and S.E.Halford (2003).
Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling.
  EMBO J, 22, 1410-1418.  
14661976 I.Goldhaber-Gordon, M.H.Early, and T.A.Baker (2003).
MuA transposase separates DNA sequence recognition from catalysis.
  Biochemistry, 42, 14633-14642.  
12784213 J.Aishima, and C.Wolberger (2003).
Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA.
  Proteins, 51, 544-551.  
12719261 J.Sun, H.Viadiu, A.K.Aggarwal, and H.Weinstein (2003).
Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex.
  Biophys J, 84, 3317-3325.  
14580211 L.M.Bowen, and C.M.Dupureur (2003).
Investigation of restriction enzyme cofactor requirements: a relationship between metal ion properties and sequence specificity.
  Biochemistry, 42, 12643-12653.  
12853636 N.Guhan, and K.Muniyappa (2003).
Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn(2+) and DNA-dependent ATPase activity.
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14523014 Q.Cui, Y.Tong, H.Xue, L.Huang, Y.Feng, and J.Wang (2003).
Two conformations of archaeal Ssh10b. The origin of its temperature-dependent interaction with DNA.
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12551981 V.S.Mikhailov, K.Okano, and G.F.Rohrmann (2003).
Baculovirus alkaline nuclease possesses a 5'-->3' exonuclease activity and associates with the DNA-binding protein LEF-3.
  J Virol, 77, 2436-2444.  
11729187 A.J.Bath, S.E.Milsom, N.A.Gormley, and S.E.Halford (2002).
Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA.
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11884629 C.Korn, S.R.Scholz, O.Gimadutdinow, A.Pingoud, and G.Meiss (2002).
Involvement of conserved histidine, lysine and tyrosine residues in the mechanism of DNA cleavage by the caspase-3 activated DNase CAD.
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12219083 C.M.Moure, F.S.Gimble, and F.A.Quiocho (2002).
Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence.
  Nat Struct Biol, 9, 764-770.
PDB codes: 1lws 1lwt
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
11875059 M.Kvaratskhelia, S.R.Budihas, and S.F.Le Grice (2002).
Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase.
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11742344 N.C.Horton, L.F.Dorner, and J.J.Perona (2002).
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
  Nat Struct Biol, 9, 42-47.
PDB code: 1kc6
11842098 S.Grazulis, M.Deibert, R.Rimseliene, R.Skirgaila, G.Sasnauskas, A.Lagunavicius, V.Repin, C.Urbanke, R.Huber, and V.Siksnys (2002).
Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
  Nucleic Acids Res, 30, 876-885.
PDB code: 1knv
11827971 V.Pingoud, E.Kubareva, G.Stengel, P.Friedhoff, J.M.Bujnicki, C.Urbanke, A.Sudina, and A.Pingoud (2002).
Evolutionary relationship between different subgroups of restriction endonucleases.
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11159430 A.H.Elcock, and J.A.McCammon (2001).
Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient.
  Biophys J, 80, 613-625.  
11180561 A.P.Demchenko (2001).
Recognition between flexible protein molecules: induced and assisted folding.
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11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11557808 B.S.Chevalier, and B.L.Stoddard (2001).
Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.
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11179886 C.M.Lukacs, and A.K.Aggarwal (2001).
BglII and MunI: what a difference a base makes.
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11170385 H.Watrob, W.Liu, Y.Chen, S.G.Bartlett, L.Jen-Jacobson, and M.D.Barkley (2001).
Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg2+ cofactor.
  Biochemistry, 40, 683-692.  
11250198 M.J.van der Woerd, J.J.Pelletier, S.Xu, and A.M.Friedman (2001).
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
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PDB code: 1dc1
11599025 O.Littlefield, and H.C.Nelson (2001).
Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex.
  Proteins, 45, 219-228.
PDB codes: 1fyk 1fyl 1fym
11726692 P.Manivasakam, J.Aubrecht, S.Sidhom, and R.H.Schiestl (2001).
Restriction enzymes increase efficiencies of illegitimate DNA integration but decrease homologous integration in mammalian cells.
  Nucleic Acids Res, 29, 4826-4833.  
11266549 S.A.Williams, and S.E.Halford (2001).
SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.
  Nucleic Acids Res, 29, 1476-1483.  
11557809 S.E.Tsutakawa, and K.Morikawa (2001).
The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.
  Nucleic Acids Res, 29, 3775-3783.  
11327870 S.L.Reid, D.Parry, H.H.Liu, and B.A.Connolly (2001).
Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization.
  Biochemistry, 40, 2484-2494.  
11113185 T.Anzai, H.Takahashi, and H.Fujiwara (2001).
Sequence-specific recognition and cleavage of telomeric repeat (TTAGG)(n) by endonuclease of non-long terminal repeat retrotransposon TRAS1.
  Mol Cell Biol, 21, 100-108.  
10911996 A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, and F.Dyda (2000).
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
  Mol Cell, 5, 1025-1034.
PDB code: 1f1z
10625479 D.Dertinger, L.S.Behlen, and O.C.Uhlenbeck (2000).
Using phosphorothioate-substituted RNA to investigate the thermodynamic role of phosphates in a sequence specific RNA-protein complex.
  Biochemistry, 39, 55-63.  
10679372 D.J.Segal, and C.F.Barbas (2000).
Design of novel sequence-specific DNA-binding proteins.
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10944205 D.M.Lilley, and M.F.White (2000).
Resolving the relationships of resolving enzymes.
  Proc Natl Acad Sci U S A, 97, 9351-9353.  
10666447 E.A.Kubareva, H.Thole, A.S.Karyagina, T.S.Oretskaya, A.Pingoud, and V.Pingoud (2000).
Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.
  Nucleic Acids Res, 28, 1085-1091.  
  10628980 H.S.Malik, and T.H.Eickbush (2000).
NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans.
  Genetics, 154, 193-203.  
10882125 H.Viadiu, and A.K.Aggarwal (2000).
Structure of BamHI bound to nonspecific DNA: a model for DNA sliding.
  Mol Cell, 5, 889-895.
PDB code: 1esg
10715131 J.J.Hlavaty, J.S.Benner, L.J.Hornstra, and I.Schildkraut (2000).
Identification of the metal-binding sites of restriction endonucleases by Fe2+-mediated oxidative cleavage.
  Biochemistry, 39, 3097-3105.  
  11206057 J.W.Cave, W.Kremer, and D.E.Wemmer (2000).
Backbone dynamics of sequence specific recognition and binding by the yeast Pho4 bHLH domain probed by NMR.
  Protein Sci, 9, 2354-2365.  
10982859 L.Aravind, K.S.Makarova, and E.V.Koonin (2000).
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
  Nucleic Acids Res, 28, 3417-3432.  
10931930 M.R.Rice, and R.M.Blumenthal (2000).
Recognition of native DNA methylation by the PvuII restriction endonuclease.
  Nucleic Acids Res, 28, 3143-3150.  
10702254 N.A.Gormley, A.J.Bath, and S.E.Halford (2000).
Reactions of BglI and other type II restriction endonucleases with discontinuous recognition sites.
  J Biol Chem, 275, 6928-6936.  
10801972 N.C.Horton, and J.J.Perona (2000).
Crystallographic snapshots along a protein-induced DNA-bending pathway.
  Proc Natl Acad Sci U S A, 97, 5729-5734.
PDB codes: 1eoo 1eop
11101527 N.P.Stanford, M.D.Szczelkun, J.F.Marko, and S.E.Halford (2000).
One- and three-dimensional pathways for proteins to reach specific DNA sites.
  EMBO J, 19, 6546-6557.  
10648519 P.C.Hsieh, J.P.Xiao, D.O'loane, and S.Y.Xu (2000).
Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.
  J Bacteriol, 182, 949-955.  
10856254 Q.Huai, J.D.Colandene, Y.Chen, F.Luo, Y.Zhao, M.D.Topal, and H.Ke (2000).
Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
  EMBO J, 19, 3110-3118.
PDB code: 1ev7
12760025 S.D.Bruner, D.P.Norman, J.C.Fromme, and G.L.Verdine (2000).
Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells.
  Cold Spring Harb Symp Quant Biol, 65, 103-111.  
11092936 T.J.O'Loughlin, Q.Xu, R.B.Kucera, L.F.Dorner, S.Sweeney, I.Schildkraut, and H.C.Guo (2000).
Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.
  Acta Crystallogr D Biol Crystallogr, 56, 1652-1655.  
10387089 A.M.Martin, N.C.Horton, S.Lusetti, N.O.Reich, and J.J.Perona (1999).
Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.
  Biochemistry, 38, 8430-8439.  
10103058 C.M.Dupureur, and L.M.Hallman (1999).
Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases.
  Eur J Biochem, 261, 261-268.  
10542216 D.J.Wright, W.E.Jack, and P.Modrich (1999).
The kinetic mechanism of EcoRI endonuclease.
  J Biol Chem, 274, 31896-31902.  
10228169 F.H.Allain, Y.M.Yen, J.E.Masse, P.Schultze, T.Dieckmann, R.C.Johnson, and J.Feigon (1999).
Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding.
  EMBO J, 18, 2563-2579.
PDB code: 1cg7
10500196 J.J.Boniface, Z.Reich, D.S.Lyons, and M.M.Davis (1999).
Thermodynamics of T cell receptor binding to peptide-MHC: evidence for a general mechanism of molecular scanning.
  Proc Natl Acad Sci U S A, 96, 11446-11451.  
10585945 J.R.Wenner, and V.A.Bloomfield (1999).
Crowding effects on EcoRV kinetics and binding.
  Biophys J, 77, 3234-3241.  
9893991 J.T.Stivers, K.W.Pankiewicz, and K.A.Watanabe (1999).
Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase.
  Biochemistry, 38, 952-963.  
10393910 J.Yang, H.S.Malik, and T.H.Eickbush (1999).
Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements.
  Proc Natl Acad Sci U S A, 96, 7847-7852.  
10350476 M.D.Sam, and J.J.Perona (1999).
Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease.
  Biochemistry, 38, 6576-6586.  
10531503 N.C.Horton, L.F.Dorner, I.Schildkraut, and J.J.Perona (1999).
Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.
  Acta Crystallogr D Biol Crystallogr, 55, 1943-1945.  
10508668 R.A.Kovall, and B.W.Matthews (1999).
Type II restriction endonucleases: structural, functional and evolutionary relationships.
  Curr Opin Chem Biol, 3, 578-583.  
10360178 S.E.Tsutakawa, T.Muto, T.Kawate, H.Jingami, N.Kunishima, M.Ariyoshi, D.Kohda, M.Nakagawa, and K.Morikawa (1999).
Crystallographic and functional studies of very short patch repair endonuclease.
  Mol Cell, 3, 621-628.
PDB code: 1vsr
10586498 T.Dahai, S.Ando, Y.Takasaki, and J.Tadano (1999).
Site-directed mutagenesis of restriction endonuclease HindIII.
  Biosci Biotechnol Biochem, 63, 1703-1707.  
9485362 A.Jeltsch, and A.Pingoud (1998).
Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA.
  Biochemistry, 37, 2160-2169.  
9461471 B.Holz, S.Klimasauskas, S.Serva, and E.Weinhold (1998).
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
  Nucleic Acids Res, 26, 1076-1083.  
9482749 C.Ban, and W.Yang (1998).
Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases.
  EMBO J, 17, 1526-1534.
PDB codes: 1azo 2azo
9558357 C.Jin, I.Marsden, X.Chen, and X.Liao (1998).
Sequence specific collective motions in a winged helix DNA binding domain detected by 15N relaxation NMR.
  Biochemistry, 37, 6179-6187.  
9822618 C.Schulze, A.Jeltsch, I.Franke, C.Urbanke, and A.Pingoud (1998).
Crosslinking the EcoRV restriction endonuclease across the DNA-binding site reveals transient intermediates and conformational changes of the enzyme during DNA binding and catalytic turnover.
  EMBO J, 17, 6757-6766.  
9485369 C.Wenz, M.Hahn, and A.Pingoud (1998).
Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site.
  Biochemistry, 37, 2234-2242.  
9724743 D.A.Wah, J.Bitinaite, I.Schildkraut, and A.K.Aggarwal (1998).
Structure of FokI has implications for DNA cleavage.
  Proc Natl Acad Sci U S A, 95, 10564-10569.
PDB code: 2fok
9548954 F.Stahl, W.Wende, C.Wenz, A.Jeltsch, and A.Pingoud (1998).
Intra- vs intersubunit communication in the homodimeric restriction enzyme EcoRV: Thr 37 and Lys 38 involved in indirect readout are only important for the catalytic activity of their own subunit.
  Biochemistry, 37, 5682-5688.  
9783752 H.Viadiu, and A.K.Aggarwal (1998).
The role of metals in catalysis by the restriction endonuclease BamHI.
  Nat Struct Biol, 5, 910-916.
PDB codes: 2bam 3bam
9601033 M.J.Schofield, D.M.Lilley, and M.F.White (1998).
Dissection of the sequence specificity of the Holliday junction endonuclease CCE1.
  Biochemistry, 37, 7733-7740.  
9736624 M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, and S.E.Phillips (1998).
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
  EMBO J, 17, 5466-5476.
PDB code: 1dmu
9705308 N.C.Horton, and J.J.Perona (1998).
Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
  J Biol Chem, 273, 21721-21729.
PDB code: 1bgb
9811827 N.C.Horton, K.J.Newberry, and J.J.Perona (1998).
Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.
  Proc Natl Acad Sci U S A, 95, 13489-13494.
PDB code: 1bss
  9684880 R.A.Albright, M.C.Mossing, and B.W.Matthews (1998).
Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein.
  Protein Sci, 7, 1485-1494.
PDB code: 3orc
9653111 R.A.Kovall, and B.W.Matthews (1998).
Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.
  Proc Natl Acad Sci U S A, 95, 7893-7897.  
9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
  Nucleic Acids Res, 26, 1906-1926.  
9759487 R.J.Roberts, and X.Cheng (1998).
Base flipping.
  Annu Rev Biochem, 67, 181-198.  
9830053 W.Cao, and F.Barany (1998).
Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage.
  J Biol Chem, 273, 33002-33010.  
9287152 A.Lagunavicius, S.Grazulis, E.Balciunaite, D.Vainius, and V.Siksnys (1997).
DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues.
  Biochemistry, 36, 11093-11099.  
9287151 A.Lagunavicius, and V.Siksnys (1997).
Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity.
  Biochemistry, 36, 11086-11092.  
9210460 A.Pingoud, and A.Jeltsch (1997).
Recognition and cleavage of DNA by type-II restriction endonucleases.
  Eur J Biochem, 246, 1.  
9298958 D.H.Groll, A.Jeltsch, U.Selent, and A.Pingoud (1997).
Does the restriction endonuclease EcoRV employ a two-metal-Ion mechanism for DNA cleavage?
  Biochemistry, 36, 11389-11401.  
9358163 D.Meierhans, M.Sieber, and R.K.Allemann (1997).
High affinity binding of MEF-2C correlates with DNA bending.
  Nucleic Acids Res, 25, 4537-4544.  
9200709 E.L.Hancox, and S.E.Halford (1997).
Kinetic analysis of a mutational hot spot in the EcoRV restriction endonuclease.
  Biochemistry, 36, 7577-7585.  
9325303 H.G.Nastri, P.D.Evans, I.H.Walker, and P.D.Riggs (1997).
Catalytic and DNA binding properties of PvuII restriction endonuclease mutants.
  J Biol Chem, 272, 25761-25767.  
9278491 H.Kong, and C.L.Smith (1997).
Substrate DNA and cofactor regulate the activities of a multi-functional restriction-modification enzyme, BcgI.
  Nucleic Acids Res, 25, 3687-3692.  
9354759 L.Jen-Jacobson (1997).
Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
  Biopolymers, 44, 153-180.  
9254693 M.Belfort, and R.J.Roberts (1997).
Homing endonucleases: keeping the house in order.
  Nucleic Acids Res, 25, 3379-3388.  
9218422 M.Oda, K.Furukawa, K.Ogata, A.Sarai, S.Ishii, Y.Nishimura, and H.Nakamura (1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
  J Biol Chem, 272, 17966-17971.  
9108149 P.H.Thorpe, D.Ternent, and N.E.Murray (1997).
The specificity of sty SKI, a type I restriction enzyme, implies a structure with rotational symmetry.
  Nucleic Acids Res, 25, 1694-1700.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9295273 R.Kovall, and B.W.Matthews (1997).
Toroidal structure of lambda-exonuclease.
  Science, 277, 1824-1827.
PDB code: 1avq
9135161 R.Shah, R.Cosstick, and S.C.West (1997).
The RuvC protein dimer resolves Holliday junctions by a dual incision mechanism that involves base-specific contacts.
  EMBO J, 16, 1464-1472.  
9200708 S.G.Erskine, G.S.Baldwin, and S.E.Halford (1997).
Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.
  Biochemistry, 36, 7567-7576.  
9063456 S.Windolph, and J.Alves (1997).
Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.
  Eur J Biochem, 244, 134-139.  
8919860 A.Jeltsch, and A.Pingoud (1996).
Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.
  J Mol Evol, 42, 91-96.  
  8890184 A.Jeltsch, C.Wenz, F.Stahl, and A.Pingoud (1996).
Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme.
  EMBO J, 15, 5104-5111.  
8621416 C.Wenz, A.Jeltsch, and A.Pingoud (1996).
Probing the indirect readout of the restriction enzyme EcoRV. Mutational analysis of contacts to the DNA backbone.
  J Biol Chem, 271, 5565-5573.  
8643494 D.B.Nikolov, H.Chen, E.D.Halay, A.Hoffman, R.G.Roeder, and S.K.Burley (1996).
Crystal structure of a human TATA box-binding protein/TATA element complex.
  Proc Natl Acad Sci U S A, 93, 4862-4867.
PDB code: 1cdw
8987994 D.Hüsken, G.Goodall, M.J.Blommers, W.Jahnke, J.Hall, R.Häner, and H.E.Moser (1996).
Creating RNA bulges: cleavage of RNA in RNA/DNA duplexes by metal ion catalysis.
  Biochemistry, 35, 16591-16600.  
8650239 F.Stahl, W.Wende, A.Jeltsch, and A.Pingoud (1996).
Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein.
  Proc Natl Acad Sci U S A, 93, 6175-6180.  
  8635475 H.Li, and A.W.Nicholson (1996).
Defining the enzyme binding domain of a ribonuclease III processing signal. Ethylation interference and hydroxyl radical footprinting using catalytically inactive RNase III mutants.
  EMBO J, 15, 1421-1433.  
8917312 H.Ruan, K.D.Lunnen, M.E.Scott, L.S.Moran, B.E.Slatko, J.J.Pelletier, E.J.Hess, J.Benner, G.G.Wilson, and S.Y.Xu (1996).
Cloning and sequence comparison of AvaI and BsoBI restriction-modification systems.
  Mol Gen Genet, 252, 695-699.  
8621526 H.Thorogood, J.A.Grasby, and B.A.Connolly (1996).
Influence of the phosphate backbone on the recognition and hydrolysis of DNA by the EcoRV restriction endonuclease. A study using oligodeoxynucleotide phosphorothioates.
  J Biol Chem, 271, 8855-8862.  
8639650 I.B.Vipond, B.J.Moon, and S.E.Halford (1996).
An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese.
  Biochemistry, 35, 1712-1721.  
8639649 I.B.Vipond, and S.E.Halford (1996).
Random mutagenesis targeted to the active site of the EcoRV restriction endonuclease.
  Biochemistry, 35, 1701-1711.  
  8665862 M.S.Junop, and D.B.Haniford (1996).
Multiple roles for divalent metal ions in DNA transposition: distinct stages of Tn10 transposition have different Mg2+ requirements.
  EMBO J, 15, 2547-2555.  
8547243 P.K.Wittmayer, and R.T.Raines (1996).
Substrate binding and turnover by the highly specific I-PpoI endonuclease.
  Biochemistry, 35, 1076-1083.  
8755524 R.A.Garcia, C.J.Bustamante, and N.O.Reich (1996).
Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.
  Proc Natl Acad Sci U S A, 93, 7618-7622.  
17029807 T.Härd, and T.Lundbäck (1996).
Thermodynamics of sequence-specific protein-DNA interactions.
  Biophys Chem, 62, 121-139.  
8600465 T.J.Boggon, E.L.Hancox, K.E.McAuley-Hecht, B.A.Connolly, W.N.Hunter, T.Brown, R.T.Walker, and G.A.Leonard (1996).
The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides.
  Nucleic Acids Res, 24, 951-961.
PDB code: 233d
8932361 W.Wende, W.Grindl, F.Christ, A.Pingoud, and V.Pingoud (1996).
Binding, bending and cleavage of DNA substrates by the homing endonuclease Pl-SceI.
  Nucleic Acids Res, 24, 4123-4132.  
7739896 A.Chen, L.M.Powell, D.T.Dryden, N.E.Murray, and T.Brown (1995).
Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.
  Nucleic Acids Res, 23, 1177-1183.  
7773784 A.K.Aggarwal (1995).
A gripping end to NF-kappa B.
  Nat Struct Biol, 2, 184-186.  
7773740 A.K.Aggarwal (1995).
Structure and function of restriction endonucleases.
  Curr Opin Struct Biol, 5, 11-19.  
8846224 B.E.Raumann, K.L.Knight, and R.T.Sauer (1995).
Dramatic changes in DNA-binding specificity caused by single residue substitutions in an Arc/Mnt hybrid repressor.
  Nat Struct Biol, 2, 1115-1122.  
7896784 B.E.Withers, and J.C.Dunbar (1995).
Sequence-specific DNA recognition by the SmaI endonuclease.
  J Biol Chem, 270, 6496-6504.  
7567471 B.E.Withers, and J.C.Dunbar (1995).
DNA determinants in sequence-specific recognition by XmaI endonuclease.
  Nucleic Acids Res, 23, 3571-3577.  
7724581 C.R.Robinson, and S.G.Sligar (1995).
Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, Pvu II, and EcoRV specificity.
  Proc Natl Acad Sci U S A, 92, 3444-3448.  
7552704 C.Venclovas, and V.Siksnys (1995).
Different enzymes with similar structures involved in Mg(2+)-mediated polynucleotidyl transfer.
  Nat Struct Biol, 2, 838-841.  
8521494 D.G.Vassylyev, T.Kashiwagi, Y.Mikami, M.Ariyoshi, S.Iwai, E.Ohtsuka, and K.Morikawa (1995).
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
  Cell, 83, 773-782.
PDB code: 1vas
  7737131 I.Brukner, R.Sánchez, D.Suck, and S.Pongor (1995).
Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
  EMBO J, 14, 1812-1818.  
7716167 J.Janin (1995).
Elusive affinities.
  Proteins, 21, 30-39.  
7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
  Biophys J, 68, 2454-2468.  
8548278 M.Oram, M.D.Szczelkun, and S.E.Halford (1995).
Recombination. Pieces of the site-specific recombination puzzle.
  Curr Biol, 5, 1106-1109.  
7664086 N.D.Arbuckle, and B.Luisi (1995).
A recipe for specificity.
  Nat Struct Biol, 2, 341-346.  
7664066 A.Athanasiadis, M.Vlassi, D.Kotsifaki, P.A.Tucker, K.S.Wilson, and M.Kokkinidis (1994).
Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.
  Nat Struct Biol, 1, 469-475.
PDB code: 1pvu
  8062817 A.Vrielink, W.Rüger, H.P.Driessen, and P.S.Freemont (1994).
Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
  EMBO J, 13, 3413-3422.
PDB codes: 1bgt 1bgu 2bgt 2bgu
8065254 C.Q.Pan, R.Landgraf, and D.S.Sigman (1994).
DNA-binding proteins as site-specific nucleases.
  Mol Microbiol, 12, 335-342.  
7892176 C.Venclovas, A.Timinskas, and V.Siksnys (1994).
Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV.
  Proteins, 20, 279-282.  
7826675 D.Suck (1994).
DNA recognition by DNase I.
  J Mol Recognit, 7, 65-70.  
7922330 D.Suck (1994).
DNA-protein interactions. Flip out and modify.
  Curr Biol, 4, 252-255.  
8081744 F.K.Winkler (1994).
DNA totally flipped-out by methylase.
  Structure, 2, 79-83.  
  7925312 H.P.Müller, and H.E.Varmus (1994).
DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes.
  EMBO J, 13, 4704-4714.  
7634103 J.L.Kim, and S.K.Burley (1994).
1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG.
  Nat Struct Biol, 1, 638-653.
PDB code: 1vto
8066089 K.Balendiran, J.Bonventre, R.Knott, W.Jack, J.Benner, I.Schildkraut, and J.E.Anderson (1994).
Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site.
  Proteins, 19, 77-79.  
7908739 L.F.Dorner, and I.Schildkraut (1994).
Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease.
  Nucleic Acids Res, 22, 1068-1074.  
8081758 M.Newman, T.Strzelecka, L.F.Dorner, I.Schildkraut, and A.K.Aggarwal (1994).
Structure of restriction endonuclease bamhi phased at 1.95 A resolution by MAD analysis.
  Structure, 2, 439-452.
PDB code: 1bam
8087558 M.Suzuki (1994).
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
  Structure, 2, 317-326.  
  8076590 X.Cheng, K.Balendiran, I.Schildkraut, and J.E.Anderson (1994).
Structure of PvuII endonuclease with cognate DNA.
  EMBO J, 13, 3927-3935.
PDB code: 1pvi
15335830 A.A.Travers, and J.W.Schwabe (1993).
Spurring on transcription?
  Curr Biol, 3, 898-900.  
8378323 A.Jeltsch, J.Alves, H.Wolfes, G.Maass, and A.Pingoud (1993).
Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes.
  Proc Natl Acad Sci U S A, 90, 8499-8503.  
8069624 C.A.Orengo, and J.M.Thornton (1993).
Alpha plus beta folds revisited: some favoured motifs.
  Structure, 1, 105-120.  
  8246971 E.L.Ellison, and V.M.Vogt (1993).
Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site.
  Mol Cell Biol, 13, 7531-7539.  
8346027 E.L.Hancox, B.A.Connolly, and R.T.Walker (1993).
Synthesis and properties of oligodeoxynucleotides containing the analogue 2'-deoxy-4'-thiothymidine.
  Nucleic Acids Res, 21, 3485-3491.  
8412677 I.B.Vipond, and S.E.Halford (1993).
Structure-function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage.
  Mol Microbiol, 9, 225-231.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.