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PDBsum entry 1rvb
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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
1rvb

 

 

 

 

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Contents
Protein chains
244 a.a.
DNA/RNA
Metals
_MG ×2
Waters ×185
PDB id:
1rvb
Name: Hydrolase/DNA
Title: Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstroms resolution
Structure: DNA (5'-d( Ap Ap Ap Gp Ap Tp Ap Tp Cp Tp T)-3'). Chain: c, d. Engineered: yes. Protein (eco rv . Chain: a, b. Engineered: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.165    
Authors: D.Kostrewa,F.K.Winkler
Key ref:
D.Kostrewa and F.K.Winkler (1995). Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution. Biochemistry, 34, 683-696. PubMed id: 7819264 DOI: 10.1021/bi00002a036
Date:
21-Oct-94     Release date:   26-Jan-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04390  (T2E5_ECOLX) -  Type II restriction enzyme EcoRV from Escherichia coli
Seq:
Struc: 		245 a.a.
244 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  A-A-A-G-A-T-A-T-C-T-T 11 bases
  A-A-A-G-A-T-A-T-C-T-T 11 bases

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.4  - type Ii site-specific deoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
      Cofactor: Mg(2+)

 

 
DOI no: 10.1021/bi00002a036 Biochemistry 34:683-696 (1995)
PubMed id: 7819264  
 
 
Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution.
D.Kostrewa, F.K.Winkler.
 
  ABSTRACT  
 
The type II restriction endonuclease EcoRV was crystallized as a complex with the substrate DNA undecamer AAAGATATCTT (recognition sequence underlined). These crystals diffract to much better resolution (2 A) than was the case for the previously reported complex with the decamer GGGATATCCC [Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., & Wilson, K. S. (1993) EMBO J. 12, 1781-1795]. The crystal structure contains one dimer complex in the asymmetric unit and was solved by molecular replacement. The same kinked DNA conformation characteristic for enzyme-bound cognate DNA is observed. Crystals, soaked with Mg2+, show the essential cofactor bound at only one active site of the dimer, and the DNA is not cleaved. The Mg2+ has one oxygen from the scissile phosphodiester group and two carboxylate oxygens, one form Asp74 and one from Asp90, in its octahedral ligand sphere. The scissile phosphodiester group is pulled by 1 A toward the Mg2+. After substrate cleavage in solution, isomorphous crystals containing the enzyme--product--Mg2+ complex were obtained. In this structure, each of the 5'-phosphate groups is bound to two Mg2+. The kinked DNA conformation is essentially maintained, but the two central adenines, 3' to the cleavage sites, form an unusual cross-strand base stacking. The structures have been refined to R factors of 0.16 at 2.1-2.0 A resolution maintaining very good stereochemistry. On the basis of these structures and inspired by recent kinetic data [Vipond, I. B., & Halford, S. E. (1994) Biochemistry (second paper of three in this issue)], we have constructed a transition state model with two metals bound to the scissile phosphorane group.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
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PDB code: 3ndh
19915993 M.J.Marcaida, I.G.Muñoz, F.J.Blanco, J.Prieto, and G.Montoya (2010).
Homing endonucleases: from basics to therapeutic applications.
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19161971 F.Xie, and C.M.Dupureur (2009).
Kinetic analysis of product release and metal ions in a metallonuclease.
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18436236 A.K.Mantha, N.Oezguen, K.K.Bhakat, T.Izumi, W.Braun, and S.Mitra (2008).
Unusual role of a cysteine residue in substrate binding and activity of human AP-endonuclease 1.
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18424798 C.M.Moure, F.S.Gimble, and F.A.Quiocho (2008).
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
  Nucleic Acids Res, 36, 3287-3296.
PDB codes: 3c0w 3c0x
17427952 N.Oezguen, C.H.Schein, S.R.Peddi, T.D.Power, T.Izumi, and W.Braun (2007).
A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1.
  Proteins, 68, 313-323.  
16981705 D.A.Hiller, and J.J.Perona (2006).
Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage.
  Biochemistry, 45, 11453-11463.
PDB code: 2ge5
16710870 K.D.Roberts, J.N.Lambert, N.J.Ede, and A.M.Bray (2006).
Efficient methodology for the cyclization of linear peptide libraries via intramolecular S-alkylation using Multipin solid phase peptide synthesis.
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16498623 K.J.Skowronek, J.Kosinski, and J.M.Bujnicki (2006).
Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.
  Proteins, 63, 1059-1068.  
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
16154091 N.McGregor, S.Ayora, S.Sedelnikova, B.Carrasco, J.C.Alonso, P.Thaw, and J.Rafferty (2005).
The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage.
  Structure, 13, 1341-1351.
PDB code: 1zp7
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
15479781 C.L.Middleton, J.L.Parker, D.J.Richard, M.F.White, and C.S.Bond (2004).
Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje.
  Nucleic Acids Res, 32, 5442-5451.
PDB codes: 1ob8 1ob9
15130133 P.A.Pribil, S.J.Wardle, and D.B.Haniford (2004).
Enhancement and rescue of target capture in Tn10 transposition by site-specific modifications in target DNA.
  Mol Microbiol, 52, 1173-1186.  
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.  
12606565 M.R.Tock, E.Frary, J.R.Sayers, and J.A.Grasby (2003).
Dynamic evidence for metal ion catalysis in the reaction mediated by a flap endonuclease.
  EMBO J, 22, 995.  
12093751 J.M.Hadden, A.C.Déclais, S.E.Phillips, and D.M.Lilley (2002).
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.
  EMBO J, 21, 3505-3515.
PDB codes: 1m0d 1m0i
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.  
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
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
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.
  Nucleic Acids Res, 29, 3757-3774.  
11148032 C.M.Dupureur, and M.A.Dominguez (2001).
The PD...(D/E)XK motif in restriction enzymes: a link between function and conformation.
  Biochemistry, 40, 387-394.  
11179886 C.M.Lukacs, and A.K.Aggarwal (2001).
BglII and MunI: what a difference a base makes.
  Curr Opin Struct Biol, 11, 14-18.  
11331763 C.S.Bond, M.Kvaratskhelia, D.Richard, M.F.White, and W.N.Hunter (2001).
Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus.
  Proc Natl Acad Sci U S A, 98, 5509-5514.
PDB code: 1hh1
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.
  Structure, 9, 133-144.
PDB code: 1dc1
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.  
11257528 W.Cao, and J.Lu (2001).
Exploring the catalytic center of TaqI endonuclease: rescuing catalytic activity by double mutations and Mn2+.
  Biochim Biophys Acta, 1546, 253-260.  
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
10978180 C.M.Dupureur, and L.H.Conlan (2000).
A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions.
  Biochemistry, 39, 10921-10927.  
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.  
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
  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.
  Genome Biol, 1, REVIEWS001.  
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
11123916 S.Schöttler, W.Wende, V.Pingoud, and A.Pingoud (2000).
Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.
  Biochemistry, 39, 15895-15900.  
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.  
10226502 G.R.Pack, L.Wong, and G.Lamm (1999).
Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations.
  Biopolymers, 49, 575-590.  
10194315 G.Sasnauskas, A.Jeltsch, A.Pingoud, and V.Siksnys (1999).
Plasmid DNA cleavage by MunI restriction enzyme: single-turnover and steady-state kinetic analysis.
  Biochemistry, 38, 4028-4036.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10220350 L.Doan, B.Handa, N.A.Roberts, and K.Klumpp (1999).
Metal ion catalysis of RNA cleavage by the influenza virus endonuclease.
  Biochemistry, 38, 5612-5619.  
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.  
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
10194360 S.F.Martin, and P.J.Hergenrother (1999).
Catalytic cycle of the phosphatidylcholine-preferring phospholipase C from Bacillus cereus. Solvent viscosity, deuterium isotope effects, and proton inventory studies.
  Biochemistry, 38, 4403-4408.  
10535916 S.Shan, A.Yoshida, S.Sun, J.A.Piccirilli, and D.Herschlag (1999).
Three metal ions at the active site of the Tetrahymena group I ribozyme.
  Proc Natl Acad Sci U S A, 96, 12299-12304.  
9521703 A.De, V.Ramesh, S.Mahadevan, and V.Nagaraja (1998).
Mg2+ mediated sequence-specific binding of transcriptional activator protein C of bacteriophage Mu to DNA.
  Biochemistry, 37, 3831-3838.  
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
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.  
9535856 C.X.Zhu, C.J.Roche, N.Papanicolaou, A.DiPietrantonio, and Y.C.Tse-Dinh (1998).
Site-directed mutagenesis of conserved aspartates, glutamates and arginines in the active site region of Escherichia coli DNA topoisomerase I.
  J Biol Chem, 273, 8783-8789.  
  9628339 F.Stahl, W.Wende, A.Jeltsch, and A.Pingoud (1998).
The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis.
  Biol Chem, 379, 467-473.  
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.  
9830061 G.Frank, J.Qiu, M.Somsouk, Y.Weng, L.Somsouk, J.P.Nolan, and B.Shen (1998).
Partial functional deficiency of E160D flap endonuclease-1 mutant in vitro and in vivo is due to defective cleavage of DNA substrates.
  J Biol Chem, 273, 33064-33072.  
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
  9628337 J.R.Horton, J.Bonventre, and X.Cheng (1998).
How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
  Biol Chem, 379, 451-458.
PDB code: 2pvi
9813108 K.Ichiyanagi, H.Iwasaki, T.Hishida, and H.Shinagawa (1998).
Mutational analysis on structure-function relationship of a holliday junction specific endonuclease RuvC.
  Genes Cells, 3, 575-586.  
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
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.  
  9628348 S.Ramchandani, P.Bigey, and M.Szyf (1998).
Genomic structure of the human DNA methyltransferase gene.
  Biol Chem, 379, 535-540.  
9512537 T.Bhaduri, D.Sikder, and V.Nagaraja (1998).
Sequence specific interaction of Mycobacterium smegmatis topoisomerase I with duplex DNA.
  Nucleic Acids Res, 26, 1668-1674.  
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.  
9689049 Y.Goldgur, F.Dyda, A.B.Hickman, T.M.Jenkins, R.Craigie, and D.R.Davies (1998).
Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium.
  Proc Natl Acad Sci U S A, 95, 9150-9154.
PDB codes: 1bis 1biu 1biz
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.  
9164457 D.Kostrewa, F.Grüninger-Leitch, A.D'Arcy, C.Broger, D.Mitchell, and A.P.van Loon (1997).
Crystal structure of phytase from Aspergillus ficuum at 2.5 A resolution.
  Nat Struct Biol, 4, 185-190.
PDB code: 1ihp
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.  
9214642 J.Lykke-Andersen, R.A.Garrett, and J.Kjems (1997).
Mapping metal ions at the catalytic centres of two intron-encoded endonucleases.
  EMBO J, 16, 3272-3281.  
9354759 L.Jen-Jacobson (1997).
Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
  Biopolymers, 44, 153-180.  
9184211 M.S.Junop, and D.B.Haniford (1997).
Factors responsible for target site selection in Tn10 transposition: a role for the DDE motif in target DNA capture.
  EMBO J, 16, 2646-2655.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
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.  
9241430 S.Nie, and R.N.Zare (1997).
Optical detection of single molecules.
  Annu Rev Biophys Biomol Struct, 26, 567-596.  
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.  
9160747 X.Duan, F.S.Gimble, and F.A.Quiocho (1997).
Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity.
  Cell, 89, 555-564.
PDB code: 1vde
9016717 Y.Goldgur, L.Mosyak, L.Reshetnikova, V.Ankilova, O.Lavrik, S.Khodyreva, and M.Safro (1997).
The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe.
  Structure, 5, 59-68.
PDB code: 1eiy
  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.  
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.  
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.  
8679635 H.Thorogood, T.R.Waters, A.W.Parker, C.W.Wharton, and B.A.Connolly (1996).
Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.
  Biochemistry, 35, 8723-8733.  
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.  
8955164 M.J.Giraud-Panis, and D.M.Lilley (1996).
T4 endonuclease VII. Importance of a histidine-aspartate cluster within the zinc-binding domain.
  J Biol Chem, 271, 33148-33155.  
8688420 M.R.Kurpiewski, M.Koziolkiewicz, A.Wilk, W.J.Stec, and L.Jen-Jacobson (1996).
Chiral phosphorothioates as probes of protein interactions with individual DNA phosphoryl oxygens: essential interactions of EcoRI endonuclease with the phosphate at pGAATTC.
  Biochemistry, 35, 8846-8854.  
  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.  
8557624 S.Cal, and B.A.Connolly (1996).
The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.
  J Biol Chem, 271, 1008-1015.  
8718874 S.Cal, R.G.Nicieza, B.A.Connolly, and J.Sánchez (1996).
Interaction of the periplasmic dG-selective Streptomyces antibioticus nuclease with oligodeoxynucleotide substrates.
  Biochemistry, 35, 10828-10836.  
8548278 M.Oram, M.D.Szczelkun, and S.E.Halford (1995).
Recombination. Pieces of the site-specific recombination puzzle.
  Curr Biol, 5, 1106-1109.  
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.

 

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