Skip to main content
SpringerLink
Log in

Restriction Endonucleases: Structure of the Conserved Catalytic Core and the Role of Metal Ions in DNA Cleavage

  • Chapter
Restriction Endonucleases

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 14))

Abstract

Type II restriction endonucleases (REases) are a fascinating group of proteins. With the REBasedatabase currently listing ≈3500 Type II REases having nearly 240 distinct DNA sequence specificities, they constitute one of the larger known families of enzymes (Roberts et al. 2003). These DNA-cleaving enzymes combine very high catalytic efficiencies (kcat/ kuncat= ≈ 1016) with exquisite DNA sequence selectivity. Restriction enzymes that are classified Type II (Welsh et al., this Vol.) cleave specifically within or close to their recognition sites, and do not require ATP hydrolysis for their nucleolytic activity. DNA cleavage by these enzymes can result in DNA with either 5′ or 3′ overhangs or blunt ends.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aggarwal AK (1995) Structure and function of restriction endonucleases. Curr Opin Struct Biol 5:11–19

    Article  PubMed  CAS  Google Scholar 

  • Athanasiadis A, Vlassi M, Kotsifaki D, Tucker PA, Wilson KS, Kokkinidis M (1994) Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Nat Struct Biol 1:469–475

    Article  PubMed  CAS  Google Scholar 

  • Baldwin GS, Sessions RB, Erskine SG, Halford SE (1999) DNA cleavage by the EcoRV restriction endonuclease: roles of divalent metal ions in specificity and catalysis. J Mol Biol 288:87–103

    Article  PubMed  CAS  Google Scholar 

  • Ban C, Yang W (1998) Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases. EMBO J 17:1526–1534

    Article  PubMed  CAS  Google Scholar 

  • Beernink PT, Segelke BW, Hadi MZ, Erzberger JP, Wilson DM 3rd, Rupp B (2001) Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Apel: implications for the catalytic mechanism. J Mol Biol 307:1023–1034

    Article  PubMed  CAS  Google Scholar 

  • Beese LS, Steitz TA (1991) Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J 10:25–33

    PubMed  CAS  Google Scholar 

  • Bhagwat AS, Lieb M (2002) Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli. Mol Microbiol 44:1421–1428

    Article  PubMed  CAS  Google Scholar 

  • Bond CS, Kvaratskhelia M, Richard D, White MF, Hunter WN (2001) Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus. Proc Natl Acad Sci USA 98:5509–5514

    Article  PubMed  CAS  Google Scholar 

  • Bozic D, Grazulis S, Siksnys V, Huber R (1996) Crystal structure of Citrobacter freundii restriction endonuclease CfrI0I at 2.15 Å resolution. J Mol Biol 255:176–186

    Article  PubMed  CAS  Google Scholar 

  • Brautigam CA, Steitz TA (1998) Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr Opin Struct Biol 8:54–63

    Article  PubMed  CAS  Google Scholar 

  • Bujnicki JM (2000) Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol 50:39–44

    PubMed  CAS  Google Scholar 

  • Bujnicki JM, Rychlewski L (2001a) Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles. J Mol Microbiol BiotechnoI 3:69–72

    CAS  Google Scholar 

  • Bujnicki JM, Rychlewski L (2001b) Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. Gene 267:183–191

    Article  PubMed  CAS  Google Scholar 

  • Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH (2003) Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix. Nucleic Acids Res 31:1633–1639

    Article  PubMed  CAS  Google Scholar 

  • Carrick KL, Topal MD (2003) Amino acid substitutions at position 43 of NaeI endonuclease-evidence for changes in NaeI structure. J Biol Chem 278:9733–9739

    Article  PubMed  CAS  Google Scholar 

  • Chandrasegaran S, Smith HO, Amzel ML, Ysern X (1986) Prelim inary X-ray diffraction analysis of HhaII endonuclease-DNA cocrystals. Proteins 1:263–266

    Article  PubMed  CAS  Google Scholar 

  • Cheetham GM, Steitz TA (2000) Insights into transcription: structure and function of single-subunit DNA-dependent RNA polymerases. Curr Opin Struct Biol 10:117–123

    Article  PubMed  CAS  Google Scholar 

  • Cheng X, Balendiran K, Schildkraut I, Anderson JE (1994) Structure of PvuII endonuclease with cognate DNA. EMBO J 13:3927–3935

    PubMed  CAS  Google Scholar 

  • Conlan LH, Dupureur CM (2002a) Dissecting the metal ion dependence of DNA binding by PvuII endonuclease. Biochemistry 41:1335–1342

    Article  PubMed  CAS  Google Scholar 

  • Conlan LH, Dupureur CM (2002b) Multiple metal ions drive DNA association by PvuII endonuclease. Biochemistry 41:14848–14855

    Article  PubMed  CAS  Google Scholar 

  • Cowan JA (1998) Metal activation of enzymes in nucleic acid biochemistry. Chem Rev 98:1067–1088

    Article  PubMed  CAS  Google Scholar 

  • Declais AC, Hadden J, Phillips SE, Lilley DM (2001) The active site of the junction-resolving enzyme T7 endonuclease J. J Mol Biol 307:1145–1158

    Article  PubMed  CAS  Google Scholar 

  • Deibert M, Grazulis S, Janulaitis A, Siksnys V, Huber R (1999) Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 Åresolution. EMBO J 18:5805–5816

    Article  PubMed  CAS  Google Scholar 

  • Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R (2000) Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat Struct Biol 7:792–799

    Article  PubMed  CAS  Google Scholar 

  • Deva T, Krishnaswamy S (2001) Structure-based sequence alignment of type-II restriction endonucleases. Biochim Biophys Acta 1544:217–228

    Article  PubMed  CAS  Google Scholar 

  • Dupureur CM, Conlan LH (2000) A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions. Biochemistry 39:10921–10927

    Article  PubMed  CAS  Google Scholar 

  • Engler LE, Sapienza P, Dorner LF, Kucera R, Schildkraut I, Jen-Jacobson L (2001) The energetics of the interaction of BamHI endonuclease with its recognition site GGATCC. J Mol Biol 307:619–636

    Article  PubMed  CAS  Google Scholar 

  • Erskine SG, Halford SE (1998) Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA. J Mol Biol 275:759–772

    Article  PubMed  CAS  Google Scholar 

  • Fedor MJ (2000) Structure and function of the hairpin ribozyme. J Mol Biol 297:269–291

    Article  PubMed  CAS  Google Scholar 

  • Freemont PS, Friedman JM, Beese LS, Sanderson MR, Steitz TA (1988) Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci USA 85:8924–8928

    Article  PubMed  CAS  Google Scholar 

  • Friedhoff P, Sheybani B, Thomas E, Merz C, Pingoud A (2002) Haemophilus influenzae and Vibrio cholerae genes for mutH are able to fully complement a mutH defect in Escherichia coli. FEMS Microbiol Lett 208:121–126

    Article  Google Scholar 

  • Friedhoff P, Thomas E, Pingoud A (2003) Tyr-212: A key residue involved in strand discrimination by the DNA mismatch repair endonuclease MutH. J Mol Biol 325:285–297

    Article  PubMed  CAS  Google Scholar 

  • Fuxreiter M, Osman R (2001) Probing the general base catalysis in the first step of BamHI action by computer simulations. Biochemistry 40:15017–023

    Article  PubMed  CAS  Google Scholar 

  • Galburt EA, Stoddard BL (2002) Catalytic mechanisms of restriction and homing endonucleases. Biochemistry 41:13851–13860

    Article  PubMed  CAS  Google Scholar 

  • Grabowski G, Jeltsch A, Wolfes H, Maass G, Alves J (1995) Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI. Gene 157:113–118

    Article  PubMed  CAS  Google Scholar 

  • Grazulis S, Deibert M, Rimseliene R, Skirgaila R, Sasnauskas G, Lagunavicius A, Repin V, Urbanke C, Huber R, Siksnys V (2002) Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucleic Acids Res 30:876–885

    Article  PubMed  CAS  Google Scholar 

  • Groll DH, Jeltsch A, Selent U, Pingoud A (1997) Does the restriction endonuclease EcoRV employ a two-metal-Ion mechanism for DNA cleavage? Biochemistry 36:11389–401

    Article  PubMed  CAS  Google Scholar 

  • Hadden JM, Convery MA, Declais AC, Lilley DM, Phillips SE (2001) Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I. Nat Struct Biol 8: 62–67

    Article  PubMed  CAS  Google Scholar 

  • Hadden JM, Declais AC, Phillips SE, Lilley DM (2002) Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I. EMBO J 21:3505–3515

    Article  PubMed  CAS  Google Scholar 

  • Haq I, O’Brien R, Lagunavicius A, Siksnys V, Ladbury JE (2001) Specific DNA recognition by the Type II restriction endonuclease MunI: the effect of pH. Biochemistry 40:14960–14967

    Article  PubMed  CAS  Google Scholar 

  • Heitman J, Ivanenko T, Kiss A (1999) DNA nicks inflicted by restriction endonucleases are repaired by a RecA-and RecB-dependent pathway in Escherichia coli. Mol Microbiol 33:1141–1151

    Article  PubMed  CAS  Google Scholar 

  • Hickman AB, Li Y, Mathew SV, May EW, Craig NL, Dyda F (2000) Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol Cell 5:1025–1034

    Article  PubMed  CAS  Google Scholar 

  • Horton JR, Cheng X (2000) Pvull endonuclease contains two calcium ions in active sites. J Mol Biol 300:1049–1056

    Article  PubMed  CAS  Google Scholar 

  • Horton NC, Dorner LF, Perona JJ (2002a) Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNAintercalation. Nat Struct Biol 9:42–47

    Article  PubMed  CAS  Google Scholar 

  • Horton NC, Newberry KJ, Perona JJ (1998) Metal ion-mediated substrate-assisted catalysis in Type II restriction endonucleases. Proc Natl Acad Sci USA 95:13489–13494

    Article  PubMed  CAS  Google Scholar 

  • Horton NC, Otey C, Lusetti S, Sam MD, Kohn J, Martin AM, Ananthnarayan V, Perona JJ (2002b) Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease. Biochemistry 41:10754–10763

    Article  PubMed  CAS  Google Scholar 

  • Huai Q, Colandene JD, Chen Y, Luo F, Zhao Y, Topal MD, Ke H (2000) Crystal structure of NaeI-an evolutionary bridge between DNAendonuclease and topoisomerase. EMBO J 19:3110–3118

    Article  PubMed  CAS  Google Scholar 

  • Huai Q, Colandene JD, Topal MD, Ke H (2001) Structure of Nael-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat Struct Biol 8:665–669

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch A, Alves J, Maass G, Pingoud A (1992) On the catalytic mechanism of EcoRI and EcoRV. A detailed proposal based on biochemical results, structural data and molecular modelling. FEBS Lett 304:4–8

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch A, Alves J, Wolfes H, Maass G, Pingoud A (1993) Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes. Proc Natl Acad Sci USA 90:8499–8503

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch A, Kroger M, Pingoud A (1995a) Evidence for an evolutionary relationship among type-II restriction endonucleases. Gene 160:7–16

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch A, Maschke H, Selent U, Wenz C, Kohler E, Connolly BA, Thorogood H, Pingoud A (1995b) DNA binding specificity of the EcoRV restriction endonuclease is increased by Mg2+ binding to a metal ion binding site distinct from the catalytic center of the enzyme. Biochemistry 34:6239–6246

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch A, Pleckaityte M, Selent U, Wolfes H, Siksnys V, Pingoud A (1995c) Evidence for substrate-assisted catalysis in the DNAcleavage of several restriction endonucleases. Gene 157:157–162

    Article  PubMed  CAS  Google Scholar 

  • Jen-Jacobson L (1997) Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state. Biopolymers 44:153–180

    Article  PubMed  CAS  Google Scholar 

  • Jo K, Topal MD (1995) DNA topoisomerase and recombinase activities in NaeI restriction endonuclease. Science 267:1817–1820

    Article  PubMed  CAS  Google Scholar 

  • Jo K, Topal MD (1996a) Changing a leucine to a lysine residue makes NaeI endonuclease hypersensitive to DNA intercalative drugs. Biochemistry 35:10014–10018

    Article  PubMed  CAS  Google Scholar 

  • Jo K, Topal MD (1996b) Effects on NaeI-DNA recognition of the leucine to lysine substitution that transforms restriction endonuclease NaeI to a topoisomerase: a model for restriction endonuclease evolution. Nucleic Acids Res 24:4171–4175

    Article  PubMed  CAS  Google Scholar 

  • Jose TJ, Conlan LH, Dupureur CM (1999) Quantitative evaluation of metal ion binding to PvuII restriction endonuclease. J Biol Inorg Chem 4:814–823

    Article  PubMed  CAS  Google Scholar 

  • Junop MS, Yang W, Funchain P, Clendenin W, Miller JH (2003) In vitro and in vivo studies of MutS, MutL and MutH mutants: correlation of mismatch repair and DNA recombination. DNA Repair (Arnst) 2:387–405

    Article  CAS  Google Scholar 

  • Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM (1990) Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science 249:13071309

    Google Scholar 

  • Komori K, Sakae S, Daiyasu H, Toh H, Morikawa K, Shinagawa H, Ishino Y (2000) Mutational analysis of the Pyrococcus furiosus Holliday junction resolvase hjc revealed functionally important residues for dimer formation, junction DNA binding, and cleavage activities. J Biol Chem 275:40385–40391

    Article  PubMed  CAS  Google Scholar 

  • Kostrewa D, Winkler FK (1995) Mg2+ binding to the active site of EcoRVendonuclease: a crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry 34:683–696

    Article  PubMed  CAS  Google Scholar 

  • Kovall R, Matthews BW (1997) Toroidal structure of lambda-exonuclease. Science 277:1824–1827

    Article  PubMed  CAS  Google Scholar 

  • Kovall RA, Matthews BW (1998) Structural, functional, and evolutionary relationships between lambda-exonuclease and the Type II restriction endonucleases. Proc Natl Acad Sci USA 95:7893–7897

    Article  PubMed  CAS  Google Scholar 

  • Kovall RA, Matthews BW (1999) Type II restriction endonucleases: structural, functional and evolutionary relationships. Curr Opin Chem Biol 3:578–583

    Article  PubMed  CAS  Google Scholar 

  • Lagunavicius A, Grazulis S, Balciunaite E, Vainius D, Siksnys V (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

    Article  PubMed  CAS  Google Scholar 

  • Lagunavicius A, Siksnys V (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

    Article  PubMed  CAS  Google Scholar 

  • Lins RD, Straatsma TP, Briggs JM (2000) Similarities in the HIV-l and ASV integrase active sites upon metal cofactor binding. Biopolymers 53:308–315

    Article  PubMed  CAS  Google Scholar 

  • Loh T, Murphy KC, Marinus MG (2001) Mutational analysis of the MutH protein from Escherichia coli. J Biol Chem 276:12113–12119

    Article  PubMed  CAS  Google Scholar 

  • Lovell S, Goryshin IY, Reznikoff WR, Rayment I (2002) Two-metal active site binding of a Tn5 transposase synaptic complex. Nat Struct Biol 9:278–281

    Article  PubMed  CAS  Google Scholar 

  • Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK (2000) Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNAsubstrate at 1.5 Å resolution. Nat Struct Biol 7:134–140

    Article  PubMed  CAS  Google Scholar 

  • Martin AM, Horton NC, Lusetti S, Reich NO, Perona JJ (1999a) Divalent metal dependence of site-specific DNA binding by EcoRVendonuclease. Biochemistry 38:8430–8439

    Article  PubMed  CAS  Google Scholar 

  • Martin AM, Sam MD, Reich NO, Perona JJ (1999b) Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. Nat Struct Biol 6:269–277

    Article  PubMed  CAS  Google Scholar 

  • Mordasini T, Curioni A, Andreoni W (2003) Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations. J Biol Chem 278:4381–4384

    Article  PubMed  CAS  Google Scholar 

  • Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE (1998) Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. EMBO J 17:5466–5476

    Article  PubMed  CAS  Google Scholar 

  • Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK (1994). Structure of restriction endonuclease BamHI phased at 1.95 Åresolution by MAD analysis. Structure 2:439–452

    Article  PubMed  CAS  Google Scholar 

  • Nishino T, Komori K, Ishino Y, Morikawa K (2001a) Dissection of the regional roles of the archaeal Holliday junction resolvase Hjc by structural and mutational analyses. J Biol Chem 276:35735–35740

    Article  PubMed  CAS  Google Scholar 

  • Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K (2001b) Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition. Structure (Camb) 9:197–204

    Article  CAS  Google Scholar 

  • Nishino T, Morikawa K (2002) Structure and function of nucleases in DNArepair: shape, grip and blade of the DNAscissors. Oncogene 21:9022–9032

    Article  PubMed  CAS  Google Scholar 

  • O’Loughlin TJ, XU Q, Kucera RB, Dorner LF, Sweeney S, Schildkraut I, Guo HC (2000) Crystallization and preliminary X-ray diffraction analysis-of MspI restriction endonuclease in complex with its cognate DNA. Acta Crystallogr D Biol Crystallogr 56 Pt 12:1652–1655

    Article  Google Scholar 

  • Perona JJ (2002) Type II restriction endonucleases. Methods 28:353–364

    Article  PubMed  CAS  Google Scholar 

  • Perona JJ, Martin AM (1997) Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis. J Mol Biol 273:207–225

    Article  PubMed  CAS  Google Scholar 

  • Pingoud A, Jeltsch A (1997) Recognition and cleavage of DNA by type-II restriction endonucleases. Eur J Biochem 246:1–22

    Article  PubMed  CAS  Google Scholar 

  • Pingoud A, Jeltsch A (2001) Structure and function of Type II restriction endonucleases. Nucleic Acids Res 29:3705–3727

    Article  PubMed  CAS  Google Scholar 

  • Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A (2002) Evolutionary relationship between different subgroups of restriction endonucleases. J Biol Chem 277:14306–14314

    Article  PubMed  CAS  Google Scholar 

  • Rice P, Craigie R, Davies DR (1996) Retroviral integrases and their cousins. Curr Opin Struct Biol 6:76–83

    Article  PubMed  CAS  Google Scholar 

  • Roberts RJ, Vincze T, Posfai J, Macelis D (2003) REBASE-restriction enzymes and methyltransferases. Nucleic Acids Res 31:418–420

    Article  PubMed  CAS  Google Scholar 

  • Rosenberg JM (1991) Structure and function of restriction endonucleases. Curr Opin Struct Biol 1:104–113

    Article  CAS  Google Scholar 

  • Sam MD, Perona JJ (1999) Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRVendonuclease. Biochemistry 38:6576–6586

    Article  PubMed  CAS  Google Scholar 

  • Sapranauskas R, Sasnauskas G, Lagunavicius A, Vilkaitis G, Lubys A, Siksnys V (2000) Novel subtype of Type lIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium. J Biol Chem 275:30878–30885

    Article  PubMed  CAS  Google Scholar 

  • Selent U, Ruter T, Kohler E, Liedtke M, Thielking V, Alves J, Oelgeschlager T, Wolfes H, Peters F, Pingoud A (1992) A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV. Biochemistry 31:4808–4815

    Article  PubMed  CAS  Google Scholar 

  • Skirgaila R, Grazulis S, Bozic D, Huber R, Siksnys V (1998) Structure-based redesign of the catalytic/metal binding site of CfrlOI restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues. J Mol Biol 279:473–481

    Article  PubMed  CAS  Google Scholar 

  • Skirgaila R, Siksnys V (1998) Ca-t-ions stimulate DNA binding specificity of Cfr10I restriction enzyme. Biol Chem 379:595–598

    PubMed  CAS  Google Scholar 

  • Soundararajan M, Chang Z, Morgan RD, Heslop P, Connolly BA(2002) DNAbinding and recognition by the lIs restriction endonuclease Mboll. J Biol Chem 277:887–895

    Article  PubMed  CAS  Google Scholar 

  • Stanford NP, Halford SE, Baldwin GS (1999) DNA cleavage by the EcoRV restriction endonuclease: pH dependence and proton transfers in catalysis. J Mol Biol 288:105–116

    Article  PubMed  CAS  Google Scholar 

  • Steitz TA (1998) A mechanism for all polymerases. Nature 391:231–232

    Article  PubMed  CAS  Google Scholar 

  • Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90:6498–6502

    Article  PubMed  CAS  Google Scholar 

  • Stoddard BL (1998) New results using Laue diffraction and time-resolved crystallography. Curr Opin Struct Biol 8:612–618

    Article  PubMed  CAS  Google Scholar 

  • Tamulaitis G, Solonin AS, Siksnys V (2002) Alternative arrangements of catalytic residues at the active sites of restriction enzymes. FEBS Lett 518:17–22

    Article  PubMed  CAS  Google Scholar 

  • Tsutakawa SE, Jingami H, Morikawa K (1999a) Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell 99:615–623

    Article  PubMed  CAS  Google Scholar 

  • Tsutakawa SE, Morikawa K(2001) The structural basis of damaged DNArecognition and endonucleolytic cleavage for very short patch repair endonuclease. Nucleic Acids Res 29:3775–3783

    Article  PubMed  CAS  Google Scholar 

  • Tsutakawa SE, Muto T, Kawate T, Jingami H, Kunishima N, Ariyoshi M, Kohda D, Nakagawa M, Morikawa K (1999b) Crystallographic and functional studies of very short patch repair endonuclease. Mol Cell 3:621–628

    Article  PubMed  CAS  Google Scholar 

  • van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM (2001) Restriction enzyme BsoBIDNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure (Camb) 9:133–144

    Article  Google Scholar 

  • Venclovas C, Timinskas A, Siksnys V (1994) Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV. Proteins 20:279–282

    Article  PubMed  CAS  Google Scholar 

  • Viadiu H, Aggarwal AK (1998) The role of metals in catalysis by the restriction endonuclease BamHI. Nat Struct Biol 5:910–916

    Article  PubMed  CAS  Google Scholar 

  • Vipond IB, Baldwin GS, Halford SE (1995) Divalent metal ions at the active sites of the EcoRVand EcoRI restriction endonucleases. Biochemistry 34:697–704

    Article  PubMed  CAS  Google Scholar 

  • Vipond IB, Halford SE (1995). Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Biochemistry 34:1113–1119

    Article  PubMed  CAS  Google Scholar 

  • Wah DA, Bitinaite J, Schildkraut I, Aggarwal AK (1998) Structure of FokI has implications for DNAcleavage. Proc Natl Acad Sci USA 95:10564–10569

    Article  PubMed  CAS  Google Scholar 

  • Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK (1997) Structure of the multimodular endonuclease FokI bound to DNA. Nature 388:97–100

    Article  PubMed  CAS  Google Scholar 

  • Winkler FK (1992) Structure and function of restriction endonucleases. Curr Opin Struct Biol 2:93–99

    Article  Google Scholar 

  • Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS (1993) The crystal structure of EcoRVendonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J 12:1781–1795

    PubMed  CAS  Google Scholar 

  • Wlodawer A (1999) Crystal structures of catalytic core domains of retroviral integrases and role of divalent cations in enzymatic activity. Adv Virus Res 52:335–350

    Article  PubMed  CAS  Google Scholar 

  • Xu Q, O’Loughlin TJ, Kucera RB, Schildkraut I, Guo H-C (2001) Structural study of restriction enzyme MspI/SDNA complex by x-ray crystallography. Biophys J 80:296a

    Google Scholar 

  • Xu SY, Schildkraut I (1991) Cofactor requirements of BamHI mutant endonuclease E77K and its suppressor mutants. J Bacteriol 173:5030–5035

    PubMed  CAS  Google Scholar 

  • Zhou EX, Reuter M, Meehan EJ, Chen L (2002) Anew crystal form of restriction endonuclease EcoRII that diffracts to 2.8 Å resolution. Acta Crystallogr D Biol Crystallogr 58:1343–1345

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, Emory University School of Medicine, 1510 Clifton, Atlanta, Georgia, 30322, USA

    J. R. Horton & X. Cheng

  2. Department of Microbiology & Immunology, and Program in Bioinformatics & Proteomics/Genomics, Medical College of Ohio, Toledo, Ohio, 43614-5806, USA

    R. M. Blumenthal

Authors
  1. J. R. Horton
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. M. Blumenthal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. X. Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Institute for Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35392, Giessen, Germany

    Alfred M. Pingoud

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Horton, J.R., Blumenthal, R.M., Cheng, X. (2004). Restriction Endonucleases: Structure of the Conserved Catalytic Core and the Role of Metal Ions in DNA Cleavage. In: Pingoud, A.M. (eds) Restriction Endonucleases. Nucleic Acids and Molecular Biology, vol 14. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18851-0_14

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-18851-0_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-62324-0

  • Online ISBN: 978-3-642-18851-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation