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EMBO J. Sep 1, 1994; 13(17): 3927–3935.
PMCID: PMC395312

Structure of PvuII endonuclease with cognate DNA.

Abstract

We have determined the structure of PvuII endonuclease complexed with cognate DNA by X-ray crystallography. The DNA substrate is bound with a single homodimeric protein, each subunit of which reveals three structural regions. The catalytic region strongly resembles structures of other restriction endonucleases, even though these regions have dissimilar primary sequences. Comparison of the active site with those of EcoRV and EcoRI endonucleases reveals a conserved triplet sequence close to the reactive phosphodiester group and a conserved acidic pair that may represent the ligands for the catalytic cofactor Mg2+. The DNA duplex is not significantly bent and maintains a B-DNA-like conformation. The subunit interface region of the homodimeric protein consists of a pseudo-three-helix bundle. Direct contacts between the protein and the base pairs of the PvuII recognition site occur exclusively in the major groove through two antiparallel beta strands from the sequence recognition region of the protein. Water-mediated contacts are made in the minor grooves to central bases of the site. If restriction enzymes do share a common ancestor, as has been proposed, their catalytic regions have been very strongly conserved, while their subunit interfaces and DNA sequence recognition regions have undergone remarkable structural variation.

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Selected References

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  • Athanasiadis A, Kokkinidis M. Purification, crystallization and preliminary X-ray diffraction studies of the PvuII endonuclease. J Mol Biol. 1991 Dec 5;222(3):451–453. [PubMed]
  • Athanasiadis A, Gregoriu M, Thanos D, Kokkinidis M, Papamatheakis J. Complete nucleotide sequence of the PvuII restriction enzyme gene from Proteus vulgaris. Nucleic Acids Res. 1990 Nov 11;18(21):6434–6434. [PMC free article] [PubMed]
  • Balendiran K, Bonventre J, Knott R, Jack W, Benner J, Schildkraut I, Anderson JE. Expression, purification, and crystallization of restriction endonuclease PvuII with DNA containing its recognition site. Proteins. 1994 May;19(1):77–79. [PubMed]
  • Blumenthal RM, Gregory SA, Cooperider JS. Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. J Bacteriol. 1985 Nov;164(2):501–509. [PMC free article] [PubMed]
  • Butkus V, Klimasauskas S, Petrauskiene L, Maneliene Z, Lebionka A, Janulaitis A. Interaction of AluI, Cfr6I and PvuII restriction-modification enzymes with substrates containing either N4-methylcytosine or 5-methylcytosine. Biochim Biophys Acta. 1987 Aug 25;909(3):201–207. [PubMed]
  • Chen DF, Liu QA, Chen XW, Zhao XL, Chen YW. The inhibition of restriction endonuclease PvuII cleavage activity by methylation outside its recognition sequence. Nucleic Acids Res. 1991 Oct 25;19(20):5703–5705. [PMC free article] [PubMed]
  • Gingeras TR, Greenough L, Schildkraut I, Roberts RJ. Two new restriction endonucleases from Proteus vulgaris. Nucleic Acids Res. 1981 Sep 25;9(18):4525–4536. [PMC free article] [PubMed]
  • Jack WE, Terry BJ, Modrich P. Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence. Proc Natl Acad Sci U S A. 1982 Jul;79(13):4010–4014. [PMC free article] [PubMed]
  • Jeltsch A, Alves J, Maass G, Pingoud A. On the catalytic mechanism of EcoRI and EcoRV. A detailed proposal based on biochemical results, structural data and molecular modelling. FEBS Lett. 1992 Jun 8;304(1):4–8. [PubMed]
  • Jeltsch A, Alves J, Wolfes H, Maass G, Pingoud A. Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes. Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8499–8503. [PMC free article] [PubMed]
  • Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. [PubMed]
  • Kim SH. Beta ribbon: a new DNA recognition motif. Science. 1992 Mar 6;255(5049):1217–1218. [PubMed]
  • Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM. Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. Science. 1990 Sep 14;249(4974):1307–1309. [PubMed]
  • Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature. 1994 Apr 14;368(6472):660–664. [PubMed]
  • Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK. Structure of restriction endonuclease bamhi phased at 1.95 A resolution by MAD analysis. Structure. 1994 May 15;2(5):439–452. [PubMed]
  • Park YW, Breslauer KJ. A spectroscopic and calorimetric study of the melting behaviors of a "bent" and a "normal" DNA duplex: [d(GA4T4C)]2 versus [d(GT4A4C)]2. Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1551–1555. [PMC free article] [PubMed]
  • Raumann BE, Rould MA, Pabo CO, Sauer RT. DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature. 1994 Feb 24;367(6465):754–757. [PubMed]
  • Selent U, Rüter T, Köhler E, Liedtke M, Thielking V, Alves J, Oelgeschläger T, Wolfes H, Peters F, Pingoud A. A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV. Biochemistry. 1992 May 26;31(20):4808–4815. [PubMed]
  • Somers WS, Phillips SE. Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands. Nature. 1992 Oct 1;359(6394):387–393. [PubMed]
  • Tao T, Blumenthal RM. Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. J Bacteriol. 1992 May;174(10):3395–3398. [PMC free article] [PubMed]
  • Tao T, Walter J, Brennan KJ, Cotterman MM, Blumenthal RM. Sequence, internal homology and high-level expression of the gene for a DNA-(cytosine N4)-methyltransferase, M.Pvu II. Nucleic Acids Res. 1989 Jun 12;17(11):4161–4175. [PMC free article] [PubMed]
  • Terry BJ, Jack WE, Modrich P. Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis. J Biol Chem. 1985 Oct 25;260(24):13130–13137. [PubMed]
  • Wang BC. Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 1985;115:90–112. [PubMed]
  • Wilson GG, Murray NE. Restriction and modification systems. Annu Rev Genet. 1991;25:585–627. [PubMed]
  • Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 1993 May;12(5):1781–1795. [PMC free article] [PubMed]

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