메뉴 건너뛰기




Volumn 21, Issue 10, 2013, Pages 1848-1858

Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; DNA;

EID: 84885411813     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.08.012     Document Type: Article
Times cited : (21)

References (57)
  • 2
    • 44949289693 scopus 로고
    • Crystallization of DNA binding proteins with oligodeoxynucleotides
    • A.K. Aggarwal Crystallization of DNA binding proteins with oligodeoxynucleotides Methods 1 1990 83 90
    • (1990) Methods , vol.1 , pp. 83-90
    • Aggarwal, A.K.1
  • 3
    • 41749092312 scopus 로고    scopus 로고
    • Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
    • S. An, R. Kumar, E.D. Sheets, and S.J. Benkovic Reversible compartmentalization of de novo purine biosynthetic complexes in living cells Science 320 2008 103 106
    • (2008) Science , vol.320 , pp. 103-106
    • An, S.1    Kumar, R.2    Sheets, E.D.3    Benkovic, S.J.4
  • 6
    • 0033579567 scopus 로고    scopus 로고
    • Reactions of type II restriction endonucleases with 8-base pair recognition sites
    • D.T. Bilcock, L.E. Daniels, A.J. Bath, and S.E. Halford Reactions of type II restriction endonucleases with 8-base pair recognition sites J. Biol. Chem. 274 1999 36379 36386
    • (1999) J. Biol. Chem. , vol.274 , pp. 36379-36386
    • Bilcock, D.T.1    Daniels, L.E.2    Bath, A.J.3    Halford, S.E.4
  • 8
    • 0037022273 scopus 로고    scopus 로고
    • Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease
    • J. Bitinaite, and I. Schildkraut Self-generated DNA termini relax the specificity of SgrAI restriction endonuclease Proc. Natl. Acad. Sci. USA 99 2002 1164 1169
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1164-1169
    • Bitinaite, J.1    Schildkraut, I.2
  • 9
    • 0034646614 scopus 로고    scopus 로고
    • Bimodal activation of acetyl-CoA carboxylase by glutamate
    • A.N. Boone, A. Chan, J.E. Kulpa, and R.W. Brownsey Bimodal activation of acetyl-CoA carboxylase by glutamate J. Biol. Chem. 275 2000 10819 10825
    • (2000) J. Biol. Chem. , vol.275 , pp. 10819-10825
    • Boone, A.N.1    Chan, A.2    Kulpa, J.E.3    Brownsey, R.W.4
  • 12
    • 0026346185 scopus 로고
    • Gel retardation
    • J. Carey Gel retardation Methods Enzymol. 208 1991 103 117
    • (1991) Methods Enzymol. , vol.208 , pp. 103-117
    • Carey, J.1
  • 13
    • 44349162159 scopus 로고    scopus 로고
    • Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures
    • Z. Chen, H. Yang, and N.P. Pavletich Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures Nature 453 2008 489 494
    • (2008) Nature , vol.453 , pp. 489-494
    • Chen, Z.1    Yang, H.2    Pavletich, N.P.3
  • 14
    • 0037470637 scopus 로고    scopus 로고
    • Subunit assembly for DNA cleavage by restriction endonuclease SgrAI
    • L.E. Daniels, K.M. Wood, D.J. Scott, and S.E. Halford Subunit assembly for DNA cleavage by restriction endonuclease SgrAI J. Mol. Biol. 327 2003 579 591
    • (2003) J. Mol. Biol. , vol.327 , pp. 579-591
    • Daniels, L.E.1    Wood, K.M.2    Scott, D.J.3    Halford, S.E.4
  • 17
    • 0029975088 scopus 로고    scopus 로고
    • SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields
    • J. Frank, M. Radermacher, P. Penczek, J. Zhu, Y. Li, M. Ladjadj, and A. Leith SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields J. Struct. Biol. 116 1996 190 199
    • (1996) J. Struct. Biol. , vol.116 , pp. 190-199
    • Frank, J.1    Radermacher, M.2    Penczek, P.3    Zhu, J.4    Li, Y.5    Ladjadj, M.6    Leith, A.7
  • 18
    • 33845348200 scopus 로고    scopus 로고
    • FREALIGN: High-resolution refinement of single particle structures
    • N. Grigorieff FREALIGN: high-resolution refinement of single particle structures J. Struct. Biol. 157 2007 117 125
    • (2007) J. Struct. Biol. , vol.157 , pp. 117-125
    • Grigorieff, N.1
  • 19
    • 0141959260 scopus 로고    scopus 로고
    • Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targets
    • K. Hingorani-Varma, and J. Bitinaite Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targets J. Biol. Chem. 278 2003 40392 40399
    • (2003) J. Biol. Chem. , vol.278 , pp. 40392-40399
    • Hingorani-Varma, K.1    Bitinaite, J.2
  • 23
    • 69249088090 scopus 로고    scopus 로고
    • Structural plasticity in actin and tubulin polymer dynamics
    • H.Y. Kueh, and T.J. Mitchison Structural plasticity in actin and tubulin polymer dynamics Science 325 2009 960 963
    • (2009) Science , vol.325 , pp. 960-963
    • Kueh, H.Y.1    Mitchison, T.J.2
  • 25
    • 78651061215 scopus 로고    scopus 로고
    • New clues in the allosteric activation of DNA cleavage by SgrAI: Structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA
    • E.J. Little, P.W. Dunten, J. Bitinaite, and N.C. Horton New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA Acta Crystallogr. D Biol. Crystallogr. 67 2011 67 74
    • (2011) Acta Crystallogr. D Biol. Crystallogr. , vol.67 , pp. 67-74
    • Little, E.J.1    Dunten, P.W.2    Bitinaite, J.3    Horton, N.C.4
  • 27
    • 84879520123 scopus 로고    scopus 로고
    • Structural analysis of activated SgrAI-DNA oligomers using ion mobility mass spectrometry
    • X. Ma, S. Shah, M. Zhou, C.K. Park, V.H. Wysocki, and N.C. Horton Structural analysis of activated SgrAI-DNA oligomers using ion mobility mass spectrometry Biochemistry 52 2013 4373 4381
    • (2013) Biochemistry , vol.52 , pp. 4373-4381
    • Ma, X.1    Shah, S.2    Zhou, M.3    Park, C.K.4    Wysocki, V.H.5    Horton, N.C.6
  • 29
    • 77955906574 scopus 로고    scopus 로고
    • Identification of novel filament-forming proteins in Saccharomyces cerevisiae and Drosophila melanogaster
    • C. Noree, B.K. Sato, R.M. Broyer, and J.E. Wilhelm Identification of novel filament-forming proteins in Saccharomyces cerevisiae and Drosophila melanogaster J. Cell Biol. 190 2010 541 551
    • (2010) J. Cell Biol. , vol.190 , pp. 541-551
    • Noree, C.1    Sato, B.K.2    Broyer, R.M.3    Wilhelm, J.E.4
  • 32
    • 77957240284 scopus 로고    scopus 로고
    • DNA curvature and flexibility in vitro and in vivo
    • J.P. Peters 3rd, and L.J. Maher DNA curvature and flexibility in vitro and in vivo Q. Rev. Biophys. 43 2010 23 63
    • (2010) Q. Rev. Biophys. , vol.43 , pp. 23-63
    • Peters III, J.P.1    Maher, L.J.2
  • 34
    • 0030911133 scopus 로고    scopus 로고
    • Recognition and cleavage of DNA by type-II restriction endonucleases
    • A. Pingoud, and A. Jeltsch Recognition and cleavage of DNA by type-II restriction endonucleases Eur. J. Biochem. 246 1997 1 22
    • (1997) Eur. J. Biochem. , vol.246 , pp. 1-22
    • Pingoud, A.1    Jeltsch, A.2
  • 35
    • 0035883723 scopus 로고    scopus 로고
    • Structure and function of type II restriction endonucleases
    • A. Pingoud, and A. Jeltsch Structure and function of type II restriction endonucleases Nucleic Acids Res. 29 2001 3705 3727
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3705-3727
    • Pingoud, A.1    Jeltsch, A.2
  • 37
    • 77952581453 scopus 로고    scopus 로고
    • Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
    • G.D. Pintilie, J. Zhang, T.D. Goddard, W. Chiu, and D.C. Gossard Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions J. Struct. Biol. 170 2010 427 438
    • (2010) J. Struct. Biol. , vol.170 , pp. 427-438
    • Pintilie, G.D.1    Zhang, J.2    Goddard, T.D.3    Chiu, W.4    Gossard, D.C.5
  • 38
    • 0023460924 scopus 로고
    • NotI and SfiI: Restriction endonucleases with octanucleotide recognition sequences
    • B.Q. Qiang, and I. Schildkraut NotI and SfiI: restriction endonucleases with octanucleotide recognition sequences Methods Enzymol. 155 1987 15 21
    • (1987) Methods Enzymol. , vol.155 , pp. 15-21
    • Qiang, B.Q.1    Schildkraut, I.2
  • 39
    • 0022605670 scopus 로고
    • A new 3-D reconstruction scheme applied to the 50S ribosomal subunit of E coli
    • M. Radermacher, T. Wagenknecht, A. Verschoor, and J. Frank A new 3-D reconstruction scheme applied to the 50S ribosomal subunit of E. coli J. Microsc. 141 1986 RP1 RP2
    • (1986) J. Microsc. , vol.141
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 40
    • 84985231782 scopus 로고
    • Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli
    • M. Radermacher, T. Wagenknecht, A. Verschoor, and J. Frank Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli J. Microsc. 146 1987 113 136
    • (1987) J. Microsc. , vol.146 , pp. 113-136
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 41
    • 75549086595 scopus 로고    scopus 로고
    • REBASE - A database for DNA restriction and modification: Enzymes, genes and genomes
    • R.J. Roberts, T. Vincze, J. Posfai, and D. Macelis REBASE - a database for DNA restriction and modification: enzymes, genes and genomes Nucleic Acids Res. 38 Database issue 2010 D234 D236
    • (2010) Nucleic Acids Res. , vol.38 , Issue.DATABASE ISSUE
    • Roberts, R.J.1    Vincze, T.2    Posfai, J.3    Macelis, D.4
  • 42
    • 0346816491 scopus 로고    scopus 로고
    • FindEM - A fast, efficient program for automatic selection of particles from electron micrographs
    • A.M. Roseman FindEM - a fast, efficient program for automatic selection of particles from electron micrographs J. Struct. Biol. 145 2004 91 99
    • (2004) J. Struct. Biol. , vol.145 , pp. 91-99
    • Roseman, A.M.1
  • 43
    • 34447649588 scopus 로고    scopus 로고
    • High-resolution electron microscopy of helical specimens: A fresh look at tobacco mosaic virus
    • C. Sachse, J.Z. Chen, P.D. Coureux, M.E. Stroupe, M. Fändrich, and N. Grigorieff High-resolution electron microscopy of helical specimens: a fresh look at tobacco mosaic virus J. Mol. Biol. 371 2007 812 835
    • (2007) J. Mol. Biol. , vol.371 , pp. 812-835
    • Sachse, C.1    Chen, J.Z.2    Coureux, P.D.3    Stroupe, M.E.4    Fändrich, M.5    Grigorieff, N.6
  • 44
    • 0033580685 scopus 로고    scopus 로고
    • Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease
    • M.D. Sam, and J.J. Perona Catalytic roles of divalent metal ions in phosphoryl transfer by EcoRV endonuclease Biochemistry 38 1999 6576 6586
    • (1999) Biochemistry , vol.38 , pp. 6576-6586
    • Sam, M.D.1    Perona, J.J.2
  • 45
    • 36749078686 scopus 로고    scopus 로고
    • Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution
    • G.F. Schröder, A.T. Brunger, and M. Levitt Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution Structure 15 2007 1630 1641
    • (2007) Structure , vol.15 , pp. 1630-1641
    • Schröder, G.F.1    Brunger, A.T.2    Levitt, M.3
  • 47
    • 78650045540 scopus 로고    scopus 로고
    • The phage-host arms race: Shaping the evolution of microbes
    • A. Stern, and R. Sorek The phage-host arms race: shaping the evolution of microbes Bioessays 33 2011 43 51
    • (2011) Bioessays , vol.33 , pp. 43-51
    • Stern, A.1    Sorek, R.2
  • 48
    • 8844219659 scopus 로고    scopus 로고
    • Noise bias in the refinement of structures derived from single particles
    • A. Stewart, and N. Grigorieff Noise bias in the refinement of structures derived from single particles Ultramicroscopy 102 2004 67 84
    • (2004) Ultramicroscopy , vol.102 , pp. 67-84
    • Stewart, A.1    Grigorieff, N.2
  • 50
    • 0025375042 scopus 로고
    • SgrAI, a novel class-II restriction endonuclease from Streptomyces griseus recognizing the octanucleotide sequence 5′-CR/CCGGYG-3′ [corrected]
    • N. Tautz, K. Kaluza, B. Frey, M. Jarsch, G.G. Schmitz, and C. Kessler SgrAI, a novel class-II restriction endonuclease from Streptomyces griseus recognizing the octanucleotide sequence 5′-CR/CCGGYG-3′ [corrected] Nucleic Acids Res. 18 1990 3087
    • (1990) Nucleic Acids Res. , vol.18 , pp. 3087
    • Tautz, N.1    Kaluza, K.2    Frey, B.3    Jarsch, M.4    Schmitz, G.G.5    Kessler, C.6
  • 51
    • 0011139817 scopus 로고
    • Studies on the mechnism of activation of acetyl coenzyme A carboxylase by citrate
    • P.R. Vagelos, A.W. Alberts, and D.B. Martin Studies on the mechnism of activation of acetyl coenzyme A carboxylase by citrate J. Biol. Chem. 238 1963 533 540
    • (1963) J. Biol. Chem. , vol.238 , pp. 533-540
    • Vagelos, P.R.1    Alberts, A.W.2    Martin, D.B.3
  • 53
    • 63649113687 scopus 로고    scopus 로고
    • DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy
    • N.R. Voss, C.K. Yoshioka, M. Radermacher, C.S. Potter, and B. Carragher DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy J. Struct. Biol. 166 2009 205 213
    • (2009) J. Struct. Biol. , vol.166 , pp. 205-213
    • Voss, N.R.1    Yoshioka, C.K.2    Radermacher, M.3    Potter, C.S.4    Carragher, B.5
  • 56
    • 20444368444 scopus 로고    scopus 로고
    • Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI
    • K.M. Wood, L.E. Daniels, and S.E. Halford Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI J. Mol. Biol. 350 2005 240 253
    • (2005) J. Mol. Biol. , vol.350 , pp. 240-253
    • Wood, K.M.1    Daniels, L.E.2    Halford, S.E.3
  • 57
    • 84863011784 scopus 로고    scopus 로고
    • Iterative stable alignment and clustering of 2D transmission electron microscope images
    • Z. Yang, J. Fang, J. Chittuluru, F.J. Asturias, and P.A. Penczek Iterative stable alignment and clustering of 2D transmission electron microscope images Structure 20 2012 237 247
    • (2012) Structure , vol.20 , pp. 237-247
    • Yang, Z.1    Fang, J.2    Chittuluru, J.3    Asturias, F.J.4    Penczek, P.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.