메뉴 건너뛰기




Volumn 81, Issue 3, 2005, Pages 183-207

Imperfect DNA mirror repeats in E. coli TnsA and other protein-coding DNA

Author keywords

DNA pattern; Mirror repeat; Molecular evolution; Secondary structure; Symmetric repeat; TnsA

Indexed keywords

AMINO ACID; DINUCLEOTIDE; NUCLEOTIDE; REPETITIVE DNA;

EID: 23644448241     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2005.03.004     Document Type: Article
Times cited : (6)

References (63)
  • 1
    • 0025879626 scopus 로고
    • Isolation and characterization of two human H1 histone genes within clusters of core histone genes
    • W. Albig, E. Kardalinou, B. Drabent, A. Zimmer, and D. Doenecke Isolation and characterization of two human H1 histone genes within clusters of core histone genes Genomics 10 1991 940 948
    • (1991) Genomics , vol.10 , pp. 940-948
    • Albig, W.1    Kardalinou, E.2    Drabent, B.3    Zimmer, A.4    Doenecke, D.5
  • 2
    • 0025836710 scopus 로고
    • Purification of TnsB, a transposition protein that binds to the ends of Tn7*
    • L.K. Arciszewska, R.L. McKown, and N.L. Craig Purification of TnsB, a transposition protein that binds to the ends of Tn7* J. Biol. Chem. 266 1991 21736 21744
    • (1991) J. Biol. Chem. , vol.266 , pp. 21736-21744
    • Arciszewska, L.K.1    McKown, R.L.2    Craig, N.L.3
  • 3
    • 0027416674 scopus 로고
    • Tn7 transposition: Target DNA recognition is mediated by multiple Tn7-encoded proteins in a purified in vitro system
    • R.J. Bainton, K.M. Kubo, J.N. Feng, and N.L. Craig Tn7 transposition: target DNA recognition is mediated by multiple Tn7-encoded proteins in a purified in vitro system Cell 72 1993 931 943
    • (1993) Cell , vol.72 , pp. 931-943
    • Bainton, R.J.1    Kubo, K.M.2    Feng, J.N.3    Craig, N.L.4
  • 8
    • 0026088263 scopus 로고
    • Tn7: A target site-specific transposon
    • N.L. Craig Tn7: a target site-specific transposon Mol. Microbiol. 5 1991 2569 2573
    • (1991) Mol. Microbiol. , vol.5 , pp. 2569-2573
    • Craig, N.L.1
  • 10
    • 0037180452 scopus 로고    scopus 로고
    • Structure of factor-inhibiting hypoxia-inducible factor 1: An asparaginyl hydroxylase involved in the hypoxic response pathway
    • C.E. Dann III, R.K. Bruick, and J. Deisenhofer Structure of factor-inhibiting hypoxia-inducible factor 1: an asparaginyl hydroxylase involved in the hypoxic response pathway Proc. Natl. Acad. Sci. USA 99 2002 15351 15356
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 15351-15356
    • Dann III, C.E.1    Bruick, R.K.2    Deisenhofer, J.3
  • 11
    • 0025230372 scopus 로고
    • Characterization of four novel ras-like genes expressed in a human teratocarcinoma cell line
    • G.T. Drivas, A. Shih, E. Coutavas, M.G. Rush, and P. D'Eustachio Characterization of four novel ras-like genes expressed in a human teratocarcinoma cell line Mol. Cell. Biol. 10 1990 1793 1798
    • (1990) Mol. Cell. Biol. , vol.10 , pp. 1793-1798
    • Drivas, G.T.1    Shih, A.2    Coutavas, E.3    Rush, M.G.4    D'Eustachio, P.5
  • 12
    • 0025894942 scopus 로고
    • A new human p34 protein kinase, CDK2, identified by complementation of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of Xenopus Eg1
    • S.J. Elledge, and M.R. Spottswood A new human p34 protein kinase, CDK2, identified by complementation of a cdc28 mutation in Saccharomyces cerevisiae, is a homolog of Xenopus Eg1 EMBO J. 10 1991 2653 2659
    • (1991) EMBO J. , vol.10 , pp. 2653-2659
    • Elledge, S.J.1    Spottswood, M.R.2
  • 14
    • 0027973061 scopus 로고
    • CPP32, a novel human apoptotic protein with homology to Caenorhabditis elegans cell death protein Ced-3 and mammalian interleukin-1 b-converting enzyme
    • T. Fernandes-Alnemri, G. Litwack, and E.S. Alnemri CPP32, a novel human apoptotic protein with homology to Caenorhabditis elegans cell death protein Ced-3 and mammalian interleukin-1 b-converting enzyme J. Biol. Chem. 269 1994 30761 30764
    • (1994) J. Biol. Chem. , vol.269 , pp. 30761-30764
    • Fernandes-Alnemri, T.1    Litwack, G.2    Alnemri, E.S.3
  • 15
    • 0025909444 scopus 로고
    • High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution
    • J.D. Forman-Kay, G.M. Clore, P.T. Wingfield, and A.M. Gronenborn High-resolution three-dimensional structure of reduced recombinant human thioredoxin in solution Biochemistry 30 1991 2685 2698
    • (1991) Biochemistry , vol.30 , pp. 2685-2698
    • Forman-Kay, J.D.1    Clore, G.M.2    Wingfield, P.T.3    Gronenborn, A.M.4
  • 17
    • 0035049521 scopus 로고    scopus 로고
    • Genome-scale compositional comparisons in eukaryotes
    • A.J. Gentles, and S. Karlin Genome-scale compositional comparisons in eukaryotes Genome Res. 11 2001 540 546
    • (2001) Genome Res. , vol.11 , pp. 540-546
    • Gentles, A.J.1    Karlin, S.2
  • 19
    • 0033634859 scopus 로고    scopus 로고
    • Unexpected structural diversity in DNA recombination: The restriction endonuclease connection
    • A.B. Hickman, Y. Li, S.V. Mathew, E.W. May, N.L. Craig, and F. Dyda Unexpected structural diversity in DNA recombination: the restriction endonuclease connection Mol. Cell. 5 2000 1025 1034
    • (2000) Mol. Cell. , vol.5 , pp. 1025-1034
    • Hickman, A.B.1    Li, Y.2    Mathew, S.V.3    May, E.W.4    Craig, N.L.5    Dyda, F.6
  • 21
    • 0031454750 scopus 로고    scopus 로고
    • A flavodoxin that is required for enzyme activation: The structure of oxidized flavodoxin from Escherichia coli at 1.8 a resolution
    • D.M. Hoover, and M.L. Ludwig A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Escherichia coli at 1.8 A resolution Protein Sci. 6 1997 2525 2537
    • (1997) Protein Sci. , vol.6 , pp. 2525-2537
    • Hoover, D.M.1    Ludwig, M.L.2
  • 22
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF - A program to identify and analyze structural motifs in proteins
    • E.G. Hutchinson, and J.M. Thornton PROMOTIF - a program to identify and analyze structural motifs in proteins Protein Sci. 5 1996 212 220
    • (1996) Protein Sci. , vol.5 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 23
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 24
    • 0035865136 scopus 로고    scopus 로고
    • Target DNA structure plays a critical role in Tn7 transposition
    • P.N. Kuduvalli, J.E. Rao, and N.L. Craig Target DNA structure plays a critical role in Tn7 transposition EMBO J. 20 2001 924 932
    • (2001) EMBO J. , vol.20 , pp. 924-932
    • Kuduvalli, P.N.1    Rao, J.E.2    Craig, N.L.3
  • 25
    • 0033614841 scopus 로고    scopus 로고
    • Binding of cardiac Troponin-I 147-163 induces a structural opening in human cardiac Troponin C
    • M.X. Li, L. Spyracopoulos, and B.D. Sykes Binding of cardiac Troponin-I 147-163 induces a structural opening in human cardiac Troponin C Biochemistry 38 1999 8289 8298
    • (1999) Biochemistry , vol.38 , pp. 8289-8298
    • Li, M.X.1    Spyracopoulos, L.2    Sykes, B.D.3
  • 27
    • 0034600960 scopus 로고    scopus 로고
    • Isolation and characterization of Tn7 transposase gain-of-function mutants: A model for transposase activation
    • F. Lu, and N.L. Craig Isolation and characterization of Tn7 transposase gain-of-function mutants: a model for transposase activation EMBO J. 19 2000 3446 3457
    • (2000) EMBO J. , vol.19 , pp. 3446-3457
    • Lu, F.1    Craig, N.L.2
  • 28
    • 0029984672 scopus 로고    scopus 로고
    • Switching from cut-and-paste to replicative Tn7 transposition
    • E.W. May, and N.L. Craig Switching from cut-and-paste to replicative Tn7 transposition Science 272 1996 401 404
    • (1996) Science , vol.272 , pp. 401-404
    • May, E.W.1    Craig, N.L.2
  • 29
    • 0035887011 scopus 로고    scopus 로고
    • FIH-1: A novel protein that interacts with HIF-1alpha and VHL to mediate repression of HIF-1 transcriptional activity
    • P.C. Mahon, K. Hirota, and G.L. Semenza FIH-1: a novel protein that interacts with HIF-1alpha and VHL to mediate repression of HIF-1 transcriptional activity Genes Dev. 15 2001 2675 2686
    • (2001) Genes Dev. , vol.15 , pp. 2675-2686
    • Mahon, P.C.1    Hirota, K.2    Semenza, G.L.3
  • 31
    • 0025009803 scopus 로고
    • Molecular cloning and expression of a G25K cDNA, the human homolog of the yeast cell cycle gene CDC42
    • S. Munemitsu, M.A. Innis, R. Clark, F. McCormick, A. Ullrich, and P. Polakis Molecular cloning and expression of a G25K cDNA, the human homolog of the yeast cell cycle gene CDC42 Mol. Cell. Biol. 10 1990 5977 5982
    • (1990) Mol. Cell. Biol. , vol.10 , pp. 5977-5982
    • Munemitsu, S.1    Innis, M.A.2    Clark, R.3    McCormick, F.4    Ullrich, A.5    Polakis, P.6
  • 32
    • 0032582395 scopus 로고    scopus 로고
    • Genes from nine genomes are separated into their organisms in the dinucleotide composition space
    • H. Nakashima, M. Ota, K. Nishikawa, and T. Ooi Genes from nine genomes are separated into their organisms in the dinucleotide composition space DNA Res. 5 1998 251 259
    • (1998) DNA Res. , vol.5 , pp. 251-259
    • Nakashima, H.1    Ota, M.2    Nishikawa, K.3    Ooi, T.4
  • 33
    • 0024818401 scopus 로고
    • Direct expression cloning of vascular cell adhesion molecule 1, a cytokine-induced endothelial protein that binds to lymphocytes
    • L. Osborn, C. Hession, R. Tizard, C. Vassallo, S. Luhowskyj, G. Chi-Rosso, and R. Lobb Direct expression cloning of vascular cell adhesion molecule 1, a cytokine-induced endothelial protein that binds to lymphocytes Cell 59 1989 1203 1211
    • (1989) Cell , vol.59 , pp. 1203-1211
    • Osborn, L.1    Hession, C.2    Tizard, R.3    Vassallo, C.4    Luhowskyj, S.5    Chi-Rosso, G.6    Lobb, R.7
  • 34
    • 0026099830 scopus 로고
    • Isolation, cloning, mapping, and nucleotide sequencing of the gene encoding flavodoxin in Escherichia coli
    • C. Osborne, L.M. Chen, and R.G. Matthews Isolation, cloning, mapping, and nucleotide sequencing of the gene encoding flavodoxin in Escherichia coli J. Bacteriol. 173 1991 1729 1737
    • (1991) J. Bacteriol. , vol.173 , pp. 1729-1737
    • Osborne, C.1    Chen, L.M.2    Matthews, R.G.3
  • 35
    • 0034636031 scopus 로고    scopus 로고
    • Recognition of triple-helical DNA structures by transposon Tn7
    • J.E. Rao, P.S. Miller, and N.L. Craig Recognition of triple-helical DNA structures by transposon Tn7 Proc. Natl. Acad. Sci. USA 97 2000 3936 3941
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 3936-3941
    • Rao, J.E.1    Miller, P.S.2    Craig, N.L.3
  • 36
    • 0035909889 scopus 로고    scopus 로고
    • Structural basis for the activation of human procaspase-7
    • S. Riedl, W. Bode, and P. Fuentes-Prior Structural basis for the activation of human procaspase-7 Proc. Natl. Acad. Sci. USA 98 2001 14790 14795
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 14790-14795
    • Riedl, S.1    Bode, W.2    Fuentes-Prior, P.3
  • 37
  • 39
    • 0029858349 scopus 로고    scopus 로고
    • The Tn7 transposase is a heteromeric complex in which DNA breakage and joining activities are distributed between different gene products
    • R.J. Sarnovsky, E.W. May, and N.L. Craig The Tn7 transposase is a heteromeric complex in which DNA breakage and joining activities are distributed between different gene products EMBO J. 15 1996 6348 6361
    • (1996) EMBO J. , vol.15 , pp. 6348-6361
    • Sarnovsky, R.J.1    May, E.W.2    Craig, N.L.3
  • 40
    • 0025372878 scopus 로고
    • Human arylsulfatase B: MOPAC cloning, nucleotide sequence of a full-length cDNA, and regions of amino acid identity with arylsulfatases a and C
    • E.H. Schuchman, C.E. Jackson, and R.J. Desnick Human arylsulfatase B: MOPAC cloning, nucleotide sequence of a full-length cDNA, and regions of amino acid identity with arylsulfatases A and C Genomics 6 1990 149 158
    • (1990) Genomics , vol.6 , pp. 149-158
    • Schuchman, E.H.1    Jackson, C.E.2    Desnick, R.J.3
  • 41
    • 0035910277 scopus 로고    scopus 로고
    • Analysis of gain-of-function mutants of an ATP-dependent regulator of Tn7 transposition
    • A.E. Stellwagen, and N.L. Craig Analysis of gain-of-function mutants of an ATP-dependent regulator of Tn7 transposition J. Mol. Biol. 305 2001 633 642
    • (2001) J. Mol. Biol. , vol.305 , pp. 633-642
    • Stellwagen, A.E.1    Craig, N.L.2
  • 42
    • 0032429191 scopus 로고    scopus 로고
    • Mobile DNA elements: Controlling transposition with ATP-dependent molecular switches
    • A.E. Stellwagen, and N.L. Craig Mobile DNA elements: controlling transposition with ATP-dependent molecular switches Trends Biochem. Sci. 23 1998 486 490
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 486-490
    • Stellwagen, A.E.1    Craig, N.L.2
  • 43
    • 0031017325 scopus 로고    scopus 로고
    • Gain-of-function mutations in TnsC, an ATP-dependent transposition protein that activates the bacterial transposon Tn7
    • A.E. Stellwagen, and N.L. Craig Gain-of-function mutations in TnsC, an ATP-dependent transposition protein that activates the bacterial transposon Tn7 Genetics 145 1997 573 585
    • (1997) Genetics , vol.145 , pp. 573-585
    • Stellwagen, A.E.1    Craig, N.L.2
  • 45
    • 0033664380 scopus 로고    scopus 로고
    • Crystal structure of a nucleosome core particle containing the variant histone H2A
    • R.K. Suto, M.J. Clarkson, D.J. Tremethick, and K. Luger Crystal structure of a nucleosome core particle containing the variant histone H2A Nat. Struct. Biol. 7 2000 1121 1124
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 1121-1124
    • Suto, R.K.1    Clarkson, M.J.2    Tremethick, D.J.3    Luger, K.4
  • 46
    • 0035889693 scopus 로고    scopus 로고
    • Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein
    • K. Takano, Y. Yamagata, and K. Yutani Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein Proteins: Struct., Funct., Genet. 45 2001 274 280
    • (2001) Proteins: Struct., Funct., Genet. , vol.45 , pp. 274-280
    • Takano, K.1    Yamagata, Y.2    Yutani, K.3
  • 47
    • 0033612390 scopus 로고    scopus 로고
    • Structural view of the Ran-Importin b interaction at 2.3 a resolution
    • I.R. Vetter, A. Arndt, U. Kutay, D. Gorlich, and A. Wittinghofer Structural view of the Ran-Importin b interaction at 2.3 A resolution Cell 97 1999 635 646
    • (1999) Cell , vol.97 , pp. 635-646
    • Vetter, I.R.1    Arndt, A.2    Kutay, U.3    Gorlich, D.4    Wittinghofer, A.5
  • 48
    • 0025673701 scopus 로고
    • Hot spots for growth hormone gene deletions in homologous regions outside of Alu repeats
    • C.L. Vnencak-Jones, and J.A. Phillips III Hot spots for growth hormone gene deletions in homologous regions outside of Alu repeats Science 250 1990 1745 1748
    • (1990) Science , vol.250 , pp. 1745-1748
    • Vnencak-Jones, C.L.1    Phillips III, J.A.2
  • 49
    • 0029046132 scopus 로고
    • The crystal structure of an N-terminal two-domain fragment of vascular cell adhesion molecule 1 (VCAM-1): A cyclic peptide based on the domain 1 C-D loop can inhibit VCAM-1-a 4 integrin interaction
    • J.H. Wang, R.B. Pepinsky, T. Stehle, J.H. Liu, M. Karpusas, B. Browning, and L. Osborn The crystal structure of an N-terminal two-domain fragment of vascular cell adhesion molecule 1 (VCAM-1): a cyclic peptide based on the domain 1 C-D loop can inhibit VCAM-1-a 4 integrin interaction Proc. Natl. Acad. Sci. USA 92 1995 5714 5718
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 5714-5718
    • Wang, J.H.1    Pepinsky, R.B.2    Stehle, T.3    Liu, J.H.4    Karpusas, M.5    Browning, B.6    Osborn, L.7
  • 50
    • 0037462647 scopus 로고    scopus 로고
    • Structural consequences of a cancer-causing BRCA1-BRCT missense mutation
    • R.S. Williams, and J.N. Glover Structural consequences of a cancer-causing BRCA1-BRCT missense mutation J. Biol. Chem. 278 2003 2630 2635
    • (2003) J. Biol. Chem. , vol.278 , pp. 2630-2635
    • Williams, R.S.1    Glover, J.N.2
  • 53
    • 85194564393 scopus 로고    scopus 로고
    • BLAST search
    • BLAST search, http://www.ncbi.nlm.nih.gov:80/BLAST/.
  • 54
    • 85194544654 scopus 로고    scopus 로고
    • Cn3D
    • Cn3D, http://www.ncbi.nlm.nih.gov:80/Structure/CN3D/cn3d.shtml.
  • 55
    • 85194548368 scopus 로고    scopus 로고
    • ELM server
    • ELM server, http://elm.eu.org/.
  • 56
    • 85194534833 scopus 로고    scopus 로고
    • ENTREZ STRUCTURE
    • ENTREZ STRUCTURE, http://www.ncbi.nih.gov/Entrez/query.fcgi?db=Structure.
  • 57
    • 85194573233 scopus 로고    scopus 로고
    • GENBANK
    • GENBANK, http://www.ncbi.nih.gov/Entrez.
  • 58
    • 85194558308 scopus 로고    scopus 로고
    • IFA SERVICES, Institute of Phonetic Sciences, University of Amsterdam.Wilcoxon test.
    • IFA SERVICES, Institute of Phonetic Sciences, University of Amsterdam.Wilcoxon test. http://www.fon.hum.uva.nl/Service/Statistics/ Signed_Rank_Test.html.
  • 59
    • 85194541922 scopus 로고    scopus 로고
    • NCBI structure database
    • NCBI structure database, http://www.ncbi.nlm.nih.gov:80/entrez/query. fcgi?db=Structure.
  • 60
    • 85194561298 scopus 로고    scopus 로고
    • PIR HMM Domain/Motif Search
    • PIR HMM Domain/Motif Search, http://pir.georgetown.edu/pirwww/search/ pirhmm.html.
  • 61
    • 85194548631 scopus 로고    scopus 로고
    • PROMOTIF, see Hutchinson and Thornton, 1996.
    • PROMOTIF, see Hutchinson and Thornton, 1996.
  • 62
    • 85194560076 scopus 로고    scopus 로고
    • PROSITE
    • PROSITE, http://us.expasy.org/prosite/.
  • 63
    • 85194557851 scopus 로고    scopus 로고
    • PROTEIN DATA BANK (PDB), Brookhaven National Laboratory PDB see Bernstein et al., 1977.
    • PROTEIN DATA BANK (PDB), http://www.rcsb.org/pdb/index.html. Brookhaven National Laboratory PDB see Bernstein et al., 1977.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.