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Volumn 51, Issue 13, 2012, Pages 2899-2910

Structural studies of E73 from a hyperthermophilic archaeal virus identify the "rH3" domain, an elaborated ribbon-helix-helix motif involved in DNA recognition

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL; BOND VECTORS; DNA BINDING; DNA RECOGNITION; DOUBLE-STRANDED DNA (DS-DNA); GENETIC DIVERSITY; HIGH THERMAL STABILITY; HOMODIMERIC PROTEINS; HOMODIMERS; HYPERTHERMOPHILIC; IN-VITRO; PICOSECONDS; PROTEIN-PROTEIN INTERACTIONS; RIGID CORE; SEQUENCE SIMILARITY; STRUCTURAL DOMAINS; STRUCTURAL STUDIES; TIME-SCALES; TRANSCRIPTIONAL REGULATION; VIRAL LIFE CYCLE;

EID: 84859408778     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201791s     Document Type: Article
Times cited : (22)

References (101)
  • 1
    • 20344382957 scopus 로고    scopus 로고
    • Here a virus, there a virus, everywhere the same virus?
    • Breitbart, M. and Rohwer, F. (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278-284
    • (2005) Trends Microbiol. , vol.13 , pp. 278-284
    • Breitbart, M.1    Rohwer, F.2
  • 2
    • 34548792911 scopus 로고    scopus 로고
    • Marine viruses: Major players in the global ecosystem
    • Suttle, C. A. (2007) Marine viruses: Major players in the global ecosystem Nat. Rev. Microbiol. 5, 801-812
    • (2007) Nat. Rev. Microbiol. , vol.5 , pp. 801-812
    • Suttle, C.A.1
  • 4
    • 33644859575 scopus 로고    scopus 로고
    • Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain
    • Forterre, P. (2006) Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain Proc. Natl. Acad. Sci. U.S.A. 103, 3669-3674
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 3669-3674
    • Forterre, P.1
  • 5
    • 0034872743 scopus 로고    scopus 로고
    • Viral eukaryogenesis: Was the ancestor of the nucleus a complex DNA virus?
    • Bell, P. J. (2001) Viral eukaryogenesis: Was the ancestor of the nucleus a complex DNA virus? J. Mol. Evol. 53, 251-256
    • (2001) J. Mol. Evol. , vol.53 , pp. 251-256
    • Bell, P.J.1
  • 8
    • 2942590839 scopus 로고    scopus 로고
    • Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: A novel virus family, the Globuloviridae
    • Haring, M., Peng, X., Brugger, K., Rachel, R., Stetter, K. O., Garrett, R. A., and Prangishvili, D. (2004) Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: A novel virus family, the Globuloviridae Virology 323, 233-242
    • (2004) Virology , vol.323 , pp. 233-242
    • Haring, M.1    Peng, X.2    Brugger, K.3    Rachel, R.4    Stetter, K.O.5    Garrett, R.A.6    Prangishvili, D.7
  • 9
    • 33744929889 scopus 로고    scopus 로고
    • His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus
    • Bath, C., Cukalac, T., Porter, K., and Dyall-Smith, M. L. (2006) His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus Virology 350, 228-239
    • (2006) Virology , vol.350 , pp. 228-239
    • Bath, C.1    Cukalac, T.2    Porter, K.3    Dyall-Smith, M.L.4
  • 10
    • 0031680647 scopus 로고    scopus 로고
    • His1, an archaeal virus of the Fuselloviridae family that infects Haloarcula hispanica
    • Bath, C. and Dyall-Smith, M. L. (1998) His1, an archaeal virus of the Fuselloviridae family that infects Haloarcula hispanica J. Virol. 72, 9392-9395
    • (1998) J. Virol. , vol.72 , pp. 9392-9395
    • Bath, C.1    Dyall-Smith, M.L.2
  • 12
    • 0035694680 scopus 로고    scopus 로고
    • Sequences and replication of genomes of the archaeal Rudiviruses SIRV1 and SIRV2: Relationships to the archaeal Lipothrixvirus SIFV and some eukaryal viruses
    • Peng, X., Blum, H., She, Q., Mallok, S., Brugger, K., Garrett, R. A., Zillig, W., and Prangishvili, D. (2001) Sequences and replication of genomes of the archaeal Rudiviruses SIRV1 and SIRV2: Relationships to the archaeal Lipothrixvirus SIFV and some eukaryal viruses Virology 291, 226-234
    • (2001) Virology , vol.291 , pp. 226-234
    • Peng, X.1    Blum, H.2    She, Q.3    Mallok, S.4    Brugger, K.5    Garrett, R.A.6    Zillig, W.7    Prangishvili, D.8
  • 15
    • 0026059368 scopus 로고
    • Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae
    • Palm, P., Schleper, C., Grampp, B., Yeats, S., McWilliam, P., Reiter, W. D., and Zillig, W. (1991) Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae Virology 185, 242-250
    • (1991) Virology , vol.185 , pp. 242-250
    • Palm, P.1    Schleper, C.2    Grampp, B.3    Yeats, S.4    McWilliam, P.5    Reiter, W.D.6    Zillig, W.7
  • 16
    • 0023148012 scopus 로고
    • Identification and characterization of the genes encoding three structural proteins of the Sulfolobus virus-like particle SSV1
    • Reiter, W. D., Palm, P., Henschen, A., Lottspeich, F., Zillig, W., and Grampp, B. (1987) Identification and characterization of the genes encoding three structural proteins of the Sulfolobus virus-like particle SSV1 Mol. Genet. Genomics 206, 144-153
    • (1987) Mol. Genet. Genomics , vol.206 , pp. 144-153
    • Reiter, W.D.1    Palm, P.2    Henschen, A.3    Lottspeich, F.4    Zillig, W.5    Grampp, B.6
  • 19
    • 0027502720 scopus 로고
    • SSV1-encoded site-specific recombination system in Sulfolobus shibatae
    • Muskhelishvili, G., Palm, P., and Zillig, W. (1993) SSV1-encoded site-specific recombination system in Sulfolobus shibatae Mol. Gen. Genet. 237, 334-342
    • (1993) Mol. Gen. Genet. , vol.237 , pp. 334-342
    • Muskhelishvili, G.1    Palm, P.2    Zillig, W.3
  • 20
    • 34047261825 scopus 로고    scopus 로고
    • The SSV1 viral integrase is not essential
    • Clore, A. J. and Stedman, K. M. (2007) The SSV1 viral integrase is not essential Virology 361, 103-111
    • (2007) Virology , vol.361 , pp. 103-111
    • Clore, A.J.1    Stedman, K.M.2
  • 21
    • 3142732363 scopus 로고    scopus 로고
    • Mutational analysis of the archaeal tyrosine recombinase SSV1 integrase suggests a mechanism of DNA cleavage in trans
    • Letzelter, C., Duguet, M., and Serre, M. C. (2004) Mutational analysis of the archaeal tyrosine recombinase SSV1 integrase suggests a mechanism of DNA cleavage in trans J. Biol. Chem. 279, 28936-28944
    • (2004) J. Biol. Chem. , vol.279 , pp. 28936-28944
    • Letzelter, C.1    Duguet, M.2    Serre, M.C.3
  • 22
    • 0037053336 scopus 로고    scopus 로고
    • Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase
    • Serre, M. C., Letzelter, C., Garel, J. R., and Duguet, M. (2002) Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase J. Biol. Chem. 277, 16758-16767
    • (2002) J. Biol. Chem. , vol.277 , pp. 16758-16767
    • Serre, M.C.1    Letzelter, C.2    Garel, J.R.3    Duguet, M.4
  • 23
    • 0026559548 scopus 로고
    • Archaebacterial virus SSV1 encodes a putative DnaA-like protein
    • Koonin, E. V. (1992) Archaebacterial virus SSV1 encodes a putative DnaA-like protein Nucleic Acids Res. 20, 1143
    • (1992) Nucleic Acids Res. , vol.20 , pp. 1143
    • Koonin, E.V.1
  • 24
    • 34250202202 scopus 로고    scopus 로고
    • Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays
    • Frols, S., Gordon, P. M., Panlilio, M. A., Schleper, C., and Sensen, C. W. (2007) Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays Virology 365, 48-59
    • (2007) Virology , vol.365 , pp. 48-59
    • Frols, S.1    Gordon, P.M.2    Panlilio, M.A.3    Schleper, C.4    Sensen, C.W.5
  • 25
    • 33645087247 scopus 로고    scopus 로고
    • Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life
    • Prangishvili, D., Garrett, R. A., and Koonin., E. V. (2006) Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life Virus Res. 117, 52-67
    • (2006) Virus Res. , vol.117 , pp. 52-67
    • Prangishvili, D.1    Garrett, R.A.2    Koonin, E.V.3
  • 28
    • 20244382943 scopus 로고    scopus 로고
    • Structure of D-63 from Sulfolobus Spindle-Shaped Virus 1: Surface Properties of the Dimeric Four-Helix Bundle Suggest an Adaptor Protein Function
    • Kraft, P., Kummel, D., Oeckinghaus, A., Gauss, G. H., Wiedenheft, B., Young, M., and Lawrence, C. M. (2004) Structure of D-63 from Sulfolobus Spindle-Shaped Virus 1: Surface Properties of the Dimeric Four-Helix Bundle Suggest an Adaptor Protein Function J. Virol. 78, 7438-7442
    • (2004) J. Virol. , vol.78 , pp. 7438-7442
    • Kraft, P.1    Kummel, D.2    Oeckinghaus, A.3    Gauss, G.H.4    Wiedenheft, B.5    Young, M.6    Lawrence, C.M.7
  • 29
    • 35548988777 scopus 로고    scopus 로고
    • A winged-helix protein from Sulfolobus turreted icosahedral virus points toward stabilizing disulfide bonds in the intracellular proteins of a hyperthermophilic virus
    • Larson, E. T., Eilers, B., Menon, S., Reiter, D., Ortmann, A., Young, M. J., and Lawrence, C. M. (2007) A winged-helix protein from Sulfolobus turreted icosahedral virus points toward stabilizing disulfide bonds in the intracellular proteins of a hyperthermophilic virus Virology 38, 249-261
    • (2007) Virology , vol.38 , pp. 249-261
    • Larson, E.T.1    Eilers, B.2    Menon, S.3    Reiter, D.4    Ortmann, A.5    Young, M.J.6    Lawrence, C.M.7
  • 30
    • 34248522373 scopus 로고    scopus 로고
    • A new DNA binding protein highly conserved in diverse crenarchaeal viruses
    • Larson, E. T., Eilers, B. J., Reiter, D., Ortmann, A. C., Young, M. J., and Lawrence., C. M. (2007) A new DNA binding protein highly conserved in diverse crenarchaeal viruses Virology 363, 387-396
    • (2007) Virology , vol.363 , pp. 387-396
    • Larson, E.T.1    Eilers, B.J.2    Reiter, D.3    Ortmann, A.C.4    Young, M.J.5    Lawrence, C.M.6
  • 31
    • 33746210125 scopus 로고    scopus 로고
    • Structure of A197 from Sulfolobus turreted icosahedral virus: A crenarchaeal viral glycosyltransferase exhibiting the GTA fold
    • Larson, E. T., Reiter, D., Young, M., and Lawrence., C. M. (2006) Structure of A197 from Sulfolobus turreted icosahedral virus: A crenarchaeal viral glycosyltransferase exhibiting the GTA fold J. Virol. 80, 7636-7644
    • (2006) J. Virol. , vol.80 , pp. 7636-7644
    • Larson, E.T.1    Reiter, D.2    Young, M.3    Lawrence, C.M.4
  • 32
    • 30044450170 scopus 로고    scopus 로고
    • Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses
    • Khayat, R., Tang, L., Larson, E. T., Lawrence, C. M., Young, M., and Johnson, J. E. (2005) Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses Proc. Natl. Acad. Sci. U.S.A. 102, 18944-18949
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 18944-18949
    • Khayat, R.1    Tang, L.2    Larson, E.T.3    Lawrence, C.M.4    Young, M.5    Johnson, J.E.6
  • 34
    • 77952731322 scopus 로고    scopus 로고
    • The Crystal Structure of D212 from Sulfolobus Spindle-shaped Virus Ragged Hills reveals a new member of the PD-(D/E)XK nuclease superfamily
    • Menon, S. K., Eilers, B. J., Young, M. J., and Lawrence., C. M. (2010) The Crystal Structure of D212 from Sulfolobus Spindle-shaped Virus Ragged Hills reveals a new member of the PD-(D/E)XK nuclease superfamily J. Virol. 84, 5890-5897
    • (2010) J. Virol. , vol.84 , pp. 5890-5897
    • Menon, S.K.1    Eilers, B.J.2    Young, M.J.3    Lawrence, C.M.4
  • 35
    • 79958754524 scopus 로고    scopus 로고
    • Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE)
    • Lintner, N. G., Kerou, M., Brumfield, S. K., Graham, S., Liu, H., Naismith, J. H., Sdano, M., Peng, N., She, Q., Copie, V., Young, M. J., White, M. F., and Lawrence, C. M. (2011) Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE) J. Biol. Chem. 286, 21643-21656
    • (2011) J. Biol. Chem. , vol.286 , pp. 21643-21656
    • Lintner, N.G.1    Kerou, M.2    Brumfield, S.K.3    Graham, S.4    Liu, H.5    Naismith, J.H.6    Sdano, M.7    Peng, N.8    She, Q.9    Copie, V.10    Young, M.J.11    White, M.F.12    Lawrence, C.M.13
  • 36
    • 0038054284 scopus 로고    scopus 로고
    • Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2
    • Stedman, K. M., She, Q., Phan, H., Arnold, H. P., Holz, I., Garrett, R. A., and Zillig., W. (2003) Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2 Res. Microbiol. 154, 295-302
    • (2003) Res. Microbiol. , vol.154 , pp. 295-302
    • Stedman, K.M.1    She, Q.2    Phan, H.3    Arnold, H.P.4    Holz, I.5    Garrett, R.A.6    Zillig, W.7
  • 37
    • 3242887157 scopus 로고    scopus 로고
    • CD-Search: Protein domain annotations on the fly
    • Marchler-Bauer, B. S. (2004) CD-Search: Protein domain annotations on the fly Nucleic Acids Res. 32, W327-W331
    • (2004) Nucleic Acids Res. , vol.32
    • Marchler-Bauer, B.S.1
  • 39
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding, J. (2005) Protein homology detection by HMM-HMM comparison Bioinformatics 21, 951-960
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 40
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding, J., Biegert, A., and Lupas, A. N. (2005) The HHpred interactive server for protein homology detection and structure prediction Nucleic Acids Res. 33, W244-W248
    • (2005) Nucleic Acids Res. , vol.33
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 41
    • 75949107791 scopus 로고    scopus 로고
    • HHsvm: Fast and accurate classification of profile-profile matches identified by HHsearch
    • Dlakic, M. (2009) HHsvm: Fast and accurate classification of profile-profile matches identified by HHsearch Bioinformatics 25, 3071-3076
    • (2009) Bioinformatics , vol.25 , pp. 3071-3076
    • Dlakic, M.1
  • 42
    • 0344826584 scopus 로고    scopus 로고
    • ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure
    • Golovanov, A. P., Barilla, D., Golovanova, M., Hayes, F., and Lian, L. Y. (2003) ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure Mol. Microbiol. 50, 1141-1153
    • (2003) Mol. Microbiol. , vol.50 , pp. 1141-1153
    • Golovanov, A.P.1    Barilla, D.2    Golovanova, M.3    Hayes, F.4    Lian, L.Y.5
  • 44
    • 33751088044 scopus 로고    scopus 로고
    • Crystal structures of the DNA binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys 9 in DNA recognition
    • Larson, J. D., Jenkins, J. L., Schuermann, J. P., Zhou, Y., Becker, D. F., and Tanner, J. J. (2006) Crystal structures of the DNA binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys 9 in DNA recognition Protein Sci. 15, 2630-2641
    • (2006) Protein Sci. , vol.15 , pp. 2630-2641
    • Larson, J.D.1    Jenkins, J.L.2    Schuermann, J.P.3    Zhou, Y.4    Becker, D.F.5    Tanner, J.J.6
  • 45
    • 70449535731 scopus 로고    scopus 로고
    • 15N backbone and side chain NMR resonance assignments for E73 from Sulfolobus spindle-shaped virus ragged hills, a hyperthermophilic crenarchaeal virus from Yellowstone National Park
    • 15N backbone and side chain NMR resonance assignments for E73 from Sulfolobus spindle-shaped virus ragged hills, a hyperthermophilic crenarchaeal virus from Yellowstone National Park Biomol. NMR Assignments 3, 219-222
    • (2009) Biomol. NMR Assignments , vol.3 , pp. 219-222
    • Schlenker, C.1    Menon, S.2    Lawrence, C.M.3    Copié, V.4
  • 46
    • 14844294424 scopus 로고    scopus 로고
    • Protein production by auto-induction in high density shaking cultures
    • Studier, F. W. (2005) Protein production by auto-induction in high density shaking cultures Protein Expression Purif. 41, 207-234
    • (2005) Protein Expression Purif. , vol.41 , pp. 207-234
    • Studier, F.W.1
  • 47
    • 70350214644 scopus 로고    scopus 로고
    • Structure-based stability analysis of an extremely stable dimeric DNA binding protein from Sulfolobus islandicus
    • Weininger, U., Zeeb, M., Neumann, P., Lowm, C., Stubbs, M. T., Lipps, G., and Balbach, J. (2009) Structure-based stability analysis of an extremely stable dimeric DNA binding protein from Sulfolobus islandicus Biochemistry 48, 10030-10037
    • (2009) Biochemistry , vol.48 , pp. 10030-10037
    • Weininger, U.1    Zeeb, M.2    Neumann, P.3    Lowm, C.4    Stubbs, M.T.5    Lipps, G.6    Balbach, J.7
  • 48
    • 0346500473 scopus 로고    scopus 로고
    • Folding and association of an extremely stable dimeric protein from Sulfolobus islandicus
    • Zeeb, M., Lipps, G., Lilie, H., and Balbach, J. (2004) Folding and association of an extremely stable dimeric protein from Sulfolobus islandicus J. Mol. Biol. 336, 227-240
    • (2004) J. Mol. Biol. , vol.336 , pp. 227-240
    • Zeeb, M.1    Lipps, G.2    Lilie, H.3    Balbach, J.4
  • 49
    • 0029812117 scopus 로고    scopus 로고
    • Kinetic study on the formation of a de novo designed heterodimeric coiled-coil: Use of surface plasmon resonance to monitor the association and dissociation of polypeptide chains
    • Chao, H., Houston, M. E., Jr., Grother, S., Kay, C. M., Oconnor-McCourt, M., Irvin, R. T., and Hodges, R. S. (1996) Kinetic study on the formation of a de novo designed heterodimeric coiled-coil: Use of surface plasmon resonance to monitor the association and dissociation of polypeptide chains Biochemistry 35, 12175-12185
    • (1996) Biochemistry , vol.35 , pp. 12175-12185
    • Chao, H.1    Houston Jr., M.E.2    Grother, S.3    Kay, C.M.4    Oconnor-Mccourt, M.5    Irvin, R.T.6    Hodges, R.S.7
  • 50
    • 44949291986 scopus 로고
    • Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins
    • Kay, L. E., Ikura, M., Tschudin, R., and Bax, A. (1990) Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins J. Magn. Reson. 89, 496-514
    • (1990) J. Magn. Reson. , vol.89 , pp. 496-514
    • Kay, L.E.1    Ikura, M.2    Tschudin, R.3    Bax, A.4
  • 51
    • 43949167657 scopus 로고
    • HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with α and proton and nitrogen resonances with α and β carbon resonances in proteins
    • Wittekind, M. and Mueller, L. (1993) HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with α and proton and nitrogen resonances with α and β carbon resonances in proteins J. Magn. Reson. 101, 201-205
    • (1993) J. Magn. Reson. , vol.101 , pp. 201-205
    • Wittekind, M.1    Mueller, L.2
  • 52
    • 44049109615 scopus 로고
    • An Efficient Experiment for Sequential Backbone Assignment of Medium-Sized Isotopically Enriched Proteins
    • Grzesiek, S. and Bax, A. (1992) An Efficient Experiment for Sequential Backbone Assignment of Medium-Sized Isotopically Enriched Proteins J. Magn. Reson. 99, 201-207
    • (1992) J. Magn. Reson. , vol.99 , pp. 201-207
    • Grzesiek, S.1    Bax, A.2
  • 54
    • 9444245493 scopus 로고
    • Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR
    • Grzesiek, S. and Bax, A. (1992) Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR J. Am. Chem. Soc. 114, 6291-6293
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 6291-6293
    • Grzesiek, S.1    Bax, A.2
  • 59
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu, G., Delaglio, F., and Bax, A. (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology J. Biomol. NMR 13, 289-302
    • (1999) J. Biomol. NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 60
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
    • Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., and Thornton, J. M. (1996) AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR J. Biomol. NMR 8, 477-486
    • (1996) J. Biomol. NMR , vol.8 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    MacArthur, M.W.3    Kaptein, R.4    Thornton, J.M.5
  • 62
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Luthy, R., Bowie, J. U., and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profiles Nature 356, 83-85
    • (1992) Nature , vol.356 , pp. 83-85
    • Luthy, R.1    Bowie, J.U.2    Eisenberg, D.3
  • 63
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
    • Wiederstein, M. and Sippl, M. J. (2007) ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins Nucleic Acids Res. 35 (Suppl. 2) W407-W410
    • (2007) Nucleic Acids Res. , vol.35 , Issue.SUPPL. 2
    • Wiederstein, M.1    Sippl, M.J.2
  • 66
    • 56649103902 scopus 로고    scopus 로고
    • Searching protein structure databases with DaliLite v.3
    • Holm, L., Kaariainen, S., Rosenstrom, P., and Schenkel, A. (2008) Searching protein structure databases with DaliLite v.3 Bioinformatics 24, 2780-2781
    • (2008) Bioinformatics , vol.24 , pp. 2780-2781
    • Holm, L.1    Kaariainen, S.2    Rosenstrom, P.3    Schenkel, A.4
  • 67
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel, E. and Henrick, K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr. D60, 2256-2268
    • (2004) Acta Crystallogr. , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 68
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch, W. (1978) A discussion of the solution for the best rotation to relate two sets of vectors Acta Crystallogr. A34, 827-828
    • (1978) Acta Crystallogr. , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 70
    • 0026748968 scopus 로고
    • 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible
    • 15N relaxation using inverse detected two-dimensional NMR spectroscopy: The central helix is flexible Biochemistry 31, 5269-5278
    • (1992) Biochemistry , vol.31 , pp. 5269-5278
    • Barbato, G.1    Ikura, M.2    Kay, L.E.3    Pastor, R.W.4    Bax, A.5
  • 71
    • 0027787894 scopus 로고
    • 2O in protein NMR: Application to sensitivity enhancement and NOE measurements
    • 2O in protein NMR: Application to sensitivity enhancement and NOE measurements J. Am. Chem. Soc. 115, 12593-12594
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 12593-12594
    • Grzesiek, S.1    Bax, A.2
  • 72
    • 0024449503 scopus 로고
    • 15N inverse detected heteronuclear NMR spectroscopy: Application to staphylococcal nuclease
    • 15N inverse detected heteronuclear NMR spectroscopy: Application to staphylococcal nuclease Biochemistry 28, 8972-8979
    • (1989) Biochemistry , vol.28 , pp. 8972-8979
    • Kay, L.E.1    Torchia, D.A.2    Bax, A.3
  • 74
    • 79958825506 scopus 로고    scopus 로고
    • Internal dynamics of the tryptophan repressor (TrpR) and two functionally distinct TrpR variants, L75F-TrpR and A77V-TrpR, in their l -Trp bound forms
    • Tripet, B. P., Goel, A., and Copié, V. (2011) Internal dynamics of the tryptophan repressor (TrpR) and two functionally distinct TrpR variants, L75F-TrpR and A77V-TrpR, in their l -Trp bound forms Biochemistry 50, 5140-5153
    • (2011) Biochemistry , vol.50 , pp. 5140-5153
    • Tripet, B.P.1    Goel, A.2    Copié, V.3
  • 75
    • 33847534249 scopus 로고
    • Effects of Diffusion on Free Precession in Nuclear Magnetic Resonance Experiments
    • Carr, H. Y. and Purcell, E. M. (1954) Effects of Diffusion on Free Precession in Nuclear Magnetic Resonance Experiments Phys. Rev. 94, 630
    • (1954) Phys. Rev. , vol.94 , pp. 630
    • Carr, H.Y.1    Purcell, E.M.2
  • 76
    • 0002899752 scopus 로고
    • Modified Spin-Echo Method for Measuring Nuclear Relaxation Times
    • Meiboom, S. and Gill, D. (1958) Modified Spin-Echo Method for Measuring Nuclear Relaxation Times Rev. Sci. Instrum. 29, 688-691
    • (1958) Rev. Sci. Instrum. , vol.29 , pp. 688-691
    • Meiboom, S.1    Gill, D.2
  • 77
    • 0029400480 scopus 로고
    • NMRPipe: A multidimensional spectral processing system based on UNIX pipes
    • Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes J. Biomol. NMR 6, 277-293
    • (1995) J. Biomol. NMR , vol.6 , pp. 277-293
    • Delaglio, F.1    Grzesiek, S.2    Vuister, G.W.3    Zhu, G.4    Pfeifer, J.5    Bax, A.6
  • 78
    • 0004040543 scopus 로고    scopus 로고
    • (2004), University of California, San Fransisco
    • Goddard, T. D. and Kneller, D. G. (2004) SPARKY 3, University of California, San Fransisco.
    • SPARKY 3
    • Goddard, T.D.1    Kneller, D.G.2
  • 79
    • 0033525126 scopus 로고    scopus 로고
    • Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: Implications for the entropy of association with DNA
    • Bracken, C., Carr, P. A., Cavanagh, J., and Palmer, A. G. (1999) Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: Implications for the entropy of association with DNA J. Mol. Biol. 285, 2133-2146
    • (1999) J. Mol. Biol. , vol.285 , pp. 2133-2146
    • Bracken, C.1    Carr, P.A.2    Cavanagh, J.3    Palmer, A.G.4
  • 80
    • 0038068865 scopus 로고    scopus 로고
    • FAST-model free: A program for rapid automated analysis of solution NMR spin-relaxation data
    • Cole, R. and Loria, J. P. (2003) FAST-model free: A program for rapid automated analysis of solution NMR spin-relaxation data J. Biomol. NMR 26, 203-213
    • (2003) J. Biomol. NMR , vol.26 , pp. 203-213
    • Cole, R.1    Loria, J.P.2
  • 81
    • 0006166990 scopus 로고    scopus 로고
    • version 4.0
    • Palmer, A. (1998) ModelFree, version 4.0, http://cpmcnet.columbia.edu/ dept/gsas/biochem/labs/palmer.
    • (1998) ModelFree
    • Palmer, A.1
  • 82
    • 33646719091 scopus 로고
    • Model-Free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules. 1. Theory and range of validity
    • Lipari, G. and Szabo, A. (1982) Model-Free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules. 1. Theory and range of validity J. Am. Chem. Soc. 104, 4546-4559
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 83
    • 33845553743 scopus 로고
    • Model-Free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules. 2. Analysis of experimental results
    • Lipari, G. and Szabo, A. (1982) Model-Free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules. 2. Analysis of experimental results J. Am. Chem. Soc. 104, 4559-4570
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4559-4570
    • Lipari, G.1    Szabo, A.2
  • 84
    • 34548046005 scopus 로고    scopus 로고
    • Ribbon-helix-helix transcription factors: Variations on a theme
    • Schreiter, E. R. and Drennan, C. L. (2007) Ribbon-helix-helix transcription factors: Variations on a theme Nat. Rev. Microbiol. 5, 710-720
    • (2007) Nat. Rev. Microbiol. , vol.5 , pp. 710-720
    • Schreiter, E.R.1    Drennan, C.L.2
  • 86
    • 0035816213 scopus 로고    scopus 로고
    • Plasmid Transcriptional Repressor CopG Oligomerises to Render Helical Superstructures Unbound and in Complexes with Oligonucleotides
    • Costa, M., Sola, M., del Solar, G., Eritja, R., Hernandez-Arriaga, A. M., Espinosa, M., Gomis-Ruth, F. X., and Coll, M. (2001) Plasmid Transcriptional Repressor CopG Oligomerises to Render Helical Superstructures Unbound and in Complexes with Oligonucleotides J. Mol. Biol. 310, 403-417
    • (2001) J. Mol. Biol. , vol.310 , pp. 403-417
    • Costa, M.1    Sola, M.2    Del Solar, G.3    Eritja, R.4    Hernandez-Arriaga, A.M.5    Espinosa, M.6    Gomis-Ruth, F.X.7    Coll, M.8
  • 87
    • 0028952291 scopus 로고
    • Crystal structure, folding, and operator binding of the hyperstable Arc repressor mutant PL8
    • Schildbach, J. F., Milla, M. E., Jeffrey, P. D., Raumann, B. E., and Sauer, R. T. (1995) Crystal structure, folding, and operator binding of the hyperstable Arc repressor mutant PL8 Biochemistry 34, 1405-1412
    • (1995) Biochemistry , vol.34 , pp. 1405-1412
    • Schildbach, J.F.1    Milla, M.E.2    Jeffrey, P.D.3    Raumann, B.E.4    Sauer, R.T.5
  • 89
    • 0034665030 scopus 로고    scopus 로고
    • Direct and indirect readout in mutant Met repressor-operator complexes
    • Garvie, C. W. and Phillips, S. E. (2000) Direct and indirect readout in mutant Met repressor-operator complexes Structure 8, 905-914
    • (2000) Structure , vol.8 , pp. 905-914
    • Garvie, C.W.1    Phillips, S.E.2
  • 90
    • 33846011436 scopus 로고    scopus 로고
    • Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs
    • Mattison, K., Wilbur, J. S., So, M., and Brennan, R. G. (2006) Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs J. Biol. Chem. 281, 37942-37951
    • (2006) J. Biol. Chem. , vol.281 , pp. 37942-37951
    • Mattison, K.1    Wilbur, J.S.2    So, M.3    Brennan, R.G.4
  • 92
    • 0025336625 scopus 로고
    • Structure of Arc represser in solution: Evidence for a family of β-sheet DMA-binding proteins
    • Breg, J. N., van Opheusden, J. H. J., Burgering, M. J. M., Boelens, R., and Kaptein, R. (1990) Structure of Arc represser in solution: Evidence for a family of β-sheet DMA-binding proteins Nature 346, 586-589
    • (1990) Nature , vol.346 , pp. 586-589
    • Breg, J.N.1    Van Opheusden, J.H.J.2    Burgering, M.J.M.3    Boelens, R.4    Kaptein, R.5
  • 93
    • 34547564386 scopus 로고    scopus 로고
    • The solution structure of ParD, the antidote of the ParDE toxin-antitoxin module, provides the structural basis for DNA and toxin binding
    • Oberer, M., Zangger, K., Gruber, K., and Keller, W. (2007) The solution structure of ParD, the antidote of the ParDE toxin-antitoxin module, provides the structural basis for DNA and toxin binding Protein Sci. 16, 1676-1688
    • (2007) Protein Sci. , vol.16 , pp. 1676-1688
    • Oberer, M.1    Zangger, K.2    Gruber, K.3    Keller, W.4
  • 94
    • 0033401440 scopus 로고    scopus 로고
    • Thermodynamic properties and DNA binding of the ParD protein from the broad host-range plasmid RK2/RP4 killing system
    • Oberer, M., Lindner, H., Glatter, O., Krafky, C., and Keller, W. (1999) Thermodynamic properties and DNA binding of the ParD protein from the broad host-range plasmid RK2/RP4 killing system J. Biol. Chem. 380, 1413-1420
    • (1999) J. Biol. Chem. , vol.380 , pp. 1413-1420
    • Oberer, M.1    Lindner, H.2    Glatter, O.3    Krafky, C.4    Keller, W.5
  • 95
    • 33748773334 scopus 로고    scopus 로고
    • NikR-operator complex structure and the mechanism of repressor activation by metal ions
    • Schreiter, E. R., Wang, S. C., Zamble, D. B., and Drennan, C. L. (2006) NikR-operator complex structure and the mechanism of repressor activation by metal ions Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 13676-13681
    • Schreiter, E.R.1    Wang, S.C.2    Zamble, D.B.3    Drennan, C.L.4
  • 96
    • 0030735429 scopus 로고    scopus 로고
    • How rolling circle plasmids control their copy number
    • Rasooly, A. and Rasooly, R. S. (1997) How rolling circle plasmids control their copy number Trends Microbiol. 5, 440-446
    • (1997) Trends Microbiol. , vol.5 , pp. 440-446
    • Rasooly, A.1    Rasooly, R.S.2
  • 97
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233, 123-138
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 99
    • 0035098779 scopus 로고    scopus 로고
    • Hyperthermophilic enzymes: Sources, uses, and molecular mechanisms for thermostability
    • Vieille, C. and Zeikus, G. J. (2001) Hyperthermophilic enzymes: Sources, uses, and molecular mechanisms for thermostability Microbiol. Mol. Biol. Rev. 65, 1-43
    • (2001) Microbiol. Mol. Biol. Rev. , vol.65 , pp. 1-43
    • Vieille, C.1    Zeikus, G.J.2
  • 100
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang, J., Edelsbrunner, H., and Woodward, C. (1998) Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design Protein Sci. 7, 1884-1897
    • (1998) Protein Sci. , vol.7 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3


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