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Volumn 386, Issue 4, 2009, Pages 1054-1065

Signatures of Protein-DNA Recognition in Free DNA Binding Sites

Author keywords

DNA structure; gene regulation; indirect readout; protein DNA interactions; transcription factors

Indexed keywords

CURVED DNA; DOUBLE STRANDED DNA;

EID: 60149104606     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.01.007     Document Type: Article
Times cited : (36)

References (53)
  • 2
    • 60149104870 scopus 로고    scopus 로고
    • Indirect readout of DNA sequence by proteins
    • Rice P.A., and Correll C.C. (Eds), Royal Society of Chemistry, Cambridge, UK
    • Lawson C.L., and Berman H.M. Indirect readout of DNA sequence by proteins. In: Rice P.A., and Correll C.C. (Eds). Protein-Nucleic Acid Interactions (2008), Royal Society of Chemistry, Cambridge, UK 66-86
    • (2008) Protein-Nucleic Acid Interactions , pp. 66-86
    • Lawson, C.L.1    Berman, H.M.2
  • 3
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • Olson W.K., Gorin A.A., Lu X.-J., Hock L.M., and Zhurkin V.B. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA 95 (1998) 11163-11168
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.-J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 6
    • 0025187081 scopus 로고
    • Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing
    • Kim Y., Grable J.C., Love R., Greene P.J., and Rosenberg J.M. Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. Science 249 (1990) 1307-1309
    • (1990) Science , vol.249 , pp. 1307-1309
    • Kim, Y.1    Grable, J.C.2    Love, R.3    Greene, P.J.4    Rosenberg, J.M.5
  • 7
    • 0027372621 scopus 로고
    • Tandem binding in crystals of a trp repressor/operator half-site complex
    • Lawson C.L., and Carey J. Tandem binding in crystals of a trp repressor/operator half-site complex. Nature 366 (1993) 178-182
    • (1993) Nature , vol.366 , pp. 178-182
    • Lawson, C.L.1    Carey, J.2
  • 8
    • 0028315988 scopus 로고
    • Determinants of repressor operator recognition from the structure of the trp operator binding site
    • Shakked Z., Guzikevich-Guerstein G., Frolow F., Rabinovich D., Joachimiak A., and Sigler P.B. Determinants of repressor operator recognition from the structure of the trp operator binding site. Nature 368 (1994) 469-473
    • (1994) Nature , vol.368 , pp. 469-473
    • Shakked, Z.1    Guzikevich-Guerstein, G.2    Frolow, F.3    Rabinovich, D.4    Joachimiak, A.5    Sigler, P.B.6
  • 9
    • 0026656038 scopus 로고
    • Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target
    • Hegde R.S., Grossman S.R., Laimins L.A., and Sigler P.B. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature 359 (1992) 505-512
    • (1992) Nature , vol.359 , pp. 505-512
    • Hegde, R.S.1    Grossman, S.R.2    Laimins, L.A.3    Sigler, P.B.4
  • 10
    • 0032417684 scopus 로고    scopus 로고
    • Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets
    • Rozenberg H., Rabinovich D., Frolow F., Hegde R.S., and Shakked Z. Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets. Proc. Natl Acad. Sci. USA 95 (1998) 15194-15199
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 15194-15199
    • Rozenberg, H.1    Rabinovich, D.2    Frolow, F.3    Hegde, R.S.4    Shakked, Z.5
  • 11
    • 0036774088 scopus 로고    scopus 로고
    • DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending
    • Bartfeld D., Shimon L., Couture G.C., Rabinovich D., Frolow F., Levanon D., Shakked Z., et al. DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending. Structure 10 (2002) 1395-1407
    • (2002) Structure , vol.10 , pp. 1395-1407
    • Bartfeld, D.1    Shimon, L.2    Couture, G.C.3    Rabinovich, D.4    Frolow, F.5    Levanon, D.6    Shakked, Z.7
  • 12
    • 0035066381 scopus 로고    scopus 로고
    • The leukemia-associated AML1 (Runx1)-CBF beta complex functions as a DNA-induced molecular clamp
    • Bravo J., Li Z., Speck N.A., and Warren A.J. The leukemia-associated AML1 (Runx1)-CBF beta complex functions as a DNA-induced molecular clamp. Nat. Struct. Biol. 8 (2001) 371-378
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 371-378
    • Bravo, J.1    Li, Z.2    Speck, N.A.3    Warren, A.J.4
  • 13
    • 24044494651 scopus 로고    scopus 로고
    • Structures of the DNA-binding site of Runt-domain transcription regulators
    • Kitayner M., Rozenberg H., Rabinovich D., and Shakked Z. Structures of the DNA-binding site of Runt-domain transcription regulators. Acta Crystallogr. D 61 (2005) 236-246
    • (2005) Acta Crystallogr. D , vol.61 , pp. 236-246
    • Kitayner, M.1    Rozenberg, H.2    Rabinovich, D.3    Shakked, Z.4
  • 14
    • 0035831044 scopus 로고    scopus 로고
    • Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta
    • Tahirov T.H., Inoue-Bungo T., Morii H., Fujikawa A., Sasaki M., Kimura K., Ogata K., et al. Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta. Cell 104 (2001) 755-767
    • (2001) Cell , vol.104 , pp. 755-767
    • Tahirov, T.H.1    Inoue-Bungo, T.2    Morii, H.3    Fujikawa, A.4    Sasaki, M.5    Kimura, K.6    Ogata, K.7
  • 15
    • 0031964687 scopus 로고    scopus 로고
    • A novel DNA recognition mode by the NF-KB p 65 homodimer
    • Chen Y.-Q., Ghosh S., and Ghosh G. A novel DNA recognition mode by the NF-KB p 65 homodimer. Nat. Struct. Biol. 5 (1998) 67-73
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 67-73
    • Chen, Y.-Q.1    Ghosh, S.2    Ghosh, G.3
  • 16
    • 12344280204 scopus 로고    scopus 로고
    • Crystal structure of a free kappa B DNA: Insights into DNA recognition by transcription factor NF-kappa B
    • Huang D.B., Phelps C.B., Fusco A.J., and Ghosh G. Crystal structure of a free kappa B DNA: Insights into DNA recognition by transcription factor NF-kappa B. J. Mol. Biol. 346 (2005) 147-160
    • (2005) J. Mol. Biol. , vol.346 , pp. 147-160
    • Huang, D.B.1    Phelps, C.B.2    Fusco, A.J.3    Ghosh, G.4
  • 17
    • 0026641755 scopus 로고
    • Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands
    • Somers W.S., and Phillips S.E.V. Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands. Nature 359 (1992) 387-393
    • (1992) Nature , vol.359 , pp. 387-393
    • Somers, W.S.1    Phillips, S.E.V.2
  • 18
    • 0034665030 scopus 로고    scopus 로고
    • Direct and indirect readout in mutant Met repressor-operator complexes
    • Garvie C.W., and Phillips S.E.V. Direct and indirect readout in mutant Met repressor-operator complexes. Struct. Fold. Des. 8 (2000) 905-914
    • (2000) Struct. Fold. Des. , vol.8 , pp. 905-914
    • Garvie, C.W.1    Phillips, S.E.V.2
  • 20
    • 0033554861 scopus 로고    scopus 로고
    • Structure and recognition of sheared tandem G × A base pairs associated with human centromere DNA sequence at atomic resolution
    • Gao Y.G., Robinson H., Sanishvili R., Joachimiak A., and Wang A.H.J. Structure and recognition of sheared tandem G × A base pairs associated with human centromere DNA sequence at atomic resolution. Biochemistry 38 (1999) 16452-16460
    • (1999) Biochemistry , vol.38 , pp. 16452-16460
    • Gao, Y.G.1    Robinson, H.2    Sanishvili, R.3    Joachimiak, A.4    Wang, A.H.J.5
  • 21
    • 0029814351 scopus 로고    scopus 로고
    • Effects of systematic variation of the minimal Escherichia coli met consensus operator site: in vivo and in vitro met repressor binding
    • Wild C.M., McNally T., Phillips S.E., and Stockley P.G. Effects of systematic variation of the minimal Escherichia coli met consensus operator site: in vivo and in vitro met repressor binding. Mol. Microbiol. 21 (1996) 1125-1135
    • (1996) Mol. Microbiol. , vol.21 , pp. 1125-1135
    • Wild, C.M.1    McNally, T.2    Phillips, S.E.3    Stockley, P.G.4
  • 22
    • 0032804235 scopus 로고    scopus 로고
    • The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions
    • Glasfeld A., Koehler A.N., Schumacher M.A., and Brennan R.G. The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions. J. Mol. Biol. 291 (1999) 347-361
    • (1999) J. Mol. Biol. , vol.291 , pp. 347-361
    • Glasfeld, A.1    Koehler, A.N.2    Schumacher, M.A.3    Brennan, R.G.4
  • 23
    • 0028173030 scopus 로고
    • Crystal structure of LacI family member, PurR, bound to DNA: minor groove binding by alpha helices
    • Schumacher M.A., Choi K.Y., Zalkin H., and Brennan R.G. Crystal structure of LacI family member, PurR, bound to DNA: minor groove binding by alpha helices. Science 266 (1994) 763-770
    • (1994) Science , vol.266 , pp. 763-770
    • Schumacher, M.A.1    Choi, K.Y.2    Zalkin, H.3    Brennan, R.G.4
  • 24
    • 0034714010 scopus 로고    scopus 로고
    • 1 Å crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium
    • Chiu T.K., and Dickerson R.E. 1 Å crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. J. Mol. Biol. 301 (2000) 915-945
    • (2000) J. Mol. Biol. , vol.301 , pp. 915-945
    • Chiu, T.K.1    Dickerson, R.E.2
  • 25
    • 0026059567 scopus 로고
    • Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G
    • Privé G.G., Yanagi K., and Dickerson R.E. Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. J. Mol. Biol. 217 (1991) 177-199
    • (1991) J. Mol. Biol. , vol.217 , pp. 177-199
    • Privé, G.G.1    Yanagi, K.2    Dickerson, R.E.3
  • 26
    • 0027910469 scopus 로고
    • Recognition by max of its cognate DNA through a dimeric b/HLH/Z domain
    • Ferré-D'Amaré A.R., Prendergast G.C., Ziff E.B., and Burley S.K. Recognition by max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363 (1993) 38-45
    • (1993) Nature , vol.363 , pp. 38-45
    • Ferré-D'Amaré, A.R.1    Prendergast, G.C.2    Ziff, E.B.3    Burley, S.K.4
  • 27
    • 0029563634 scopus 로고
    • Crystal structure of a bZIP/DNA complex at 2.2 Å: determinants of DNA specific recognition
    • Keller W., Konig P., and Richmond T.J. Crystal structure of a bZIP/DNA complex at 2.2 Å: determinants of DNA specific recognition. J. Mol. Biol. 254 (1995) 657-667
    • (1995) J. Mol. Biol. , vol.254 , pp. 657-667
    • Keller, W.1    Konig, P.2    Richmond, T.J.3
  • 28
    • 0032522662 scopus 로고    scopus 로고
    • High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition
    • Elrod-Erickson M., Benson T.E., and Pabo C.O. High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure 6 (1998) 451-464
    • (1998) Structure , vol.6 , pp. 451-464
    • Elrod-Erickson, M.1    Benson, T.E.2    Pabo, C.O.3
  • 29
    • 0002183131 scopus 로고    scopus 로고
    • Polynucleotide secondary structures: an historical perspective
    • Neidle S. (Ed), Oxford University Press, Oxford, UK
    • Arnott S. Polynucleotide secondary structures: an historical perspective. In: Neidle S. (Ed). Oxford Handbook of Nucleic Acid Structure (1999), Oxford University Press, Oxford, UK 1-38
    • (1999) Oxford Handbook of Nucleic Acid Structure , pp. 1-38
    • Arnott, S.1
  • 30
    • 0043203406 scopus 로고    scopus 로고
    • Crystal structures of A-DNA duplexes
    • Wahl M.C., and Sundaralingam M. Crystal structures of A-DNA duplexes. Biopolymers 44 (1997) 45-63
    • (1997) Biopolymers , vol.44 , pp. 45-63
    • Wahl, M.C.1    Sundaralingam, M.2
  • 31
    • 0034698001 scopus 로고    scopus 로고
    • A-form conformational motifs in ligand-bound DNA structures
    • Lu X.-J., Shakked Z., and Olson W.K. A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300 (2000) 819-840
    • (2000) J. Mol. Biol. , vol.300 , pp. 819-840
    • Lu, X.-J.1    Shakked, Z.2    Olson, W.K.3
  • 32
    • 0033614015 scopus 로고    scopus 로고
    • Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features
    • Malinina L., Fernandez L.G., Huynh-Dinh T., and Subirana J.A. Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features. J. Mol. Biol. 285 (1999) 1679-1690
    • (1999) J. Mol. Biol. , vol.285 , pp. 1679-1690
    • Malinina, L.1    Fernandez, L.G.2    Huynh-Dinh, T.3    Subirana, J.A.4
  • 34
    • 0035912812 scopus 로고    scopus 로고
    • A crystallographic map of the transition from B-DNA to A-DNA
    • Vargason J.M., Henderson K., and Ho P.S. A crystallographic map of the transition from B-DNA to A-DNA. Proc. Natl Acad. Sci. USA 98 (2001) 7265-7270
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 7265-7270
    • Vargason, J.M.1    Henderson, K.2    Ho, P.S.3
  • 37
    • 0037106324 scopus 로고    scopus 로고
    • Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG
    • Ng H.L., and Dickerson R.E. Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG. Nucl. Acids Res. 30 (2002) 4061-4067
    • (2002) Nucl. Acids Res. , vol.30 , pp. 4061-4067
    • Ng, H.L.1    Dickerson, R.E.2
  • 38
    • 0034008772 scopus 로고    scopus 로고
    • The structure of a stable intermediate in the A ↔ B DNA helix transition
    • Ng H.L., Kopka M.L., and Dickerson R.E. The structure of a stable intermediate in the A ↔ B DNA helix transition. Proc. Natl Acad. Sci. USA 97 (2000) 2035-2039
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 2035-2039
    • Ng, H.L.1    Kopka, M.L.2    Dickerson, R.E.3
  • 39
    • 0035193091 scopus 로고    scopus 로고
    • Sequence-dependent B to A transition in DNA evaluated with dimeric and trimeric scales
    • Tolstorukov M.Y., Ivanov V.I., Malenkov G.G., Jernigan R.L., and Zhurkin V.B. Sequence-dependent B to A transition in DNA evaluated with dimeric and trimeric scales. Biophys. J. 81 (2001) 3409-3421
    • (2001) Biophys. J. , vol.81 , pp. 3409-3421
    • Tolstorukov, M.Y.1    Ivanov, V.I.2    Malenkov, G.G.3    Jernigan, R.L.4    Zhurkin, V.B.5
  • 40
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 43
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47 (1991) 110-119
    • (1991) Acta Crystallogr. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard4
  • 44
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density
    • McRee D.E. XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
    • (1999) J. Struct. Biol. , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 45
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu X.J., and Olson W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31 (2003) 5108-5121
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2
  • 46
    • 0033081529 scopus 로고    scopus 로고
    • Rapid automated molecular replacement by evolutionary search
    • Kissinger C.R., Gehlhaar D.K., and Fogel D.B. Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D 55 (1999) 484-491
    • (1999) Acta Crystallogr. D , vol.55 , pp. 484-491
    • Kissinger, C.R.1    Gehlhaar, D.K.2    Fogel, D.B.3
  • 47
    • 0035182073 scopus 로고    scopus 로고
    • Use of TLS parameters to model anisotropic displacements in macromolecular refinement
    • Winn M.D., Isupov M.N., and Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D 57 (2001) 122-133
    • (2001) Acta Crystallogr. D , vol.57 , pp. 122-133
    • Winn, M.D.1    Isupov, M.N.2    Murshudov, G.N.3
  • 48
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53 (1997) 240-255
    • (1997) Acta Crystallogr. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 49
    • 0002634621 scopus 로고
    • Maximum likelihood refinement of heavy atom parameters
    • Wolf W., Evans P.R., and Leslie A.G.W. (Eds), SERC Daresbury Laboratory, Warrington, UK
    • Otwinowski Z. Maximum likelihood refinement of heavy atom parameters. In: Wolf W., Evans P.R., and Leslie A.G.W. (Eds). Proceedings of the CCP4 Study Weekend (1991), SERC Daresbury Laboratory, Warrington, UK 80-86
    • (1991) Proceedings of the CCP4 Study Weekend , pp. 80-86
    • Otwinowski, Z.1
  • 50
    • 0002583957 scopus 로고
    • DM: an automated procedure for phase improvement by density modification
    • Cowtan K. DM: an automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newsletter Protein Crystallogr. 31 (1994) 34-38
    • (1994) Joint CCP4 ESF-EACBM Newsletter Protein Crystallogr. , vol.31 , pp. 34-38
    • Cowtan, K.1
  • 51
    • 84920325457 scopus 로고
    • AMoRe: an automated package for molecular replacement
    • Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50 (1994) 157-163
    • (1994) Acta Crystallogr. A , vol.50 , pp. 157-163
    • Navaza, J.1
  • 52
    • 0032534539 scopus 로고    scopus 로고
    • X-ray crystal structures of half the human papilloma virus E2 binding site: d(GACCGCGCTC)
    • Finley J.B., and Luo M. X-ray crystal structures of half the human papilloma virus E2 binding site: d(GACCGCGCTC). Nucleic Acids Res. 26 (1998) 5719-5727
    • (1998) Nucleic Acids Res. , vol.26 , pp. 5719-5727
    • Finley, J.B.1    Luo, M.2


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