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Volumn 48, Issue 6, 2009, Pages 1148-1155

Structural basis for DNA recognition by the human PAX3 homeodomain

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOMAL TRANSLOCATIONS; DNA HELIXES; DNA RECOGNITION; DNA-BINDING DOMAINS; FUSION GENES; HOMEODOMAIN; MEDIATED INTERACTIONS; MINOR GROOVES; MOLECULAR MECHANISMS; MYOGENESIS; N TERMINALS; NEUROGENESIS; PAIRED DOMAINS; PALINDROMIC; PHOSPHATE BACKBONES; PROTEIN-DNA INTERACTIONS; REGULATORY PROTEINS; RHABDOMYOSARCOMA; STRUCTURAL BASIS; WATER MOLECULES;

EID: 64349102568     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi802052y     Document Type: Article
Times cited : (36)

References (43)
  • 1
    • 36248952802 scopus 로고    scopus 로고
    • The role of Pax genes in the development of tissues and organs: Pax3 and Pax7 regulate muscle progenitor cell functions
    • Buckingham, M., and Relaix, F. (2007) The role of Pax genes in the development of tissues and organs: Pax3 and Pax7 regulate muscle progenitor cell functions. Annu. Rev. Cell Dev. Biol. 23, 645-673.
    • (2007) Annu. Rev. Cell Dev. Biol , vol.23 , pp. 645-673
    • Buckingham, M.1    Relaix, F.2
  • 3
    • 0026602124 scopus 로고
    • Waardenburg's syndrome patients have mutations in the human homologue of the Pax-3 paired box gene
    • Tassabehji, M., Read, A. P., Newton, V. E., Harris, R., Balling, R., Gruss, P., and Strachan, T. (1992) Waardenburg's syndrome patients have mutations in the human homologue of the Pax-3 paired box gene. Nature 355, 635-636.
    • (1992) Nature , vol.355 , pp. 635-636
    • Tassabehji, M.1    Read, A.P.2    Newton, V.E.3    Harris, R.4    Balling, R.5    Gruss, P.6    Strachan, T.7
  • 4
    • 0026584439 scopus 로고
    • An exonic mutation in the HuP2 paired domain gene causes Waardenburg's syndrome
    • Baldwin, C. T., Hoth, C. F., Amos, J. A., da-Silva, E. O., and Milunsky, A. (1992) An exonic mutation in the HuP2 paired domain gene causes Waardenburg's syndrome. Nature 355, 637-638.
    • (1992) Nature , vol.355 , pp. 637-638
    • Baldwin, C.T.1    Hoth, C.F.2    Amos, J.A.3    da-Silva, E.O.4    Milunsky, A.5
  • 6
    • 0028854798 scopus 로고
    • Further elucidation of the genomic structure of PAX3, and identification of two different point mutations within the PAX3 homeobox that cause Waardenburg syndrome type 1 in two families
    • Lalwani, A. K., Brister, J. R., Fex, J., Grundfast, K. M., Ploplis, B., San Agustin, T. B., and Wilcox, E. R. (1995) Further elucidation of the genomic structure of PAX3, and identification of two different point mutations within the PAX3 homeobox that cause Waardenburg syndrome type 1 in two families. Am. J. Hum. Genet. 56, 75-83.
    • (1995) Am. J. Hum. Genet , vol.56 , pp. 75-83
    • Lalwani, A.K.1    Brister, J.R.2    Fex, J.3    Grundfast, K.M.4    Ploplis, B.5    San Agustin, T.B.6    Wilcox, E.R.7
  • 8
    • 64349094976 scopus 로고    scopus 로고
    • A novel missense mutation in the PAX3 gene in a case of Waardenburg syndrome type I
    • in press
    • Nakamura, M., Ishikawa, O., and Tokura, Y. (2008) A novel missense mutation in the PAX3 gene in a case of Waardenburg syndrome type I. J. Eur. Acad. Dermatol. Venereol. (in press).
    • (2008) J. Eur. Acad. Dermatol. Venereol
    • Nakamura, M.1    Ishikawa, O.2    Tokura, Y.3
  • 9
    • 64349120595 scopus 로고    scopus 로고
    • Novel mutation in PAX3 gene in Waardenburg syndrome accompanied by unilateral macular degeneration
    • in press
    • Kozawa, M., Kondo, H., Tahira, T., Hayashi, K., and Uchio, E. (2008) Novel mutation in PAX3 gene in Waardenburg syndrome accompanied by unilateral macular degeneration. Eye (in press).
    • (2008) Eye
    • Kozawa, M.1    Kondo, H.2    Tahira, T.3    Hayashi, K.4    Uchio, E.5
  • 10
    • 0035839886 scopus 로고    scopus 로고
    • Gene fusions involving PAX and FOX family members in alveolar rhabdomyosarcoma
    • Barr, F. G. (2001) Gene fusions involving PAX and FOX family members in alveolar rhabdomyosarcoma. Oncogene 20, 5736-5746.
    • (2001) Oncogene , vol.20 , pp. 5736-5746
    • Barr, F.G.1
  • 12
    • 0026002757 scopus 로고
    • Crystal structure of a MATa2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions
    • Wolberger, C., Vershon, A. K., Liu, B., Johnson, A. D., and Pabo, C. O. (1991) Crystal structure of a MATa2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell 67, 517-528.
    • (1991) Cell , vol.67 , pp. 517-528
    • Wolberger, C.1    Vershon, A.K.2    Liu, B.3    Johnson, A.D.4    Pabo, C.O.5
  • 13
    • 0027787519 scopus 로고
    • Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex
    • Billeter, M., Qian, Y. Q., Otting, G., Müller, M., Gehring, W., and Wüthrich, K. (1993) Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. J. Mol. Biol. 234, 1084-1093.
    • (1993) J. Mol. Biol , vol.234 , pp. 1084-1093
    • Billeter, M.1    Qian, Y.Q.2    Otting, G.3    Müller, M.4    Gehring, W.5    Wüthrich, K.6
  • 14
    • 0028828745 scopus 로고
    • Crystal structure of the MATa1/MATa2 homeodomain heterodimer bound to DNA
    • Li, T., Stark, M. R., Johnson, A. D., and Wolberger, C. (1995) Crystal structure of the MATa1/MATa2 homeodomain heterodimer bound to DNA. Science 270, 262-269.
    • (1995) Science , vol.270 , pp. 262-269
    • Li, T.1    Stark, M.R.2    Johnson, A.D.3    Wolberger, C.4
  • 15
    • 0029160486 scopus 로고
    • High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA
    • Wilson, D. S., Guenther, B., Desplan, C., and Kuriyan, J. (1995) High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell 82, 709-719.
    • (1995) Cell , vol.82 , pp. 709-719
    • Wilson, D.S.1    Guenther, B.2    Desplan, C.3    Kuriyan, J.4
  • 16
    • 0029595248 scopus 로고
    • Structure of the even-skipped homeodomain complexed to AT-rich DNA: New perspectives on homeodomain specificity
    • Hirsch, J. A., and Aggarwal, A. K. (1995) Structure of the even-skipped homeodomain complexed to AT-rich DNA: New perspectives on homeodomain specificity. EMBO J. 14, 6280-6291.
    • (1995) EMBO J , vol.14 , pp. 6280-6291
    • Hirsch, J.A.1    Aggarwal, A.K.2
  • 17
    • 0032573434 scopus 로고    scopus 로고
    • Engrailed homeodomain-DNA complex at 2.2 Å resolution: A detailed view of the interface and comparison with other engrailed structures
    • Fraenkel, E., Rould, M. A., Chambers, K. A., and Pabo, C. O. (1998) Engrailed homeodomain-DNA complex at 2.2 Å resolution: A detailed view of the interface and comparison with other engrailed structures. J. Mol. Biol. 284, 351-361.
    • (1998) J. Mol. Biol , vol.284 , pp. 351-361
    • Fraenkel, E.1    Rould, M.A.2    Chambers, K.A.3    Pabo, C.O.4
  • 18
    • 0033602242 scopus 로고    scopus 로고
    • Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex
    • Passner, J. M., Ryoo, H. D., Shen, L., Mann, R. S., and Aggarwal, A. K. (1999) Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. Nature 397, 714-719.
    • (1999) Nature , vol.397 , pp. 714-719
    • Passner, J.M.1    Ryoo, H.D.2    Shen, L.3    Mann, R.S.4    Aggarwal, A.K.5
  • 19
    • 0033582545 scopus 로고    scopus 로고
    • Structure of a HoxB1-Pbx1 heterodimer bound to DNA: Role of the hexapeptide and a fourth homeodomain helix in complex formation
    • Piper, D. E., Batchelor, A. H., Chang, C. P., Cleary, M. L., and Wolberger, C. (1999) Structure of a HoxB1-Pbx1 heterodimer bound to DNA: Role of the hexapeptide and a fourth homeodomain helix in complex formation. Cell 96, 587-597.
    • (1999) Cell , vol.96 , pp. 587-597
    • Piper, D.E.1    Batchelor, A.H.2    Chang, C.P.3    Cleary, M.L.4    Wolberger, C.5
  • 20
    • 0033546260 scopus 로고    scopus 로고
    • The three-dimensional structure of the vnd/ NK-2 homeodomain-DNA complex by NMR spectroscopy
    • Gruschus, J. M., Tsao, D. H., Wang, L. H., Nirenberg, M., and Ferretti, J. A. (1999) The three-dimensional structure of the vnd/ NK-2 homeodomain-DNA complex by NMR spectroscopy. J. Mol. Biol. 289, 529-545.
    • (1999) J. Mol. Biol , vol.289 , pp. 529-545
    • Gruschus, J.M.1    Tsao, D.H.2    Wang, L.H.3    Nirenberg, M.4    Ferretti, J.A.5
  • 21
    • 0035834053 scopus 로고    scopus 로고
    • Crystal structure of the Msx-1 homeodomain/DNA complex
    • Hovde, S., Abate-Shen, C., and Geiger, J. H. (2001) Crystal structure of the Msx-1 homeodomain/DNA complex. Biochemistry 40, 12013-12021.
    • (2001) Biochemistry , vol.40 , pp. 12013-12021
    • Hovde, S.1    Abate-Shen, C.2    Geiger, J.H.3
  • 22
    • 18844432177 scopus 로고    scopus 로고
    • Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome
    • Chaney, B. A., Clark-Baldwin, K., Dave, V., Ma, J., and Rance, M. (2005) Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome. Biochemistry 44, 7497-7511.
    • (2005) Biochemistry , vol.44 , pp. 7497-7511
    • Chaney, B.A.1    Clark-Baldwin, K.2    Dave, V.3    Ma, J.4    Rance, M.5
  • 23
    • 32044460394 scopus 로고    scopus 로고
    • The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site
    • Baird-Titus, J. M., Clark-Baldwin, K., Dave, V., Caperelli, C. A., Ma, J., and Rance, M. (2006) The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. J. Mol. Biol. 356, 1137-1151.
    • (2006) J. Mol. Biol , vol.356 , pp. 1137-1151
    • Baird-Titus, J.M.1    Clark-Baldwin, K.2    Dave, V.3    Caperelli, C.A.4    Ma, J.5    Rance, M.6
  • 25
    • 33947408340 scopus 로고    scopus 로고
    • Structural basis for induced fit mechanisms in DNA recognition by the Pdx1 homeodomain
    • Longo, A., Guanga, G. P., and Rose, R. B. (2007) Structural basis for induced fit mechanisms in DNA recognition by the Pdx1 homeodomain. Biochemistry 46, 2948-2957.
    • (2007) Biochemistry , vol.46 , pp. 2948-2957
    • Longo, A.1    Guanga, G.P.2    Rose, R.B.3
  • 26
    • 0027332476 scopus 로고
    • Cooperative dimerization of paired class homeodomains on DNA
    • Wilson, D., Sheng, G., Lecuit, T., Dostatni, N., and Desplan, C. (1993) Cooperative dimerization of paired class homeodomains on DNA. Genes Dev. 7, 2120-2134.
    • (1993) Genes Dev , vol.7 , pp. 2120-2134
    • Wilson, D.1    Sheng, G.2    Lecuit, T.3    Dostatni, N.4    Desplan, C.5
  • 27
    • 0028108227 scopus 로고
    • Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50
    • Ades, S. E., and Sauer, R. T. (1994) Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50. Biochemistry 33, 9187-9194.
    • (1994) Biochemistry , vol.33 , pp. 9187-9194
    • Ades, S.E.1    Sauer, R.T.2
  • 28
    • 0029951161 scopus 로고    scopus 로고
    • Conservation and diversification in homeodomain-DNA interactions: A comparative genetic analysis
    • Wilson, D. S., Sheng, G., Jun, S., and Desplan, C. (1996) Conservation and diversification in homeodomain-DNA interactions: A comparative genetic analysis. Proc. Natl. Acad. Sci. U.S.A. 93, 6886-6891.
    • (1996) Proc. Natl. Acad. Sci. U.S.A , vol.93 , pp. 6886-6891
    • Wilson, D.S.1    Sheng, G.2    Jun, S.3    Desplan, C.4
  • 29
    • 0032126885 scopus 로고    scopus 로고
    • Hiremath, C. N., and Ladias, J. A. A. (1998) Expression and purification of recombinant hRPABC25, hRPABC17, and hR-PABC14.4, three essential subunits of human RNA polymerases I, II, and III. Protein Expression Purif. 13, 198-204.
    • Hiremath, C. N., and Ladias, J. A. A. (1998) Expression and purification of recombinant hRPABC25, hRPABC17, and hR-PABC14.4, three essential subunits of human RNA polymerases I, II, and III. Protein Expression Purif. 13, 198-204.
  • 30
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
    • (1997) Methods Enzymol , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 31
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An Automated Program for Molecular Replacement
    • Vagin, A., and Teplyakov, A. (1997) MOLREP: An Automated Program for Molecular Replacement. J. Appl. Crystallogr. 30, 1022-1025.
    • (1997) J. Appl. Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 33
    • 0032964481 scopus 로고    scopus 로고
    • Automated protein model building combined with iterative structure refinement
    • Perrakis, A., Morris, R., and Lamzin, V. S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458-463.
    • (1999) Nat. Struct. Biol , vol.6 , pp. 458-463
    • Perrakis, A.1    Morris, R.2    Lamzin, V.S.3
  • 34
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132.
    • (2004) Acta Crystallogr , vol.D60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 35
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255.
    • (1997) Acta Crystallogr , vol.D53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 37
    • 0030729548 scopus 로고    scopus 로고
    • Reciprocal effect of Waardenburg syndrome mutations on DNA binding by the Pax-3 paired domain and homeodomain
    • Fortin, A. S., Underhill, D. A., and Gros, P. (1997) Reciprocal effect of Waardenburg syndrome mutations on DNA binding by the Pax-3 paired domain and homeodomain. Hum. Mol. Genet. 6, 1781-1790.
    • (1997) Hum. Mol. Genet , vol.6 , pp. 1781-1790
    • Fortin, A.S.1    Underhill, D.A.2    Gros, P.3
  • 38
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 39
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
    • Esnouf, R. M. (1997) An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J. Mol. Graphics Modell. 15, 132-134.
    • (1997) J. Mol. Graphics Modell , vol.15 , pp. 132-134
    • Esnouf, R.M.1
  • 40
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A., Sharp, K. A., and Honig, B. (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 41
    • 0024058085 scopus 로고
    • The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
    • Lavery, R., and Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6, 63-91.
    • (1988) J. Biomol. Struct. Dyn , vol.6 , pp. 63-91
    • Lavery, R.1    Sklenar, H.2
  • 42
    • 50349085962 scopus 로고    scopus 로고
    • 3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
    • Lu, X. J., and Olson, W. K. (2008) 3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat. Protoc. 3, 1213-1227.
    • (2008) Nat. Protoc , vol.3 , pp. 1213-1227
    • Lu, X.J.1    Olson, W.K.2
  • 43
    • 0038243196 scopus 로고    scopus 로고
    • Povscript+: A program for model and data visualization using persistence of vision ray-tracing
    • Fenn, T. D., Ringe, D., and Petsko, G. A. (2003) Povscript+: A program for model and data visualization using persistence of vision ray-tracing. J. Appl. Crystallogr. 36, 944-947.
    • (2003) J. Appl. Crystallogr , vol.36 , pp. 944-947
    • Fenn, T.D.1    Ringe, D.2    Petsko, G.A.3


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