메뉴 건너뛰기




Volumn 383, Issue 5, 2008, Pages 1156-1170

Solution Structure and Characterization of the DNA-Binding Activity of the B3BP-Smr Domain

Author keywords

DNA repair; DNA binding domain; DNase I; IF3C fold; NMR

Indexed keywords

BINDING PROTEIN; ENDONUCLEASE; PROTEIN MUTS; SINGLE STRANDED DNA; SMALL MUTS RELATED; UNCLASSIFIED DRUG;

EID: 53549103560     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.09.005     Document Type: Article
Times cited : (16)

References (58)
  • 1
    • 0032808820 scopus 로고    scopus 로고
    • Smr: a bacterial and eukaryotic homologue of the C-terminal region of the MutS2 family
    • Moreira D., and Philippe H. Smr: a bacterial and eukaryotic homologue of the C-terminal region of the MutS2 family. Trends Biochem. Sci. 24 (1999) 298-300
    • (1999) Trends Biochem. Sci. , vol.24 , pp. 298-300
    • Moreira, D.1    Philippe, H.2
  • 2
    • 0032530155 scopus 로고    scopus 로고
    • A phylogenomic study of the MutS family of proteins
    • Eisen J.A. A phylogenomic study of the MutS family of proteins. Nucleic Acids Res. 26 (1998) 4291-4300
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4291-4300
    • Eisen, J.A.1
  • 3
    • 0035696150 scopus 로고    scopus 로고
    • MutS recognition: multiple mismatches and sequence context effects
    • Joshi A., and Rao B.J. MutS recognition: multiple mismatches and sequence context effects. J. Biosci. 26 (2001) 595-606
    • (2001) J. Biosci. , vol.26 , pp. 595-606
    • Joshi, A.1    Rao, B.J.2
  • 4
    • 0034283838 scopus 로고    scopus 로고
    • Dual recognition-incision enzymes might be involved in mismatch repair and meiosis
    • Malik H.S., and Henikoff S. Dual recognition-incision enzymes might be involved in mismatch repair and meiosis. Trends Biochem. Sci. 25 (2000) 414-418
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 414-418
    • Malik, H.S.1    Henikoff, S.2
  • 5
    • 1942488240 scopus 로고    scopus 로고
    • Thermus thermophilus MutS2, a MutS paralogue, possesses an endonuclease activity promoted by MutL
    • Fukui K., Masui R., and Kuramitsu S. Thermus thermophilus MutS2, a MutS paralogue, possesses an endonuclease activity promoted by MutL. J. Biochem. (Tokyo) 135 (2004) 375-384
    • (2004) J. Biochem. (Tokyo) , vol.135 , pp. 375-384
    • Fukui, K.1    Masui, R.2    Kuramitsu, S.3
  • 7
    • 18244400420 scopus 로고    scopus 로고
    • Structural and functional divergence of MutS2 from bacterial MutS1 and eukaryotic MSH4-MSH5 homologs
    • Kang J., Huang S., and Blaser M.J. Structural and functional divergence of MutS2 from bacterial MutS1 and eukaryotic MSH4-MSH5 homologs. J. Bacteriol. 187 (2005) 3528-3537
    • (2005) J. Bacteriol. , vol.187 , pp. 3528-3537
    • Kang, J.1    Huang, S.2    Blaser, M.J.3
  • 9
    • 0034641947 scopus 로고    scopus 로고
    • The crystal structure of DNA mismatch repair protein MutS binding to a GxT mismatch
    • Lamers M.H., Perrakis A., Enzlin J.H., Winterwerp H.H., de Wind N., and Sixma T.K. The crystal structure of DNA mismatch repair protein MutS binding to a GxT mismatch. Nature 407 (2000) 711-717
    • (2000) Nature , vol.407 , pp. 711-717
    • Lamers, M.H.1    Perrakis, A.2    Enzlin, J.H.3    Winterwerp, H.H.4    de Wind, N.5    Sixma, T.K.6
  • 10
    • 0034641938 scopus 로고    scopus 로고
    • Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA
    • Obmolova G., Ban C., Hsieh P., and Yang W. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407 (2000) 703-710
    • (2000) Nature , vol.407 , pp. 703-710
    • Obmolova, G.1    Ban, C.2    Hsieh, P.3    Yang, W.4
  • 11
    • 0037830413 scopus 로고    scopus 로고
    • Identification and characterization of BCL-3-binding protein: implications for transcription and DNA repair or recombination
    • Watanabe N., Wachi S., and Fujita T. Identification and characterization of BCL-3-binding protein: implications for transcription and DNA repair or recombination. J. Biol. Chem. 278 (2003) 26102-26110
    • (2003) J. Biol. Chem. , vol.278 , pp. 26102-26110
    • Watanabe, N.1    Wachi, S.2    Fujita, T.3
  • 12
    • 33847378477 scopus 로고    scopus 로고
    • Nuclease activity of the MutS homologue MutS2 from Thermus thermophilus is confined to the Smr domain
    • Fukui K., Kosaka H., Kuramitsu S., and Masui R. Nuclease activity of the MutS homologue MutS2 from Thermus thermophilus is confined to the Smr domain. Nucleic Acids Res. 35 (2007) 850-860
    • (2007) Nucleic Acids Res. , vol.35 , pp. 850-860
    • Fukui, K.1    Kosaka, H.2    Kuramitsu, S.3    Masui, R.4
  • 13
    • 0037169521 scopus 로고    scopus 로고
    • Identification of developmentally expressed proteins that functionally interact with Nedd4 ubiquitin ligase
    • Murillas R., Simms K.S., Hatakeyama S., Weissman A.M., and Kuehn M.R. Identification of developmentally expressed proteins that functionally interact with Nedd4 ubiquitin ligase. J. Biol. Chem. 277 (2002) 2897-2907
    • (2002) J. Biol. Chem. , vol.277 , pp. 2897-2907
    • Murillas, R.1    Simms, K.S.2    Hatakeyama, S.3    Weissman, A.M.4    Kuehn, M.R.5
  • 14
    • 34548037713 scopus 로고    scopus 로고
    • Haplotype of gene Nedd4 binding protein 2 associated with sporadic nasopharyngeal carcinoma in the Southern Chinese population
    • Zheng M.Z., Qin H.D., Yu X.J., Zhang R.H., Chen L.Z., Feng Q.S., and Zeng Y.X. Haplotype of gene Nedd4 binding protein 2 associated with sporadic nasopharyngeal carcinoma in the Southern Chinese population. J. Transl. Med. 5 (2007) 36
    • (2007) J. Transl. Med. , vol.5 , pp. 36
    • Zheng, M.Z.1    Qin, H.D.2    Yu, X.J.3    Zhang, R.H.4    Chen, L.Z.5    Feng, Q.S.6    Zeng, Y.X.7
  • 15
    • 36248989248 scopus 로고    scopus 로고
    • The Nedd4-like family of E3 ubiquitin ligases and cancer
    • Chen C., and Matesic L.E. The Nedd4-like family of E3 ubiquitin ligases and cancer. Cancer Metastasis Rev. 26 (2007) 587-604
    • (2007) Cancer Metastasis Rev. , vol.26 , pp. 587-604
    • Chen, C.1    Matesic, L.E.2
  • 17
    • 33748929006 scopus 로고    scopus 로고
    • Thermofluor-based high-throughput stability optimization of proteins for structural studies
    • Ericsson U.B., Hallberg B.M., Detitta G.T., Dekker N., and Nordlund P. Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal. Biochem. 357 (2006) 289-298
    • (2006) Anal. Biochem. , vol.357 , pp. 289-298
    • Ericsson, U.B.1    Hallberg, B.M.2    Detitta, G.T.3    Dekker, N.4    Nordlund, P.5
  • 21
    • 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. 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 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 23
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    • Arnold K., Bordoli L., Kopp J., and Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22 (2006) 195-201
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 24
    • 0029918694 scopus 로고    scopus 로고
    • The FSSP database: fold classification based on structure-structure alignment of proteins
    • Holm L., and Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24 (1996) 206-209
    • (1996) Nucleic Acids Res. , vol.24 , pp. 206-209
    • Holm, L.1    Sander, C.2
  • 26
    • 33846033844 scopus 로고    scopus 로고
    • The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
    • Greene L.H., Lewis T.E., Addou S., Cuff A., Dallman T., Dibley M., et al. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 35 (2007) D291-D297
    • (2007) Nucleic Acids Res. , vol.35
    • Greene, L.H.1    Lewis, T.E.2    Addou, S.3    Cuff, A.4    Dallman, T.5    Dibley, M.6
  • 27
    • 0029111710 scopus 로고
    • X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix
    • Biou V., Shu F., and Ramakrishnan V. X-ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha-helix. EMBO J. 14 (1995) 4056-4064
    • (1995) EMBO J. , vol.14 , pp. 4056-4064
    • Biou, V.1    Shu, F.2    Ramakrishnan, V.3
  • 28
    • 0032899119 scopus 로고    scopus 로고
    • Identification of the ribosome binding sites of translation initiation factor IF3 by multidimensional heteronuclear NMR spectroscopy
    • Sette M., Spurio R., van Tilborg P., Gualerzi C.O., and Boelens R. Identification of the ribosome binding sites of translation initiation factor IF3 by multidimensional heteronuclear NMR spectroscopy. RNA 5 (1999) 82-92
    • (1999) RNA , vol.5 , pp. 82-92
    • Sette, M.1    Spurio, R.2    van Tilborg, P.3    Gualerzi, C.O.4    Boelens, R.5
  • 29
    • 0034711380 scopus 로고    scopus 로고
    • High precision NMR structure of YhhP, a novel Escherichia coli protein implicated in cell division
    • Katoh E., Hatta T., Shindo H., Ishii Y., Yamada H., Mizuno T., and Yamazaki T. High precision NMR structure of YhhP, a novel Escherichia coli protein implicated in cell division. J. Mol. Biol. 304 (2000) 219-229
    • (2000) J. Mol. Biol. , vol.304 , pp. 219-229
    • Katoh, E.1    Hatta, T.2    Shindo, H.3    Ishii, Y.4    Yamada, H.5    Mizuno, T.6    Yamazaki, T.7
  • 30
    • 0030587524 scopus 로고    scopus 로고
    • Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution
    • Davies C., Ramakrishnan V., and White S.W. Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution. Structure 4 (1996) 1093-1104
    • (1996) Structure , vol.4 , pp. 1093-1104
    • Davies, C.1    Ramakrishnan, V.2    White, S.W.3
  • 31
    • 2442702832 scopus 로고    scopus 로고
    • The structure of a ribosomal protein S8/spc operon mRNA complex
    • Merianos H.J., Wang J., and Moore P.B. The structure of a ribosomal protein S8/spc operon mRNA complex. RNA 10 (2004) 954-964
    • (2004) RNA , vol.10 , pp. 954-964
    • Merianos, H.J.1    Wang, J.2    Moore, P.B.3
  • 32
    • 0035838973 scopus 로고    scopus 로고
    • Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii
    • Tishchenko S., Nikulin A., Fomenkova N., Nevskaya N., Nikonov O., Dumas P., et al. Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii. J. Mol. Biol. 311 (2001) 311-324
    • (2001) J. Mol. Biol. , vol.311 , pp. 311-324
    • Tishchenko, S.1    Nikulin, A.2    Fomenkova, N.3    Nevskaya, N.4    Nikonov, O.5    Dumas, P.6
  • 33
    • 1842832249 scopus 로고    scopus 로고
    • Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins
    • Ostheimer G.J., Barkan A., and Matthews B.W. Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins. Structure 10 (2002) 1593-1601
    • (2002) Structure , vol.10 , pp. 1593-1601
    • Ostheimer, G.J.1    Barkan, A.2    Matthews, B.W.3
  • 35
    • 0032167733 scopus 로고    scopus 로고
    • The R3H motif: a domain that binds single-stranded nucleic acids
    • Grishin N.V. The R3H motif: a domain that binds single-stranded nucleic acids. Trends Biochem. Sci. 23 (1998) 329-330
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 329-330
    • Grishin, N.V.1
  • 36
    • 0026354983 scopus 로고
    • DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex
    • Lahm A., and Suck D. DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. J. Mol. Biol. 222 (1991) 645-667
    • (1991) J. Mol. Biol. , vol.222 , pp. 645-667
    • Lahm, A.1    Suck, D.2
  • 37
    • 0023038391 scopus 로고
    • Crystallographic refinement and structure of DNase I at 2 A resolution
    • Oefner C., and Suck D. Crystallographic refinement and structure of DNase I at 2 A resolution. J. Mol. Biol. 192 (1986) 605-632
    • (1986) J. Mol. Biol. , vol.192 , pp. 605-632
    • Oefner, C.1    Suck, D.2
  • 38
    • 0029945421 scopus 로고    scopus 로고
    • The dimerization property of glutathione S-transferase partially reactivates Bcr-Abl lacking the oligomerization domain
    • Maru Y., Afar D.E., Witte O.N., and Shibuya M. The dimerization property of glutathione S-transferase partially reactivates Bcr-Abl lacking the oligomerization domain. J. Biol. Chem. 271 (1996) 15353-15357
    • (1996) J. Biol. Chem. , vol.271 , pp. 15353-15357
    • Maru, Y.1    Afar, D.E.2    Witte, O.N.3    Shibuya, M.4
  • 39
    • 0037009516 scopus 로고    scopus 로고
    • Structure of Alba: an archaeal chromatin protein modulated by acetylation
    • Wardleworth B.N., Russell R.J., Bell S.D., Taylor G.L., and White M.F. Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J. 21 (2002) 4654-4662
    • (2002) EMBO J. , vol.21 , pp. 4654-4662
    • Wardleworth, B.N.1    Russell, R.J.2    Bell, S.D.3    Taylor, G.L.4    White, M.F.5
  • 41
    • 3543148406 scopus 로고    scopus 로고
    • Expression screening, protein purification and NMR analysis of human protein domains for structural genomics
    • Folkers G.E., van Buuren B.N., and Kaptein R. Expression screening, protein purification and NMR analysis of human protein domains for structural genomics. J. Struct. Funct. Genomics 5 (2004) 119-131
    • (2004) J. Struct. Funct. Genomics , vol.5 , pp. 119-131
    • Folkers, G.E.1    van Buuren, B.N.2    Kaptein, R.3
  • 43
    • 0029245364 scopus 로고
    • Site-directed mutagenesis by double polymerase chain reaction
    • Barik S. Site-directed mutagenesis by double polymerase chain reaction. Mol. Biotechnol. 3 (1995) 1-7
    • (1995) Mol. Biotechnol. , vol.3 , pp. 1-7
    • Barik, S.1
  • 45
    • 0033610857 scopus 로고    scopus 로고
    • Promoter architecture, cofactors, and orphan receptors contribute to cell-specific activation of the retinoic acid receptor beta2 promoter
    • Folkers G.E., van der Burg B., and van der Saag P.T. Promoter architecture, cofactors, and orphan receptors contribute to cell-specific activation of the retinoic acid receptor beta2 promoter. J. Biol. Chem. 273 (1998) 32200-32212
    • (1998) J. Biol. Chem. , vol.273 , pp. 32200-32212
    • Folkers, G.E.1    van der Burg, B.2    van der Saag, P.T.3
  • 47
    • 0028112295 scopus 로고
    • Protein-structure determination with 3-dimensional and 4-dimensional NMR-spectroscopy
    • Oschkinat H., Muller T., and Dieckmann T. Protein-structure determination with 3-dimensional and 4-dimensional NMR-spectroscopy. Angew Chem. Int. Ed. 33 (1994) 277-293
    • (1994) Angew Chem. Int. Ed. , vol.33 , pp. 277-293
    • Oschkinat, H.1    Muller, T.2    Dieckmann, T.3
  • 48
    • 0347722841 scopus 로고    scopus 로고
    • Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients
    • Sattler M., Schleucher J., and Griesinger C. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog. Nucl. Magn. Res. Spectrosc. 34 (1999) 93-158
    • (1999) Prog. Nucl. Magn. Res. Spectrosc. , vol.34 , pp. 93-158
    • Sattler, M.1    Schleucher, J.2    Griesinger, C.3
  • 49
    • 0032694547 scopus 로고    scopus 로고
    • An efficient strategy for assignment of cross-peaks in 3D heteronuclear NOESY experiments
    • Diercks T., Coles M., and Kessler H. An efficient strategy for assignment of cross-peaks in 3D heteronuclear NOESY experiments. J. Biomol. NMR 15 (1999) 177-180
    • (1999) J. Biomol. NMR , vol.15 , pp. 177-180
    • Diercks, T.1    Coles, M.2    Kessler, H.3
  • 50
    • 0027456412 scopus 로고
    • Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIGlc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques
    • Pelton J.G., Torchia D.A., Meadow N.D., and Roseman S. Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIGlc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques. Protein Sci. 2 (1993) 543-558
    • (1993) Protein Sci. , vol.2 , pp. 543-558
    • Pelton, J.G.1    Torchia, D.A.2    Meadow, N.D.3    Roseman, S.4
  • 51
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • Herrmann T., Güntert P., and Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319 (2002) 209-227
    • (2002) J. Mol. Biol. , vol.319 , pp. 209-227
    • Herrmann, T.1    Güntert, P.2    Wüthrich, K.3
  • 52
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • Güntert P., Mumenthaler C., and Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273 (1997) 283-298
    • (1997) J. Mol. Biol. , vol.273 , pp. 283-298
    • Güntert, P.1    Mumenthaler, C.2    Wüthrich, K.3
  • 53
    • 33745096027 scopus 로고    scopus 로고
    • Direct use of unassigned resonances in NMR structure calculations with proxy residues
    • AB E., Pugh D.J., Kaptein R., Boelens R., and Bonvin A.M. Direct use of unassigned resonances in NMR structure calculations with proxy residues. J. Am. Chem. Soc. 128 (2006) 7566-7571
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 7566-7571
    • AB, E.1    Pugh, D.J.2    Kaptein, R.3    Boelens, R.4    Bonvin, A.M.5
  • 54
    • 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. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13 (1999) 289-302
    • (1999) J. Biomol. NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 56
    • 21044449889 scopus 로고    scopus 로고
    • RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
    • Nederveen A.J., Doreleijers J.F., Vranken W., Miller Z., Spronk C.A., Nabuurs S.B., et al. RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59 (2005) 662-672
    • (2005) Proteins , vol.59 , pp. 662-672
    • Nederveen, A.J.1    Doreleijers, J.F.2    Vranken, W.3    Miller, Z.4    Spronk, C.A.5    Nabuurs, S.B.6
  • 57
    • 0025398721 scopus 로고
    • WHAT IF-a molecular modeling and drug design program
    • Vriend G. WHAT IF-a molecular modeling and drug design program. J. Mol. Graphics 8 (1990) 52-58
    • (1990) J. Mol. Graphics , vol.8 , pp. 52-58
    • Vriend, G.1
  • 58
    • 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. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996) 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.