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Volumn 376, Issue 5, 2008, Pages 1237-1250

Structure of the N-Terminal Oligomerization Domain of DnaD Reveals a Unique Tetramerization Motif and Provides Insights into Scaffold Formation

Author keywords

Bacillus subtilis; crystal structure; DNA replication; DnaD; primosomal

Indexed keywords

DNA; PROTEIN; PROTEIN DNAD; UNCLASSIFIED DRUG;

EID: 39149084042     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.12.045     Document Type: Article
Times cited : (23)

References (58)
  • 1
    • 33750312968 scopus 로고    scopus 로고
    • DnaA: controlling the initiation of bacterial DNA replication and more
    • Kaguni J.M. DnaA: controlling the initiation of bacterial DNA replication and more. Annu. Rev. Microbiol. 60 (2006) 351-375
    • (2006) Annu. Rev. Microbiol. , vol.60 , pp. 351-375
    • Kaguni, J.M.1
  • 2
    • 0013371151 scopus 로고    scopus 로고
    • Chromosome replication and segregation
    • Sonenshein A.L., Hoch J.A., and Losick R. (Eds), ASM Press, Washington, DC
    • Lemon K.P., Moriya S., Ogasawara N., and Grossman A.D. Chromosome replication and segregation. In: Sonenshein A.L., Hoch J.A., and Losick R. (Eds). Bacillus subtilis and Its Closest Relatives (2002), ASM Press, Washington, DC 73-86
    • (2002) Bacillus subtilis and Its Closest Relatives , pp. 73-86
    • Lemon, K.P.1    Moriya, S.2    Ogasawara, N.3    Grossman, A.D.4
  • 3
    • 0026777126 scopus 로고
    • Prokaryotic DNA replication
    • Marians K.J. Prokaryotic DNA replication. Annu. Rev. Biochem. 61 (1992) 673-719
    • (1992) Annu. Rev. Biochem. , vol.61 , pp. 673-719
    • Marians, K.J.1
  • 4
    • 33745192288 scopus 로고    scopus 로고
    • Origin inactivation in bacterial DNA replication control
    • Paulsson J., and Chattoraj D.K. Origin inactivation in bacterial DNA replication control. Mol. Microbiol. 61 (2006) 9-15
    • (2006) Mol. Microbiol. , vol.61 , pp. 9-15
    • Paulsson, J.1    Chattoraj, D.K.2
  • 5
    • 0033786801 scopus 로고    scopus 로고
    • Structure and function of hexameric helicases
    • Patel S.S., and Picha K.M. Structure and function of hexameric helicases. Annu. Rev. Biochem. 69 (2000) 651-697
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 651-697
    • Patel, S.S.1    Picha, K.M.2
  • 6
    • 0033988501 scopus 로고    scopus 로고
    • Role of PriA in replication fork reactivation in Escherichia coli
    • Sandler S.J., and Marians K.J. Role of PriA in replication fork reactivation in Escherichia coli. J. Bacteriol. 182 (2000) 9-13
    • (2000) J. Bacteriol. , vol.182 , pp. 9-13
    • Sandler, S.J.1    Marians, K.J.2
  • 7
    • 0029003406 scopus 로고
    • Primosome assembly site in Bacillus subtilis
    • Bruand C., Ehrlich S.D., and Janniere L. Primosome assembly site in Bacillus subtilis. EMBO J. 14 (1995) 2642-2650
    • (1995) EMBO J. , vol.14 , pp. 2642-2650
    • Bruand, C.1    Ehrlich, S.D.2    Janniere, L.3
  • 8
    • 0035725265 scopus 로고    scopus 로고
    • DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome
    • Bruand C., Farache M., McGovern S., Ehrlich S.D., and Polard P. DnaB, DnaD and DnaI proteins are components of the Bacillus subtilis replication restart primosome. Mol. Microbiol. 42 (2001) 245-255
    • (2001) Mol. Microbiol. , vol.42 , pp. 245-255
    • Bruand, C.1    Farache, M.2    McGovern, S.3    Ehrlich, S.D.4    Polard, P.5
  • 9
    • 0028969032 scopus 로고
    • Nucleotide sequence of the Bacillus subtilis dnaD gene
    • Bruand C., Sorokin A., Serror P., and Ehrlich S.D. Nucleotide sequence of the Bacillus subtilis dnaD gene. Microbiology 141 (1995) 321-322
    • (1995) Microbiology , vol.141 , pp. 321-322
    • Bruand, C.1    Sorokin, A.2    Serror, P.3    Ehrlich, S.D.4
  • 10
    • 3042538224 scopus 로고    scopus 로고
    • Identification of temperature-sensitive dnaD mutants of Staphylococcus aureus that are defective in chromosomal DNA replication
    • Li Y., Kurokawa K., Matsuo M., Fukuhara N., Murakami K., and Sekimizu K. Identification of temperature-sensitive dnaD mutants of Staphylococcus aureus that are defective in chromosomal DNA replication. Mol. Genet. Genomics 271 (2004) 447-457
    • (2004) Mol. Genet. Genomics , vol.271 , pp. 447-457
    • Li, Y.1    Kurokawa, K.2    Matsuo, M.3    Fukuhara, N.4    Murakami, K.5    Sekimizu, K.6
  • 11
    • 0035108406 scopus 로고    scopus 로고
    • DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication
    • Ishigo-Oka D., Ogasawara N., and Moriya S. DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication. J. Bacteriol. 183 (2001) 2148-2150
    • (2001) J. Bacteriol. , vol.183 , pp. 2148-2150
    • Ishigo-Oka, D.1    Ogasawara, N.2    Moriya, S.3
  • 13
    • 0842295026 scopus 로고
    • Nucleotide sequence of Bacillus subtilis dnaB: a gene essential for DNA replication initiation and membrane attachment
    • Hoshino T., McKenzie T., Schmidt S., Tanaka T., and Sueoka N. Nucleotide sequence of Bacillus subtilis dnaB: a gene essential for DNA replication initiation and membrane attachment. Proc. Natl. Acad. Sci. USA 84 (1987) 653-657
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 653-657
    • Hoshino, T.1    McKenzie, T.2    Schmidt, S.3    Tanaka, T.4    Sueoka, N.5
  • 14
    • 3042548131 scopus 로고    scopus 로고
    • Control of DNA replication initiation by recruitment of an essential initiation protein to the membrane of Bacillus subtilis
    • Rokop M.E., Auchtung J.M., and Grossman A.D. Control of DNA replication initiation by recruitment of an essential initiation protein to the membrane of Bacillus subtilis. Mol. Microbiol. 52 (2004) 1757-1767
    • (2004) Mol. Microbiol. , vol.52 , pp. 1757-1767
    • Rokop, M.E.1    Auchtung, J.M.2    Grossman, A.D.3
  • 15
    • 33750983641 scopus 로고    scopus 로고
    • Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading Bacillus subtilis
    • Ioannou C., Schaeffer P.M., Dixon N.E., and Soultanas P. Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading Bacillus subtilis. Nucleic Acids Res. 34 (2006) 5247-5258
    • (2006) Nucleic Acids Res. , vol.34 , pp. 5247-5258
    • Ioannou, C.1    Schaeffer, P.M.2    Dixon, N.E.3    Soultanas, P.4
  • 16
    • 33847337926 scopus 로고    scopus 로고
    • Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase
    • Nunez-Ramirez R., Velten M., Rivas G., Polard P., Carazo J.M., and Donate L.E. Loading a ring: structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase. J. Mol. Biol. 367 (2007) 764-769
    • (2007) J. Mol. Biol. , vol.367 , pp. 764-769
    • Nunez-Ramirez, R.1    Velten, M.2    Rivas, G.3    Polard, P.4    Carazo, J.M.5    Donate, L.E.6
  • 17
    • 0037082430 scopus 로고    scopus 로고
    • A functional interaction between the putative primosomal protein DnaI and the main replicative DNA helicase DnaB in Bacillus
    • Soultanas P. A functional interaction between the putative primosomal protein DnaI and the main replicative DNA helicase DnaB in Bacillus. Nucleic Acids Res. 30 (2002) 966-974
    • (2002) Nucleic Acids Res. , vol.30 , pp. 966-974
    • Soultanas, P.1
  • 18
    • 0038637844 scopus 로고    scopus 로고
    • A two-protein strategy for the functional loading of a cellular replicative DNA helicase
    • Velten M., McGovern S., Marsin S., Ehrlich S.D., Noirot P., and Polard P. A two-protein strategy for the functional loading of a cellular replicative DNA helicase. Mol. Cell 11 (2003) 1009-1020
    • (2003) Mol. Cell , vol.11 , pp. 1009-1020
    • Velten, M.1    McGovern, S.2    Marsin, S.3    Ehrlich, S.D.4    Noirot, P.5    Polard, P.6
  • 19
    • 14544302666 scopus 로고    scopus 로고
    • Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and re-initiation of DNA replication
    • Bruand C., Velten M., McGovern S., Marsin S., Serena C., Ehrlich S.D., and Polard P. Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and re-initiation of DNA replication. Mol. Microbiol. 55 (2005) 1138-1150
    • (2005) Mol. Microbiol. , vol.55 , pp. 1138-1150
    • Bruand, C.1    Velten, M.2    McGovern, S.3    Marsin, S.4    Serena, C.5    Ehrlich, S.D.6    Polard, P.7
  • 20
    • 0034101584 scopus 로고    scopus 로고
    • Control of initiation of sporulation by replication initiation genes in Bacillus subtilis
    • Lemon K.P., Kurtser I., Wu J., and Grossman A.D. Control of initiation of sporulation by replication initiation genes in Bacillus subtilis. J. Bacteriol. 182 (2000) 2989-2991
    • (2000) J. Bacteriol. , vol.182 , pp. 2989-2991
    • Lemon, K.P.1    Kurtser, I.2    Wu, J.3    Grossman, A.D.4
  • 21
    • 33746640515 scopus 로고    scopus 로고
    • The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA
    • Zhang W., Allen S., Roberts C.J., and Soultanas P. The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA. J. Bacteriol. 188 (2006) 5487-5493
    • (2006) J. Bacteriol. , vol.188 , pp. 5487-5493
    • Zhang, W.1    Allen, S.2    Roberts, C.J.3    Soultanas, P.4
  • 22
    • 22044451587 scopus 로고    scopus 로고
    • The Bacillus subtilis DnaD and DnaB proteins exhibit different DNA remodelling activities
    • Zhang W., Carneiro M.J., Turner I.J., Allen S., Roberts C.J., and Soultanas P. The Bacillus subtilis DnaD and DnaB proteins exhibit different DNA remodelling activities. J. Mol. Biol. 351 (2005) 66-75
    • (2005) J. Mol. Biol. , vol.351 , pp. 66-75
    • Zhang, W.1    Carneiro, M.J.2    Turner, I.J.3    Allen, S.4    Roberts, C.J.5    Soultanas, P.6
  • 23
    • 8844266092 scopus 로고    scopus 로고
    • The Bacillus subtilis DnaD protein: a putative link between DNA remodelling and initiation of DNA replication
    • Turner I.J., Scott D.J., Allen S., Roberts C.J., and Soultanas P. The Bacillus subtilis DnaD protein: a putative link between DNA remodelling and initiation of DNA replication. FEBS Lett. 577 (2004) 460-464
    • (2004) FEBS Lett. , vol.577 , pp. 460-464
    • Turner, I.J.1    Scott, D.J.2    Allen, S.3    Roberts, C.J.4    Soultanas, P.5
  • 24
    • 33646431990 scopus 로고    scopus 로고
    • The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains
    • Carneiro M.J., Zhang W., Ioannou C., Scott D.J., Allen S., Roberts C.J., and Soultanas P. The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains. Mol. Microbiol. 60 (2006) 917-924
    • (2006) Mol. Microbiol. , vol.60 , pp. 917-924
    • Carneiro, M.J.1    Zhang, W.2    Ioannou, C.3    Scott, D.J.4    Allen, S.5    Roberts, C.J.6    Soultanas, P.7
  • 25
    • 0021346918 scopus 로고
    • Protein HU in the enzymatic replication of the chromosomal origin of E. coli
    • Dixon N.E., and Kornberg A. Protein HU in the enzymatic replication of the chromosomal origin of E. coli. Proc. Natl. Acad. Sci. USA 81 (1984) 424-428
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 424-428
    • Dixon, N.E.1    Kornberg, A.2
  • 26
    • 0026463867 scopus 로고
    • Opening of the replication origin of E. coli by DnaA protein with HU or IHF
    • Hwang D.S., and Kornberg A. Opening of the replication origin of E. coli by DnaA protein with HU or IHF. J. Biol. Chem. 267 (1992) 23083-23086
    • (1992) J. Biol. Chem. , vol.267 , pp. 23083-23086
    • Hwang, D.S.1    Kornberg, A.2
  • 27
    • 0031555485 scopus 로고    scopus 로고
    • Complexes at the replication of B. subtilis with homologous and heterologous DnaA protein
    • Krause M., Ruckert B., Lurz R., and Messer W. Complexes at the replication of B. subtilis with homologous and heterologous DnaA protein. J. Mol. Biol. 274 (1997) 365-380
    • (1997) J. Mol. Biol. , vol.274 , pp. 365-380
    • Krause, M.1    Ruckert, B.2    Lurz, R.3    Messer, W.4
  • 28
    • 0028575868 scopus 로고    scopus 로고
    • Functions of histone-like proteins in the initiation of DNA replication at oriC of Escherichia coli
    • Roth A., Urmoneit B., and Messer W. Functions of histone-like proteins in the initiation of DNA replication at oriC of Escherichia coli. Biochimie 76 (1999) 917-923
    • (1999) Biochimie , vol.76 , pp. 917-923
    • Roth, A.1    Urmoneit, B.2    Messer, W.3
  • 30
    • 0029797932 scopus 로고    scopus 로고
    • The nucleoid protein H-NS facilitates chromosome DNA replication in E. coli dnaA mutants
    • Katayama T., Takata M., and Sekimizu K. The nucleoid protein H-NS facilitates chromosome DNA replication in E. coli dnaA mutants. J. Bacteriol. 178 (1996) 5790-5792
    • (1996) J. Bacteriol. , vol.178 , pp. 5790-5792
    • Katayama, T.1    Takata, M.2    Sekimizu, K.3
  • 31
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 (1993) 123-138
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 33
    • 14244256059 scopus 로고    scopus 로고
    • Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons
    • Safo M.K., Zhao Q., Ko T.P., Musayev F.N., Robinson H., Scarsdale N., et al. Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons. J. Bacteriol. 187 (2005) 1833-1844
    • (2005) J. Bacteriol. , vol.187 , pp. 1833-1844
    • Safo, M.K.1    Zhao, Q.2    Ko, T.P.3    Musayev, F.N.4    Robinson, H.5    Scarsdale, N.6
  • 34
    • 0033546005 scopus 로고    scopus 로고
    • Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA
    • Schwartz T., Rould M.A., Lowenhaupt K., Herbert A., and Rich A. Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284 (1999) 1841-1845
    • (1999) Science , vol.284 , pp. 1841-1845
    • Schwartz, T.1    Rould, M.A.2    Lowenhaupt, K.3    Herbert, A.4    Rich, A.5
  • 35
    • 0033019592 scopus 로고    scopus 로고
    • Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex
    • Jin C., Marsden I., Chen X., and Liao X. Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex. J. Mol. Biol. 289 (1999) 683-690
    • (1999) J. Mol. Biol. , vol.289 , pp. 683-690
    • Jin, C.1    Marsden, I.2    Chen, X.3    Liao, X.4
  • 37
    • 5044245523 scopus 로고    scopus 로고
    • ESCRT-II, an endosome-associated complex required for protein sorting: crystal structure and interactions with ESCRT-III and membranes
    • Teo H., Perisic O., Gonzalez B., and Williams R.L. ESCRT-II, an endosome-associated complex required for protein sorting: crystal structure and interactions with ESCRT-III and membranes. Dev. Cell 7 (2004) 559-569
    • (2004) Dev. Cell , vol.7 , pp. 559-569
    • Teo, H.1    Perisic, O.2    Gonzalez, B.3    Williams, R.L.4
  • 39
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF-a program to identify and analyze structural motifs in proteins
    • Hutchinson E.G., and Thornton J.M. 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
  • 40
    • 0027339355 scopus 로고
    • Accommodating sequence changes in beta-hairpins in proteins
    • Sibanda B.L., and Thornton J.M. Accommodating sequence changes in beta-hairpins in proteins. J. Mol. Biol. 229 (1993) 428-447
    • (1993) J. Mol. Biol. , vol.229 , pp. 428-447
    • Sibanda, B.L.1    Thornton, J.M.2
  • 41
    • 0032006708 scopus 로고    scopus 로고
    • Formation and stability of beta-hairpin structures in polypeptides
    • Blanco F., Ramirez-Alvarado M., and Serrano L. Formation and stability of beta-hairpin structures in polypeptides. Curr. Opin. Struct. Biol. 8 (1998) 107-111
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 107-111
    • Blanco, F.1    Ramirez-Alvarado, M.2    Serrano, L.3
  • 43
    • 0004235822 scopus 로고
    • McPherson M.J., Quirke P., and Taylor G.R. (Eds), IRL Press, Oxford, UK
    • Clackson T., Gussow D., and Jones P.T. In: McPherson M.J., Quirke P., and Taylor G.R. (Eds). PCR-A Practical Approach (1991), IRL Press, Oxford, UK
    • (1991) PCR-A Practical Approach
    • Clackson, T.1    Gussow, D.2    Jones, P.T.3
  • 44
    • 33847098779 scopus 로고    scopus 로고
    • Crystallization and X-ray diffraction analysis of the DNA-remodelling protein DnaD from Bacillus subtilis
    • Schneider S., Carneiro M.J.V.M., Ioannou C., Soultanas P., and Paoli M. Crystallization and X-ray diffraction analysis of the DNA-remodelling protein DnaD from Bacillus subtilis. Acta Crystallogr., Sect. F F63 (2007) 110-113
    • (2007) Acta Crystallogr., Sect. F , vol.F63 , pp. 110-113
    • Schneider, S.1    Carneiro, M.J.V.M.2    Ioannou, C.3    Soultanas, P.4    Paoli, M.5
  • 45
    • 0025262173 scopus 로고
    • Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three dimensional structure
    • Hendrickson W.A., Horton J.R., and LeMaster D.M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three dimensional structure. EMBO J. 9 (1990) 1665-1672
    • (1990) EMBO J. , vol.9 , pp. 1665-1672
    • Hendrickson, W.A.1    Horton, J.R.2    LeMaster, D.M.3
  • 48
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • CCP4
    • CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 (1994) 760-763
    • (1994) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.50 , pp. 760-763
  • 50
    • 0031058188 scopus 로고    scopus 로고
    • Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods
    • de La Fortelle E., and Bricogne G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods in Enzymology 276 (1997) 472-494
    • (1997) Methods in Enzymology , vol.276 , pp. 472-494
    • de La Fortelle, E.1    Bricogne, G.2
  • 52
    • 0013461295 scopus 로고    scopus 로고
    • Macromolecular TLS refinement in REFMAC at moderate resolutions
    • Winn M.D., Murshudov G.N., and Papiz M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374 (2003) 300-321
    • (2003) Methods Enzymol. , vol.374 , pp. 300-321
    • Winn, M.D.1    Murshudov, G.N.2    Papiz, M.Z.3
  • 54
    • 33645158291 scopus 로고    scopus 로고
    • TLSMD web server for the generation of multi-group TLS models
    • Painter J., and Merritt E.A. TLSMD web server for the generation of multi-group TLS models. J. Appl. Crystallogr. 39 (2006) 109-111
    • (2006) J. Appl. Crystallogr. , vol.39 , pp. 109-111
    • Painter, J.1    Merritt, E.A.2
  • 55
    • 3242886389 scopus 로고    scopus 로고
    • MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    • Davis I.W., Murray L.W., Richardson J.S., and Richardson D.C. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res. 32 (2004) W615-W619
    • (2004) Nucleic Acids Res. , vol.32
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 57
    • 0028922586 scopus 로고
    • LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
    • Wallace A.C., Laskowski R.A., and Thornton J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8 (1995) 127-134
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3


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