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Volumn 37, Issue 20, 2009, Pages 6960-6969

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: Implications for DNA restriction and translocation activity

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; BACTERIAL DNA; RECA PROTEIN; RESTRICTION ENDONUCLEASE; DNA; PROTEIN SUBUNIT; TYPE I SITE SPECIFIC DEOXYRIBONUCLEASE;

EID: 73349100057     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp603     Document Type: Article
Times cited : (23)

References (48)
  • 1
    • 0034130457 scopus 로고    scopus 로고
    • Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)
    • Murray, N.E. (2000) Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol. Mol. Biol. Rev., 64, 412-434.
    • (2000) Microbiol. Mol. Biol. Rev. , vol.64 , pp. 412-434
    • Murray, N.E.1
  • 2
    • 0035883536 scopus 로고    scopus 로고
    • Nucleoside triphosphate-dependent restriction enzymes
    • Dryden, D.T.F., Murray, N.E. and Rao, D.N. (2001) Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res., 29, 3728-3741.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3728-3741
    • Dryden, D.T.F.1    Murray, N.E.2    Rao, D.N.3
  • 3
    • 2442549510 scopus 로고    scopus 로고
    • S-Adenosyl-L-methionine-dependent restriction enzymes
    • Sistla, S. and Rao, D.N. (2004) S-Adenosyl-L-methionine-dependent restriction enzymes. Crit. Rev. Biochem. Mol. Biol., 39, 1-19.
    • (2004) Crit. Rev. Biochem. Mol. Biol. , vol.39 , pp. 1-19
    • Sistla, S.1    Rao, D.N.2
  • 4
    • 0026338873 scopus 로고
    • Restriction and modification systems
    • Wilson, G.G. and Murray, N.E. (1991) Restriction and modification systems. Annu. Rev. Genet., 25, 585-627.
    • (1991) Annu. Rev. Genet. , vol.25 , pp. 585-627
    • Wilson, G.G.1    Murray, N.E.2
  • 5
    • 19544389295 scopus 로고    scopus 로고
    • KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system
    • Chin, V., Valinluck, V., Magaki, S. and Ryu, J. (2004) KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system. Nucleic Acids Res., 32, e138.
    • (2004) Nucleic Acids Res. , vol.32
    • Chin, V.1    Valinluck, V.2    Magaki, S.3    Ryu, J.4
  • 6
    • 0026503940 scopus 로고
    • Purification and biochemical characterisation of the EcoR124 type I modification methylase
    • Taylor, I.P.J., Firman, K. and Kneale, G. (1992) Purification and biochemical characterisation of the EcoR124 type I modification methylase. Nucleic Acids Res., 20, 179-186.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 179-186
    • Taylor, I.P.J.1    Firman, K.2    Kneale, G.3
  • 7
    • 0032509099 scopus 로고    scopus 로고
    • The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutation of its polypeptide chain
    • Janscak, P. and Bickle, T.A. (1998) The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutation of its polypeptide chain. J. Mol. Biol., 284, 937-948.
    • (1998) J. Mol. Biol. , vol.284 , pp. 937-948
    • Janscak, P.1    Bickle, T.A.2
  • 8
    • 0034595208 scopus 로고    scopus 로고
    • Measuring motion on DNA by the type I restriction endonuclease EcoR1241 using triplex displacement
    • Firman, K. and Szczelkun, M.D. (2000) Measuring motion on DNA by the type I restriction endonuclease EcoR1241 using triplex displacement. EMBO J., 19, 2094-2102.
    • (2000) EMBO J. , vol.19 , pp. 2094-2102
    • Firman, K.1    Szczelkun, M.D.2
  • 10
    • 0027497325 scopus 로고
    • Purification and Characterization of the methyltransferase from the Type 1 Restriction and Modification System of Escherichia coli K12
    • Dryden, D.T., Cooper, L.P. and Murray, N.E. (1993) Purification and Characterization of the methyltransferase from the Type 1 Restriction and Modification System of Escherichia coli K12. J. Biol. Chem., 268, 13228-13236.
    • (1993) J. Biol. Chem. , vol.268 , pp. 13228-13236
    • Dryden, D.T.1    Cooper, L.P.2    Murray, N.E.3
  • 12
    • 0033522512 scopus 로고    scopus 로고
    • DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes
    • Janscak, P., MacWilliams, M.P., Sandmeier, U. and Nagaraja, V. (1999) DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes. EMBO J., 18, 2638-2647.
    • (1999) EMBO J. , vol.18 , pp. 2638-2647
    • Janscak, P.1    MacWilliams, M.P.2    Sandmeier, U.3    Nagaraja, V.4
  • 14
    • 14744267674 scopus 로고    scopus 로고
    • Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications
    • USA
    • Kim, J.S., DeGiovanni, A., Jancarik, J., Adams, P.D., Yokota, H., Kim, R. and Kim, S.H. (2005) Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc. Natl Acad. Sci. USA, 102, 3248-3253.
    • (2005) Proc. Natl Acad. Sci. , vol.102 , pp. 3248-3253
    • Kim, J.S.1    DeGiovanni, A.2    Jancarik, J.3    Adams, P.D.4    Yokota, H.5    Kim, R.6    Kim, S.H.7
  • 15
    • 23444459393 scopus 로고    scopus 로고
    • Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium
    • Calisto, R.M., Pich, O.Q., Pinol, J., Fita, I., Querol, E. and Carpena, X. (2005) Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium. J. Mol. Biol., 351, 749-762.
    • (2005) J. Mol. Biol. , vol.351 , pp. 749-762
    • Calisto, R.M.1    Pich, O.Q.2    Pinol, J.3    Fita, I.4    Querol, E.5    Carpena, X.6
  • 17
    • 38349125372 scopus 로고    scopus 로고
    • HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modeling
    • Obarska-Kosinska, A., Taylor, J.E., Callow, P., Orlowski, J., Bujnicki, J.M. and Kneale, G.G. (2008) HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modeling. J. Mol. Biol., 376, 438-452.
    • (2008) J. Mol. Biol. , vol.376 , pp. 438-452
    • Obarska-Kosinska, A.1    Taylor, J.E.2    Callow, P.3    Orlowski, J.4    Bujnicki, J.M.5    Kneale, G.G.6
  • 19
    • 47249088354 scopus 로고    scopus 로고
    • A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I
    • Sisakova, E., Stanley, L.K., Weiserova, M. and Szczelkun, M.D. (2008) A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I. Nucleic Acids Res., 36, 3939-3949.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3939-3949
    • Sisakova, E.1    Stanley, L.K.2    Weiserova, M.3    Szczelkun, M.D.4
  • 20
    • 53749084424 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray diffraction analysis of HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
    • Nguyen, T.U., Nishi, K., Park, S.Y., Choi, J.W., Lee, H.J. and Kim, J.S. (2008) Crystallization and preliminary X-ray diffraction analysis of HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016. Acta Crystallogr. Sect. F., 64, 926-928.
    • (2008) Acta Crystallogr. Sect. F. , vol.64 , pp. 926-928
    • Nguyen, T.U.1    Nishi, K.2    Park, S.Y.3    Choi, J.W.4    Lee, H.J.5    Kim, J.S.6
  • 21
    • 0031059866 scopus 로고    scopus 로고
    • Procession of x-ray diffraction data collected in oscillation mode
    • Otwinowski, Z. and Minor, W. (1997) Procession 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
  • 24
  • 25
    • 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, Z.Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A., 47, 110-117.
    • (1991) Acta Crystallogr. A. , vol.47 , pp. 110-117
    • Jones, T.A.1    Zou, Z.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 26
    • 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. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr., 57, 122-133.
    • (2001) Acta Crystallogr. D Biol. Crystallogr. , vol.57 , pp. 122-133
    • Winn, M.D.1    Isupov, M.N.2    Murshudov, G.N.3
  • 28
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski, R., MacArthur, M., Hutchinson, E. and Thorton, J. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.1    MacArthur, M.2    Hutchinson, E.3    Thorton, J.4
  • 30
    • 0032502894 scopus 로고    scopus 로고
    • Crystal structure and evolution of a transfer RNA splicing enzyme
    • Li, H., Trotta, C.R. and Abelson, J. (1998) Crystal structure and evolution of a transfer RNA splicing enzyme. Science, 280, 279-284.
    • (1998) Science , vol.280 , pp. 279-284
    • Li, H.1    Trotta, C.R.2    Abelson, J.3
  • 31
    • 0032555574 scopus 로고    scopus 로고
    • Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts
    • Horton, N.C. and Perona, J.J. (1998) Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts. J. Biol. Chem., 273, 21721-21729.
    • (1998) J. Biol. Chem. , vol.273 , pp. 21721-21729
    • Horton, N.C.1    Perona, J.J.2
  • 32
    • 0033818703 scopus 로고    scopus 로고
    • Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA
    • Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V. and Huber, R. (2000) Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat. Struct. Biol., 7, 792-799.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 792-799
    • Deibert, M.1    Grazulis, S.2    Sasnauskas, G.3    Siksnys, V.4    Huber, R.5
  • 33
  • 35
    • 33645988522 scopus 로고    scopus 로고
    • Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair
    • Fan, L., Arvai, A., Cooper, P.K., Iwai, S., Hanaoka, F. and Tainer, J.A. (2006) Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Mol. Cell., 22, 27-37.
    • (2006) Mol. Cell. , vol.22 , pp. 27-37
    • Fan, L.1    Arvai, A.2    Cooper, P.K.3    Iwai, S.4    Hanaoka, F.5    Tainer, J.A.6
  • 36
    • 18844457346 scopus 로고    scopus 로고
    • X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA
    • Durr, H., Korner, C., Muller, M., Hickmann, V. and Hopfner, K.P. (2005) X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell, 121, 363-373.
    • (2005) Cell , vol.121 , pp. 363-373
    • Durr, H.1    Korner, C.2    Muller, M.3    Hickmann, V.4    Hopfner, K.P.5
  • 37
    • 0032717259 scopus 로고    scopus 로고
    • Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus
    • Machius, M., Henry, L., Palnitkar, M. and Deisenhofer, J. (1999) Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus. Proc. Natl Acad. Sci. USA, 96, 11717-11722.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 11717-11722
    • Machius, M.1    Henry, L.2    Palnitkar, M.3    Deisenhofer, J.4
  • 40
    • 0032518490 scopus 로고    scopus 로고
    • Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding
    • Kim, J.L., Morgenstern, K.A., Griffith, J.P., Dwyer, M.D., Thomson, J.A., Murcko, M.A., Lin, C. and Caron, P.R. (1998) Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure, 6, 89-100.
    • (1998) Structure , vol.6 , pp. 89-100
    • Kim, J.L.1    Morgenstern, K.A.2    Griffith, J.P.3    Dwyer, M.D.4    Thomson, J.A.5    Murcko, M.A.6    Lin, C.7    Caron, P.R.8
  • 42
    • 11144222543 scopus 로고    scopus 로고
    • Crystal structure of the human ATP-dependent splicing and export factor UAP56
    • Shi, H., Cordin, O., Minder, C.M., Linder, P. and Xu, R.M. (2004) Crystal structure of the human ATP-dependent splicing and export factor UAP56. Proc. Natl Acad. Sci. USA, 101, 17628-17633.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17628-17633
    • Shi, H.1    Cordin, O.2    Minder, C.M.3    Linder, P.4    Xu, R.M.5
  • 43
    • 0023732866 scopus 로고
    • Model for how type-I restriction enzymes select cleavage sites in DNA
    • Studier, F.W. and Bandyopadhyay, P.K. (1988) Model for how type-I restriction enzymes select cleavage sites in DNA. Proc. Natl Acad. Sci. USA, 85, 4677-4681.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 4677-4681
    • Studier, F.W.1    Bandyopadhyay, P.K.2
  • 44
    • 0033918211 scopus 로고    scopus 로고
    • Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy
    • Berge, T., Ellis, D.J., Dryden, D.T., Edwardson, J.M. and Henderson, R.M. (2000) Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy. Biophys. J., 79, 479-484.
    • (2000) Biophys. J. , vol.79 , pp. 479-484
    • Berge, T.1    Ellis, D.J.2    Dryden, D.T.3    Edwardson, J.M.4    Henderson, R.M.5
  • 45
    • 0033515425 scopus 로고    scopus 로고
    • Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism
    • Velankar, S.S., Soultanas, P., Dillingham, M.S., Subramanya, H.S. and Wigley, D.B. (1999) Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell, 97, 75-98.
    • (1999) Cell , vol.97 , pp. 75-98
    • Velankar, S.S.1    Soultanas, P.2    Dillingham, M.S.3    Subramanya, H.S.4    Wigley, D.B.5
  • 47
    • 0034723157 scopus 로고    scopus 로고
    • DNA supercoiling during ATP-dependent DNA translocation by the Type I restriction enzyme EcoAI
    • Janscak, P. and Bickle, T.A. (2000) DNA supercoiling during ATP-dependent DNA translocation by the Type I restriction enzyme EcoAI. J. Mol. Biol., 295, 1089-1099.
    • (2000) J. Mol. Biol. , vol.295 , pp. 1089-1099
    • Janscak, P.1    Bickle, T.A.2
  • 48
    • 56849134577 scopus 로고    scopus 로고
    • The interrelationship of helicase and nuclease domains during DNA translocation by the molecular motor EcoR124I
    • Sisáková, E., Weiserová, M., Dekker, C., Seidel, R. and Szczelkun, M.D. (2008) The interrelationship of helicase and nuclease domains during DNA translocation by the molecular motor EcoR124I. J. Mol. Biol., 384, 1273-1286.
    • (2008) J. Mol. Biol. , vol.384 , pp. 1273-1286
    • Sisáková, E.1    Weiserová, M.2    Dekker, C.3    Seidel, R.4    Szczelkun, M.D.5


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