메뉴 건너뛰기




Volumn 36, Issue 19, 2008, Pages 6109-6117

Central base pair flipping and discrimination by PspGI

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA; GUANOSINE; PROTEIN PSPGI; RESTRICTION ENDONUCLEASE; THYMINE; UNCLASSIFIED DRUG;

EID: 56049121435     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn622     Document Type: Article
Times cited : (31)

References (33)
  • 2
    • 0031685558 scopus 로고    scopus 로고
    • Characterization of an extremely thermostable restriction enzyme, PspGI, from a Pyrococcus strain and cloning of the PspGI restriction-modification system in Escherichia coli
    • Morgan,R., Xiao,J. and Xu,S. (1998) Characterization of an extremely thermostable restriction enzyme, PspGI, from a Pyrococcus strain and cloning of the PspGI restriction-modification system in Escherichia coli. Appl. Environ. Microbiol., 64, 3669-3673.
    • (1998) Appl. Environ. Microbiol , vol.64 , pp. 3669-3673
    • Morgan, R.1    Xiao, J.2    Xu, S.3
  • 3
    • 0015891545 scopus 로고
    • Recognition sequence of a restriction enzyme
    • Bigger,C.H., Murray,K. and Murray,N.E. (1973) Recognition sequence of a restriction enzyme. Nat. New Biol., 244, 7-10.
    • (1973) Nat. New Biol , vol.244 , pp. 7-10
    • Bigger, C.H.1    Murray, K.2    Murray, N.E.3
  • 4
    • 0015806892 scopus 로고
    • DNA substrate site for the EcoRII restriction endonuclease and modi.cation methylase
    • Boyer,H.W., Chow,L.T., Dugaiczyk,A., Hedgpeth,J. and Goodman,H.M. (1973) DNA substrate site for the EcoRII restriction endonuclease and modi.cation methylase. Nat. New Biol., 244, 40-43.
    • (1973) Nat. New Biol , vol.244 , pp. 40-43
    • Boyer, H.W.1    Chow, L.T.2    Dugaiczyk, A.3    Hedgpeth, J.4    Goodman, H.M.5
  • 7
    • 0037531222 scopus 로고    scopus 로고
    • PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: Structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes
    • Pingoud,V., Conzelmann,C., Kinzebach,S., Sudina,A., Metelev,V., Kubareva,E., Bujnicki,J.M., Lurz,R., Luder,G., Xu,S.Y. et al. (2003) PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: Structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. J. Mol. Biol., 329, 913-929.
    • (2003) J. Mol. Biol , vol.329 , pp. 913-929
    • Pingoud, V.1    Conzelmann, C.2    Kinzebach, S.3    Sudina, A.4    Metelev, V.5    Kubareva, E.6    Bujnicki, J.M.7    Lurz, R.8    Luder, G.9    Xu, S.Y.10
  • 8
    • 0037042192 scopus 로고    scopus 로고
    • Alternative arrangements of catalytic residues at the active sites of restriction enzymes
    • Tamulaitis,G., Solonin,A.S. and Siksnys,V. (2002) Alternative arrangements of catalytic residues at the active sites of restriction enzymes. FEBS Lett., 518, 17-22.
    • (2002) FEBS Lett , vol.518 , pp. 17-22
    • Tamulaitis, G.1    Solonin, A.S.2    Siksnys, V.3
  • 9
    • 33344465796 scopus 로고    scopus 로고
    • Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes
    • Tamulaitis,G., Mucke,M. and Siksnys,V. (2006) Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes. FEBS Lett., 580, 1665-1671.
    • (2006) FEBS Lett , vol.580 , pp. 1665-1671
    • Tamulaitis, G.1    Mucke, M.2    Siksnys, V.3
  • 10
    • 0345549459 scopus 로고    scopus 로고
    • Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold
    • Zhou,X.E., Wang,Y., Reuter,M., Mucke,M., Kruger,D.H., Meehan,E.J. and Chen,L. (2004) Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J. Mol. Biol., 335, 307-319.
    • (2004) J. Mol. Biol , vol.335 , pp. 307-319
    • Zhou, X.E.1    Wang, Y.2    Reuter, M.3    Mucke, M.4    Kruger, D.H.5    Meehan, E.J.6    Chen, L.7
  • 12
    • 34547862040 scopus 로고    scopus 로고
    • Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence
    • Tamulaitis,G., Zaremba,M., Szczepanowski,R.H., Bochtler,M. and Siksnys,V. (2007) Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence. Nucleic Acids Res., 35 4792-4799.
    • (2007) Nucleic Acids Res , vol.35 , pp. 4792-4799
    • Tamulaitis, G.1    Zaremba, M.2    Szczepanowski, R.H.3    Bochtler, M.4    Siksnys, V.5
  • 13
    • 52649140087 scopus 로고    scopus 로고
    • DNA base flipping by both members of the PspGI restriction-modification system
    • Carpenter,M.A. and Bhagwat,A.S. (2008) DNA base flipping by both members of the PspGI restriction-modification system. Nucleic Acids Res.
    • (2008) Nucleic Acids Res
    • Carpenter, M.A.1    Bhagwat, A.S.2
  • 14
    • 33748754281 scopus 로고    scopus 로고
    • Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI
    • Carpenter,M., Divvela,P., Pingoud,V., Bujnicki,J. and Bhagwat,A.S. (2006) Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI. Nucleic Acids Res. 34, 3762-3770.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3762-3770
    • Carpenter, M.1    Divvela, P.2    Pingoud, V.3    Bujnicki, J.4    Bhagwat, A.S.5
  • 17
    • 0038210935 scopus 로고    scopus 로고
    • Advances in direct methods for protein crystallography
    • Uson,I. and Sheldrick,G.M. (1999) Advances in direct methods for protein crystallography. Curr. Opin. Struct. Biol., 9, 643-648.
    • (1999) Curr. Opin. Struct. Biol , vol.9 , pp. 643-648
    • Uson, I.1    Sheldrick, G.M.2
  • 18
    • 0013054388 scopus 로고    scopus 로고
    • Macromolecular phasing with SHELXE
    • Sheldrick,G.M. (2002) Macromolecular phasing with SHELXE. Z Kristallogr, 217, 644-650.
    • (2002) Z Kristallogr , vol.217 , pp. 644-650
    • Sheldrick, G.M.1
  • 19
    • 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
  • 20
    • 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. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2
  • 21
    • 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,M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A, 47(Pt 2), 110-119.
    • (1991) Acta Crystallogr. A , vol.47 , Issue.PART 2 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 22
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/X.t - a versatile program for manipulating atomic coordinates and electron density
    • McRee,D.E. (1999) XtalView/X.t - a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol., 125 156-165.
    • (1999) J. Struct. Biol , vol.125 , pp. 156-165
    • McRee, D.E.1
  • 23
    • 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 Cryst., D53, 240-255.
    • (1997) Acta Cryst , vol.D53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 25
    • 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
  • 26
    • 0028010888 scopus 로고
    • HhaI methyltransferase flips its target base out of the DNA helix
    • Klimasauskas,S., Kumar,S., Roberts,R.J. and Cheng,X. (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369.
    • (1994) Cell , vol.76 , pp. 357-369
    • Klimasauskas, S.1    Kumar, S.2    Roberts, R.J.3    Cheng, X.4
  • 27
    • 0029904839 scopus 로고    scopus 로고
    • A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
    • Slupphaug,G., Mol,C.D., Kavli,B., Arvai,A.S., Krokan,H.E. and Tainer,J.A. (1996) A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature, 384, 87-92.
    • (1996) Nature , vol.384 , pp. 87-92
    • Slupphaug, G.1    Mol, C.D.2    Kavli, B.3    Arvai, A.S.4    Krokan, H.E.5    Tainer, J.A.6
  • 28
    • 0037675807 scopus 로고    scopus 로고
    • Crystal structures of the T4 phage beta-glucosyltransferase and the D100A mutant in complex with UDP-glucose: Glucose binding and identification of the catalytic base for a direct displacement mechanism
    • Lariviere,L., Gueguen-Chaignon,V. and Morera,S. (2003) Crystal structures of the T4 phage beta-glucosyltransferase and the D100A mutant in complex with UDP-glucose: Glucose binding and identification of the catalytic base for a direct displacement mechanism. J. Mol. Biol., 330, 1077-1086.
    • (2003) J. Mol. Biol , vol.330 , pp. 1077-1086
    • Lariviere, L.1    Gueguen-Chaignon, V.2    Morera, S.3
  • 30
    • 0027318463 scopus 로고
    • Sequence-dependent DNA structure. The role of base stacking interactions
    • Hunter,C.A. (1993) Sequence-dependent DNA structure. The role of base stacking interactions. J. Mol. Biol., 230, 1025-1054.
    • (1993) J. Mol. Biol , vol.230 , pp. 1025-1054
    • Hunter, C.A.1
  • 31
    • 0028963346 scopus 로고
    • Enthalpy-entropy compensation in DNA melting thermodynamics
    • Petruska,J. and Goodman,M.F. (1995) Enthalpy-entropy compensation in DNA melting thermodynamics. J. Biol. Chem., 270, 746-750.
    • (1995) J. Biol. Chem , vol.270 , pp. 746-750
    • Petruska, J.1    Goodman, M.F.2
  • 32
    • 0037335588 scopus 로고    scopus 로고
    • Base pair opening within B-DNA: Free energy pathways for GC and AT pairs from umbrella sampling simulations
    • Giudice,E., Varnai,P. and Lavery,R. (2003) Base pair opening within B-DNA: Free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Res., 31, 1434-1443.
    • (2003) Nucleic Acids Res , vol.31 , pp. 1434-1443
    • Giudice, E.1    Varnai, P.2    Lavery, R.3
  • 33
    • 1842479316 scopus 로고    scopus 로고
    • Linear free energy correlations for enzymatic base flipping: How do damaged base pairs facilitate speci.c recognition?
    • Krosky,D.J., Schwarz,F.P. and Stivers,J.T. (2004) Linear free energy correlations for enzymatic base flipping: How do damaged base pairs facilitate speci.c recognition? Biochemistry, 43, 4188-4195.
    • (2004) Biochemistry , vol.43 , pp. 4188-4195
    • Krosky, D.J.1    Schwarz, F.P.2    Stivers, J.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.