메뉴 건너뛰기




Volumn 16, Issue 4, 2008, Pages 558-569

Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding

Author keywords

DNA

Indexed keywords

GENOMIC DNA; IRON; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE NOTI; UNCLASSIFIED DRUG;

EID: 41449117713     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.01.017     Document Type: Article
Times cited : (32)

References (53)
  • 2
    • 0029123025 scopus 로고
    • Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 Å resolution: a novel non-heme iron protein structure
    • Archer M., Huber R., Tavares P., Moura I., Moura J.J., Carrondo M.A., Sieker L.C., LeGall J., and Romao M.J. Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 Å resolution: a novel non-heme iron protein structure. J. Mol. Biol. 251 (1995) 690-702
    • (1995) J. Mol. Biol. , vol.251 , pp. 690-702
    • Archer, M.1    Huber, R.2    Tavares, P.3    Moura, I.4    Moura, J.J.5    Carrondo, M.A.6    Sieker, L.C.7    LeGall, J.8    Romao, M.J.9
  • 3
  • 4
  • 6
    • 0036880785 scopus 로고    scopus 로고
    • Complex restriction enzymes: NTP-driven molecular motors
    • Bourniquel A.A., and Bickle T.A. Complex restriction enzymes: NTP-driven molecular motors. Biochimie 84 (2002) 1047-1059
    • (2002) Biochimie , vol.84 , pp. 1047-1059
    • Bourniquel, A.A.1    Bickle, T.A.2
  • 7
    • 0035066732 scopus 로고    scopus 로고
    • The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites
    • Chevalier B.S., Monnat Jr. R.J., and Stoddard B.L. The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nat. Struct. Biol. 8 (2001) 312-316
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 312-316
    • Chevalier, B.S.1    Monnat Jr., R.J.2    Stoddard, B.L.3
  • 8
    • 0033745660 scopus 로고    scopus 로고
    • Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease
    • Chinen A., Naito Y., Handa N., and Kobayashi I. Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease. Mol. Biol. Evol. 17 (2000) 1610-1619
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1610-1619
    • Chinen, A.1    Naito, Y.2    Handa, N.3    Kobayashi, I.4
  • 10
    • 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. Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat. Struct. Biol. 7 (2000) 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
  • 11
    • 0029949340 scopus 로고    scopus 로고
    • The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains
    • deMare F., Kurtz Jr. D.M., and Nordlund P. The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains. Nat. Struct. Biol. 3 (1996) 539-546
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 539-546
    • deMare, F.1    Kurtz Jr., D.M.2    Nordlund, P.3
  • 12
    • 0026601976 scopus 로고
    • Artificial mobile DNA element constructed from the EcoRI endonuclease gene
    • Eddy S.R., and Gold L. Artificial mobile DNA element constructed from the EcoRI endonuclease gene. Proc. Natl. Acad. Sci. USA 89 (1992) 1544-1547
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 1544-1547
    • Eddy, S.R.1    Gold, L.2
  • 13
    • 0033806414 scopus 로고    scopus 로고
    • Barriers to intron promiscuity in bacteria
    • Edgell D.R., Belfort M., and Shub D.A. Barriers to intron promiscuity in bacteria. J. Bacteriol. 182 (2000) 5281-5289
    • (2000) J. Bacteriol. , vol.182 , pp. 5281-5289
    • Edgell, D.R.1    Belfort, M.2    Shub, D.A.3
  • 14
    • 33846035027 scopus 로고    scopus 로고
    • The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated
    • Ferrer M., Golyshina O.V., Beloqui A., Golyshin P.N., and Timmis K.N. The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 445 (2007) 91-94
    • (2007) Nature , vol.445 , pp. 91-94
    • Ferrer, M.1    Golyshina, O.V.2    Beloqui, A.3    Golyshin, P.N.4    Timmis, K.N.5
  • 15
    • 0001531847 scopus 로고    scopus 로고
    • Iron-sulfur proteins with nonredox functions
    • Flint D.H., and Allen R.M. Iron-sulfur proteins with nonredox functions. Chem. Rev. 96 (1996) 2315-2334
    • (1996) Chem. Rev. , vol.96 , pp. 2315-2334
    • Flint, D.H.1    Allen, R.M.2
  • 17
    • 27644485012 scopus 로고    scopus 로고
    • Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease
    • Grazulis S., Manakova E., Roessle M., Bochtler M., Tamulaitiene G., Huber R., and Siksnys V. Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease. Proc. Natl. Acad. Sci. USA 102 (2005) 15797-15802
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15797-15802
    • Grazulis, S.1    Manakova, E.2    Roessle, M.3    Bochtler, M.4    Tamulaitiene, G.5    Huber, R.6    Siksnys, V.7
  • 18
    • 0032728707 scopus 로고    scopus 로고
    • Post-segregational killing by restriction modification gene complexes: observations of individual cell deaths
    • Handa N., and Kobayashi I. Post-segregational killing by restriction modification gene complexes: observations of individual cell deaths. Biochimie 81 (1999) 931-938
    • (1999) Biochimie , vol.81 , pp. 931-938
    • Handa, N.1    Kobayashi, I.2
  • 19
    • 0034034023 scopus 로고    scopus 로고
    • Cellular responses to postsegregational killing by restriction-modification genes
    • Handa N., Ichige A., Kusano K., and Kobayashi I. Cellular responses to postsegregational killing by restriction-modification genes. J. Bacteriol. 182 (2000) 2218-2229
    • (2000) J. Bacteriol. , vol.182 , pp. 2218-2229
    • Handa, N.1    Ichige, A.2    Kusano, K.3    Kobayashi, I.4
  • 20
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L., and Sander C. Mapping the protein universe. Science 273 (1996) 595-603
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 22
    • 33645065589 scopus 로고    scopus 로고
    • Iron-sulphur clusters and the problem with oxygen
    • Imlay J.A. Iron-sulphur clusters and the problem with oxygen. Mol. Microbiol. 59 (2006) 1073-1082
    • (2006) Mol. Microbiol. , vol.59 , pp. 1073-1082
    • Imlay, J.A.1
  • 24
    • 20744446399 scopus 로고    scopus 로고
    • Structure, function, and formation of biological iron-sulfur clusters
    • Johnson D.C., Dean D.R., Smith A.D., and Johnson M.K. Structure, function, and formation of biological iron-sulfur clusters. Annu. Rev. Biochem. 74 (2005) 247-281
    • (2005) Annu. Rev. Biochem. , vol.74 , pp. 247-281
    • Johnson, D.C.1    Dean, D.R.2    Smith, A.D.3    Johnson, M.K.4
  • 25
    • 0035883519 scopus 로고    scopus 로고
    • Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
    • Kobayashi I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res. 29 (2001) 3742-3746
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3742-3746
    • Kobayashi, I.1
  • 27
    • 0033981010 scopus 로고    scopus 로고
    • Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 Å resolution
    • Lukacs C.M., Kucera R., Schildkraut I., and Aggarwal A.K. Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 Å resolution. Nat. Struct. Biol. 7 (2000) 134-140
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 134-140
    • Lukacs, C.M.1    Kucera, R.2    Schildkraut, I.3    Aggarwal, A.K.4
  • 28
    • 16344377473 scopus 로고    scopus 로고
    • A role for iron-sulfur clusters in DNA repair
    • Lukianova O.A., and David S.S. A role for iron-sulfur clusters in DNA repair. Curr. Opin. Chem. Biol. 9 (2005) 145-151
    • (2005) Curr. Opin. Chem. Biol. , vol.9 , pp. 145-151
    • Lukianova, O.A.1    David, S.S.2
  • 33
    • 0023460924 scopus 로고
    • NotI and SfiI: restriction endonucleases with octanucleotide recognition sequences
    • Qiang B.Q., and Schildkraut I. NotI and SfiI: restriction endonucleases with octanucleotide recognition sequences. Methods Enzymol. 155 (1987) 15-21
    • (1987) Methods Enzymol. , vol.155 , pp. 15-21
    • Qiang, B.Q.1    Schildkraut, I.2
  • 36
    • 9144246375 scopus 로고    scopus 로고
    • Comparative study of methyl-CpG-binding domain proteins
    • 10.1186/1471-2164-4-1 Published online January 16 2003
    • Roloff T.C., Ropers H.H., and Nuber U.A. Comparative study of methyl-CpG-binding domain proteins. BMC Genomics 4 (2003) 1 10.1186/1471-2164-4-1 Published online January 16 2003
    • (2003) BMC Genomics , vol.4 , pp. 1
    • Roloff, T.C.1    Ropers, H.H.2    Nuber, U.A.3
  • 37
    • 0037102325 scopus 로고    scopus 로고
    • Restriction landmark genomic scanning for DNA methylation in cancer: past, present, and future applications
    • Rush L.J., and Plass C. Restriction landmark genomic scanning for DNA methylation in cancer: past, present, and future applications. Anal. Biochem. 307 (2002) 191-201
    • (2002) Anal. Biochem. , vol.307 , pp. 191-201
    • Rush, L.J.1    Plass, C.2
  • 38
    • 33644868063 scopus 로고    scopus 로고
    • Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants
    • Samuelson J.C., Morgan R.D., Benner J.S., Claus T.E., Packard S.L., and Xu S.Y. Engineering a rare-cutting restriction enzyme: genetic screening and selection of NotI variants. Nucleic Acids Res. 34 (2006) 796-805
    • (2006) Nucleic Acids Res. , vol.34 , pp. 796-805
    • Samuelson, J.C.1    Morgan, R.D.2    Benner, J.S.3    Claus, T.E.4    Packard, S.L.5    Xu, S.Y.6
  • 39
    • 11344267268 scopus 로고    scopus 로고
    • Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily
    • Saravanan M., Bujnicki J.M., Cymerman I.A., Rao D.N., and Nagaraja V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucleic Acids Res. 32 (2004) 6129-6135
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6129-6135
    • Saravanan, M.1    Bujnicki, J.M.2    Cymerman, I.A.3    Rao, D.N.4    Nagaraja, V.5
  • 40
    • 0032486108 scopus 로고    scopus 로고
    • Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues
    • Skirgaila R., Grazulis S., Bozic D., Huber R., and Siksnys V. Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues. J. Mol. Biol. 279 (1998) 473-481
    • (1998) J. Mol. Biol. , vol.279 , pp. 473-481
    • Skirgaila, R.1    Grazulis, S.2    Bozic, D.3    Huber, R.4    Siksnys, V.5
  • 41
    • 0037068375 scopus 로고    scopus 로고
    • The study of aberrant methylation in cancer via restriction landmark genomic scanning
    • Smiraglia D.J., and Plass C. The study of aberrant methylation in cancer via restriction landmark genomic scanning. Oncogene 21 (2002) 5414-5426
    • (2002) Oncogene , vol.21 , pp. 5414-5426
    • Smiraglia, D.J.1    Plass, C.2
  • 42
    • 0025648526 scopus 로고
    • The structure of rubredoxin from Desulfovibrio desulfuricans strain 27,774 at 1.5 Å resolution
    • Stenkamp R.E., Sieker L.C., and Jensen L.H. The structure of rubredoxin from Desulfovibrio desulfuricans strain 27,774 at 1.5 Å resolution. Proteins 8 (1990) 352-364
    • (1990) Proteins , vol.8 , pp. 352-364
    • Stenkamp, R.E.1    Sieker, L.C.2    Jensen, L.H.3
  • 43
    • 0024297455 scopus 로고
    • The characterization and cloning of the EagI restriction-modification system
    • Sznyter L.A., and Brooks J.E. The characterization and cloning of the EagI restriction-modification system. Gene 74 (1988) 53
    • (1988) Gene , vol.74 , pp. 53
    • Sznyter, L.A.1    Brooks, J.E.2
  • 44
    • 33748310747 scopus 로고    scopus 로고
    • The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture
    • Tamulaitiene G., Jakubauskas A., Urbanke C., Huber R., Grazulis S., and Siksnys V. The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture. Structure 14 (2006) 1389-1400
    • (2006) Structure , vol.14 , pp. 1389-1400
    • Tamulaitiene, G.1    Jakubauskas, A.2    Urbanke, C.3    Huber, R.4    Grazulis, S.5    Siksnys, V.6
  • 45
    • 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
  • 46
    • 1942425560 scopus 로고    scopus 로고
    • Crystal structure of BstYI at 1.85 Å resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII
    • Townson S.A., Samuelson J.C., Vanamee E.S., Edwards T.A., Escalante C.R., Xu S.Y., and Aggarwal A.K. Crystal structure of BstYI at 1.85 Å resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII. J. Mol. Biol. 338 (2004) 725-733
    • (2004) J. Mol. Biol. , vol.338 , pp. 725-733
    • Townson, S.A.1    Samuelson, J.C.2    Vanamee, E.S.3    Edwards, T.A.4    Escalante, C.R.5    Xu, S.Y.6    Aggarwal, A.K.7
  • 47
    • 28644435380 scopus 로고    scopus 로고
    • A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA
    • Vanamee E.S., Viadiu H., Kucera R., Dorner L., Picone S., Schildkraut I., and Aggarwal A.K. A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J. 24 (2005) 4198-4208
    • (2005) EMBO J. , vol.24 , pp. 4198-4208
    • Vanamee, E.S.1    Viadiu, H.2    Kucera, R.3    Dorner, L.4    Picone, S.5    Schildkraut, I.6    Aggarwal, A.K.7
  • 49
    • 4444373591 scopus 로고    scopus 로고
    • An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site
    • Xu Q.S., Kucera R.B., Roberts R.J., and Guo H.C. An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure 12 (2004) 1741-1747
    • (2004) Structure , vol.12 , pp. 1741-1747
    • Xu, Q.S.1    Kucera, R.B.2    Roberts, R.J.3    Guo, H.C.4
  • 50
    • 0025865885 scopus 로고
    • Isolation of BamHI variants with reduced cleavage activities
    • Xu S.-Y., and Schildkraut I. Isolation of BamHI variants with reduced cleavage activities. J. Biol. Chem. 266 (1991) 4425-4429
    • (1991) J. Biol. Chem. , vol.266 , pp. 4425-4429
    • Xu, S.-Y.1    Schildkraut, I.2
  • 51
    • 36248983896 scopus 로고    scopus 로고
    • Rational design of a chimeric endonuclease targeted to NotI recognition site
    • 10.1093/protein/gzm049 Published online October 20 2007
    • Zhang P., Bao Y., Higgins L., and Xu S.-Y. Rational design of a chimeric endonuclease targeted to NotI recognition site. Protein Eng. Des. Sel. 20 (2007) 497-504 10.1093/protein/gzm049 Published online October 20 2007
    • (2007) Protein Eng. Des. Sel. , vol.20 , pp. 497-504
    • Zhang, P.1    Bao, Y.2    Higgins, L.3    Xu, S.-Y.4
  • 52
    • 34247628027 scopus 로고    scopus 로고
    • The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif
    • Zhao L., Bonocora R.P., Shub D.A., and Stoddard B.L. The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. EMBO J. 26 (2007) 2432-2442
    • (2007) EMBO J. , vol.26 , pp. 2432-2442
    • Zhao, L.1    Bonocora, R.P.2    Shub, D.A.3    Stoddard, B.L.4
  • 53
    • 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. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J. Mol. Biol. 335 (2004) 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.