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Volumn 40, Issue 15, 2012, Pages 7016-7045

SURVEY AND SUMMARY: Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHODIESTERASE; PROTEIN COG1395; PROTEIN COG5482; PROTEIN DUF3883; PROTEIN DUF4263; PROTEIN DUF4420; PROTEIN ECO711; PROTEIN HAELL; PROTEIN HPAII; PROTEIN REPLIC RELAX; PROTEIN SCAL; PROTEIN TSP451; TRANSFER RNA; UNCLASSIFIED DRUG; RESTRICTION ENDONUCLEASE;

EID: 84867287187     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks382     Document Type: Review
Times cited : (112)

References (163)
  • 1
    • 46349101158 scopus 로고    scopus 로고
    • Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
    • Orlowski, J. and Bujnicki, J. M. (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res., 36, 3552-3569.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3552-3569
    • Orlowski, J.1    Bujnicki, J.M.2
  • 2
    • 0031587825 scopus 로고    scopus 로고
    • Another bridge between kingdoms: Trna splicing in archaea and eukaryotes
    • Belfort, M. and Weiner, A. (1997) Another bridge between kingdoms: tRNA splicing in archaea and eukaryotes. Cell, 89, 1003-1006.
    • (1997) Cell , vol.89 , pp. 1003-1006
    • Belfort, M.1    Weiner, A.2
  • 3
    • 0033634859 scopus 로고    scopus 로고
    • Unexpected structural diversity in DNA recombination: The restriction endonuclease connection
    • Hickman, A. B., Li, Y., Mathew, S. V., May, E. W., Craig, N. L. and Dyda, F. (2000) Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol. Cell, 5, 1025-1034.
    • (2000) Mol. Cell , vol.5 , pp. 1025-1034
    • Hickman, A.B.1    Li, Y.2    Mathew, S.V.3    May, E.W.4    Craig, N.L.5    Dyda, F.6
  • 4
    • 70350435285 scopus 로고    scopus 로고
    • Crystal structure of the shutoff and exonuclease protein from the oncogenic Kaposi's sarcoma-associated herpesvirus
    • Dahlroth, S. L., Gurmu, D., Schmitzberger, F., Engman, H., Haas, J., Erlandsen, H. and Nordlund, P. (2009) Crystal structure of the shutoff and exonuclease protein from the oncogenic Kaposi's sarcoma-associated herpesvirus. FEBS J., 276, 6636-6645.
    • (2009) FEBS J. , vol.276 , pp. 6636-6645
    • Dahlroth, S.L.1    Gurmu, D.2    Schmitzberger, F.3    Engman, H.4    Haas, J.5    Erlandsen, H.6    Nordlund, P.7
  • 5
    • 0034664813 scopus 로고    scopus 로고
    • SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: Identification of new families, phyletic distribution and evolutionary trajectories
    • Aravind, L., Makarova, K. S. and Koonin, E. V. (2000) SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res., 28, 3417-3432.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 3417-3432
    • Aravind, L.1    Makarova, K.S.2    Koonin, E.V.3
  • 6
    • 0032473571 scopus 로고    scopus 로고
    • Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases
    • Ban, C. and Yang, W. (1998) Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases. EMBO J., 17, 1526-1534.
    • (1998) EMBO J. , vol.17 , pp. 1526-1534
    • Ban, C.1    Yang, W.2
  • 7
    • 64749111945 scopus 로고    scopus 로고
    • Structure and function of the 5'->3' exoribonuclease Rat1 and its activating partner Rai1
    • Xiang, S., Cooper-Morgan, A., Jiao, X., Kiledjian, M., Manley, J. L. and Tong, L. (2009) Structure and function of the 5'->3' exoribonuclease Rat1 and its activating partner Rai1. Nature, 458, 784-788.
    • (2009) Nature , vol.458 , pp. 784-788
    • Xiang, S.1    Cooper-Morgan, A.2    Jiao, X.3    Kiledjian, M.4    Manley, J.L.5    Tong, L.6
  • 8
    • 0034612217 scopus 로고    scopus 로고
    • Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target
    • Todone, F., Weinzierl, R. O., Brick, P. and Onesti, S. (2000) Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proc. Natl Acad. Sci. USA, 97, 6306-6310.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 6306-6310
    • Todone, F.1    Weinzierl, R.O.2    Brick, P.3    Onesti, S.4
  • 9
    • 12444336898 scopus 로고    scopus 로고
    • X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: Similarity between its endonuclease domain and restriction enzymes
    • Nishino, T., Komori, K., Ishino, Y. and Morikawa, K. (2003) X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease: similarity between its endonuclease domain and restriction enzymes. Structure, 11, 445-457.
    • (2003) Structure , vol.11 , pp. 445-457
    • Nishino, T.1    Komori, K.2    Ishino, Y.3    Morikawa, K.4
  • 10
    • 25444501004 scopus 로고    scopus 로고
    • Identification of a new family of putative PD-(D/E) XK nucleases with unusual phylogenomic distribution and a new type of the active site
    • Feder, M. and Bujnicki, J. M. (2005) Identification of a new family of putative PD-(D/E) XK nucleases with unusual phylogenomic distribution and a new type of the active site. BMC Genomics, 6, 21.
    • (2005) BMC Genomics , vol.6 , pp. 21
    • Feder, M.1    Bujnicki, J.M.2
  • 11
    • 79952318529 scopus 로고    scopus 로고
    • Identification of new homologs of PD-(D/E) XK nucleases by support vector machines trained on data derived from profile-profile alignments
    • Laganeckas, M., Margelevicius, M. and Venclovas, C. (2011) Identification of new homologs of PD-(D/E) XK nucleases by support vector machines trained on data derived from profile-profile alignments. Nucleic Acids Res., 39, 1187-1196.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 1187-1196
    • Laganeckas, M.1    Margelevicius, M.2    Venclovas, C.3
  • 12
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G., Brenner, S. E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 13
    • 17044403057 scopus 로고    scopus 로고
    • Type II restriction endonucleases: Structure and mechanism
    • Pingoud, A., Fuxreiter, M., Pingoud, V. and Wende, W. (2005) Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci., 62, 685-707.
    • (2005) Cell. Mol. Life Sci. , vol.62 , pp. 685-707
    • Pingoud, A.1    Fuxreiter, M.2    Pingoud, V.3    Wende, W.4
  • 15
    • 33745727120 scopus 로고    scopus 로고
    • Structural diversity of domain superfamilies in the CATH database
    • Reeves, G. A., Dallman, T. J., Redfern, O. C., Akpor, A. and Orengo, C. A. (2006) Structural diversity of domain superfamilies in the CATH database. J. Mol. Biol., 360, 725-741.
    • (2006) J. Mol. Biol. , vol.360 , pp. 725-741
    • Reeves, G.A.1    Dallman, T.J.2    Redfern, O.C.3    Akpor, A.4    Orengo, C.A.5
  • 16
    • 9144271294 scopus 로고    scopus 로고
    • Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks
    • Singleton, M. R., Dillingham, M. S., Gaudier, M., Kowalczykowski, S. C. and Wigley, D. B. (2004) Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature, 432, 187-193.
    • (2004) Nature , vol.432 , pp. 187-193
    • Singleton, M.R.1    Dillingham, M.S.2    Gaudier, M.3    Kowalczykowski, S.C.4    Wigley, D.B.5
  • 17
    • 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
  • 21
    • 0027324744 scopus 로고
    • Biology of DNA restriction
    • Bickle, T. A. and Kruger, D. H. (1993) Biology of DNA restriction. Microbiol. Rev., 57, 434-450.
    • (1993) Microbiol. Rev. , vol.57 , pp. 434-450
    • Bickle, T.A.1    Kruger, D.H.2
  • 22
    • 0029940857 scopus 로고    scopus 로고
    • Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems
    • Jeltsch, A. and Pingoud, A. (1996) Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems. J. Mol. Evol., 42, 91-96.
    • (1996) J. Mol. Evol. , vol.42 , pp. 91-96
    • Jeltsch, A.1    Pingoud, A.2
  • 23
    • 25844494491 scopus 로고    scopus 로고
    • MutH complexed with hemi-and unmethylated DNAs: Coupling base recognition and DNA cleavage
    • Lee, J. Y., Chang, J., Joseph, N., Ghirlando, R., Rao, D. N. and Yang, W. (2005) MutH complexed with hemi-and unmethylated DNAs: coupling base recognition and DNA cleavage. Mol. Cell, 20, 155-166.
    • (2005) Mol. Cell , vol.20 , pp. 155-166
    • Lee, J.Y.1    Chang, J.2    Joseph, N.3    Ghirlando, R.4    Rao, D.N.5    Yang, W.6
  • 25
    • 24344457115 scopus 로고    scopus 로고
    • The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage
    • McGregor, N., Ayora, S., Sedelnikova, S., Carrasco, B., Alonso, J. C., Thaw, P. and Rafferty, J. (2005) The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage. Structure, 13, 1341-1351.
    • (2005) Structure , vol.13 , pp. 1341-1351
    • McGregor, N.1    Ayora, S.2    Sedelnikova, S.3    Carrasco, B.4    Alonso, J.C.5    Thaw, P.6    Rafferty, J.7
  • 28
    • 42149183549 scopus 로고    scopus 로고
    • Crystal structure of the Mus81-Eme1 complex
    • Chang, J. H., Kim, J. J., Choi, J. M., Lee, J. H. and Cho, Y. (2008) Crystal structure of the Mus81-Eme1 complex. Genes Dev., 22, 1093-1106.
    • (2008) Genes Dev. , vol.22 , pp. 1093-1106
    • Chang, J.H.1    Kim, J.J.2    Choi, J.M.3    Lee, J.H.4    Cho, Y.5
  • 30
    • 68149163563 scopus 로고    scopus 로고
    • A bridge crosses the active-site canyon of the Epstein-Barr virus nuclease with DNase and RNase activities
    • Buisson, M., Geoui, T., Flot, D., Tarbouriech, N., Ressing, M. E., Wiertz, E. J. and Burmeister, W. P. (2009) A bridge crosses the active-site canyon of the Epstein-Barr virus nuclease with DNase and RNase activities. J. Mol. Biol., 391, 717-728.
    • (2009) J. Mol. Biol. , vol.391 , pp. 717-728
    • Buisson, M.1    Geoui, T.2    Flot, D.3    Tarbouriech, N.4    Ressing, M.E.5    Wiertz, E.J.6    Burmeister, W.P.7
  • 31
    • 0030881051 scopus 로고    scopus 로고
    • Toroidal structure of lambda-exonuclease
    • Kovall, R. and Matthews, B. W. (1997) Toroidal structure of lambda-exonuclease. Science, 277, 1824-1827.
    • (1997) Science , vol.277 , pp. 1824-1827
    • Kovall, R.1    Matthews, B.W.2
  • 32
    • 42949101518 scopus 로고    scopus 로고
    • Pet127 governs a 5' -> 3'-exonuclease important in maturation of apocytochrome b mRNA in Saccharomyces cerevisiae
    • Fekete, Z., Ellis, T. P., Schonauer, M. S. and Dieckmann, C. L. (2008) Pet127 governs a 5' -> 3'-exonuclease important in maturation of apocytochrome b mRNA in Saccharomyces cerevisiae. J. Biol. Chem., 283, 3767-3772.
    • (2008) J. Biol. Chem. , vol.283 , pp. 3767-3772
    • Fekete, Z.1    Ellis, T.P.2    Schonauer, M.S.3    Dieckmann, C.L.4
  • 34
    • 79960350167 scopus 로고    scopus 로고
    • The xeroderma pigmentosum pathway: Decision tree analysis of DNA quality
    • Naegeli, H. and Sugasawa, K. (2011) The xeroderma pigmentosum pathway: decision tree analysis of DNA quality. DNA Repair, 10, 673-683.
    • (2011) DNA Repair , vol.10 , pp. 673-683
    • Naegeli, H.1    Sugasawa, K.2
  • 35
    • 72149090671 scopus 로고    scopus 로고
    • FANCM connects the genome instability disorders Bloom's Syndrome and Fanconi Anemia
    • Deans, A. J. and West, S. C. (2009) FANCM connects the genome instability disorders Bloom's Syndrome and Fanconi Anemia. Mol. Cell, 36, 943-953.
    • (2009) Mol. Cell , vol.36 , pp. 943-953
    • Deans, A.J.1    West, S.C.2
  • 36
    • 34447128115 scopus 로고    scopus 로고
    • Realm of PD-(D/E) XK nuclease superfamily revisited: Detection of novel families with modified transitive meta profile searches
    • Knizewski, L., Kinch, L. N., Grishin, N. V., Rychlewski, L. and Ginalski, K. (2007) Realm of PD-(D/E) XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches. BMC Struct. Biol., 7, 40.
    • (2007) BMC Struct. Biol. , vol.7 , pp. 40
    • Knizewski, L.1    Kinch, L.N.2    Grishin, N.V.3    Rychlewski, L.4    Ginalski, K.5
  • 37
    • 33144466677 scopus 로고    scopus 로고
    • Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E) XK endonuclease
    • Knizewski, L., Kinch, L., Grishin, N. V., Rychlewski, L. and Ginalski, K. (2006) Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E) XK endonuclease. J. Virol., 80, 2575-2577.
    • (2006) J. Virol. , vol.80 , pp. 2575-2577
    • Knizewski, L.1    Kinch, L.2    Grishin, N.V.3    Rychlewski, L.4    Ginalski, K.5
  • 38
    • 1542316315 scopus 로고    scopus 로고
    • NERD: A DNA processing-related domain present in the anthrax virulence plasmid, pXO1
    • Grynberg, M. and Godzik, A. (2004) NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1. Trends Biochem. Sci., 29, 106-110.
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 106-110
    • Grynberg, M.1    Godzik, A.2
  • 39
    • 21344435463 scopus 로고    scopus 로고
    • Identification of novel restriction endonuclease-like fold families among hypothetical proteins
    • Kinch, L. N., Ginalski, K., Rychlewski, L. and Grishin, N. V. (2005) Identification of novel restriction endonuclease-like fold families among hypothetical proteins. Nucleic Acids Res., 33, 3598-3605.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 3598-3605
    • Kinch, L.N.1    Ginalski, K.2    Rychlewski, L.3    Grishin, N.V.4
  • 41
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski, K., Elofsson, A., Fischer, D. and Rychlewski, L. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics, 19, 1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 43
    • 0037433034 scopus 로고    scopus 로고
    • PCMA: Fast and accurate multiple sequence alignment based on profile consistency
    • Pei, J., Sadreyev, R. and Grishin, N. V. (2003) PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics, 19, 427-428.
    • (2003) Bioinformatics , vol.19 , pp. 427-428
    • Pei, J.1    Sadreyev, R.2    Grishin, N.V.3
  • 44
    • 0242267511 scopus 로고    scopus 로고
    • Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
    • Ginalski, K. and Rychlewski, L. (2003) Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment. Proteins, 53(Suppl 6), 410-417.
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 410-417
    • Ginalski, K.1    Rychlewski, L.2
  • 45
    • 34447332520 scopus 로고    scopus 로고
    • Searching for three-dimensional secondary structural patterns in proteins with ProSMoS
    • Shi, S., Zhong, Y., Majumdar, I., Sri Krishna, S. and Grishin, N. V. (2007) Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. Bioinformatics, 23, 1331-1338.
    • (2007) Bioinformatics , vol.23 , pp. 1331-1338
    • Shi, S.1    Zhong, Y.2    Majumdar, I.3    Krishna, S.S.4    Grishin, N.V.5
  • 47
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., Dao, P., Sahinalp, S. C., Ester, M., Foster, L. J. et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 26, 1608-1615.
    • (2010) Bioinformatics , vol.26 , pp. 1608-1615
    • Yu, N.Y.1    Wagner, J.R.2    Laird, M.R.3    Melli, G.4    Rey, S.5    Lo, R.6    Dao, P.7    Sahinalp, S.C.8    Ester, M.9    Foster, L.J.10
  • 48
    • 1942505330 scopus 로고    scopus 로고
    • Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions
    • Yu, C. S., Lin, C. J. and Hwang, J. K. (2004) Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci., 13, 1402-1406.
    • (2004) Protein Sci. , vol.13 , pp. 1402-1406
    • Yu, C.S.1    Lin, C.J.2    Hwang, J.K.3
  • 50
    • 33646861792 scopus 로고    scopus 로고
    • MultiLoc: Prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
    • Hoglund, A., Donnes, P., Blum, T., Adolph, H. W. and Kohlbacher, O. (2006) MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics, 22, 1158-1165.
    • (2006) Bioinformatics , vol.22 , pp. 1158-1165
    • Hoglund, A.1    Donnes, P.2    Blum, T.3    Adolph, H.W.4    Kohlbacher, O.5
  • 54
    • 10044222704 scopus 로고    scopus 로고
    • CLANS: A Java application for visualizing protein families based on pairwise similarity
    • Frickey, T. and Lupas, A. (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics, 20, 3702-3704.
    • (2004) Bioinformatics , vol.20 , pp. 3702-3704
    • Frickey, T.1    Lupas, A.2
  • 56
    • 11244346041 scopus 로고    scopus 로고
    • NARG2 encodes a novel nuclear protein with (S/T) PXX motifs that is expressed during development
    • Sugiura, N., Dadashev, V. and Corriveau, R. A. (2004) NARG2 encodes a novel nuclear protein with (S/T) PXX motifs that is expressed during development. Eur. J. Biochem., 271, 4629-4637.
    • (2004) Eur. J. Biochem. , vol.271 , pp. 4629-4637
    • Sugiura, N.1    Dadashev, V.2    Corriveau, R.A.3
  • 58
    • 0034660061 scopus 로고    scopus 로고
    • Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase
    • Huai, Q., Colandene, J. D., Chen, Y., Luo, F., Zhao, Y., Topal, M. D. and Ke, H. (2000) Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase. EMBO J., 19, 3110-3118.
    • (2000) EMBO J. , vol.19 , pp. 3110-3118
    • Huai, Q.1    Colandene, J.D.2    Chen, Y.3    Luo, F.4    Zhao, Y.5    Topal, M.D.6    Ke, H.7
  • 59
    • 0032530311 scopus 로고    scopus 로고
    • Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence
    • Newman, M., Lunnen, K., Wilson, G., Greci, J., Schildkraut, I. and Phillips, S. E. (1998) Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. EMBO J., 17, 5466-5476.
    • (1998) EMBO J. , vol.17 , pp. 5466-5476
    • Newman, M.1    Lunnen, K.2    Wilson, G.3    Greci, J.4    Schildkraut, I.5    Phillips, S.E.6
  • 60
    • 33744546367 scopus 로고    scopus 로고
    • DNA looping by two-site restriction endonucleases: Heterogeneous probability distributions for loop size and unbinding force
    • Gemmen, G. J., Millin, R. and Smith, D. E. (2006) DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. Nucleic Acids Res., 34, 2864-2877.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2864-2877
    • Gemmen, G.J.1    Millin, R.2    Smith, D.E.3
  • 61
    • 0028998124 scopus 로고
    • Restriction and modification systems of Neisseria gonorrhoeae
    • Stein, D. C., Gunn, J. S., Radlinska, M. and Piekarowicz, A. (1995) Restriction and modification systems of Neisseria gonorrhoeae. Gene, 157, 19-22.
    • (1995) Gene , vol.157 , pp. 19-22
    • Stein, D.C.1    Gunn, J.S.2    Radlinska, M.3    Piekarowicz, A.4
  • 63
    • 34249866596 scopus 로고    scopus 로고
    • A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering
    • Kosinski, J., Kubareva, E. and Bujnicki, J. M. (2007) A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering. Proteins, 68, 324-336.
    • (2007) Proteins , vol.68 , pp. 324-336
    • Kosinski, J.1    Kubareva, E.2    Bujnicki, J.M.3
  • 65
    • 0018260789 scopus 로고
    • A new restriction endonuclease from Streptomyces albus G
    • Arrand, J. R., Myers, P. A. and Roberts, R. J. (1978) A new restriction endonuclease from Streptomyces albus G. J. Mol. Biol., 118, 127-135.
    • (1978) J. Mol. Biol. , vol.118 , pp. 127-135
    • Arrand, J.R.1    Myers, P.A.2    Roberts, R.J.3
  • 66
    • 0022422393 scopus 로고
    • Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products
    • Theriault, G., Roy, P. H., Howard, K. A., Benner, J. S., Brooks, J. E., Waters, A. F. and Gingeras, T. R. (1985) Nucleotide sequence of the PaeR7 restriction/modification system and partial characterization of its protein products. Nucleic Acids Res., 13, 8441-8461.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 8441-8461
    • Theriault, G.1    Roy, P.H.2    Howard, K.A.3    Benner, J.S.4    Brooks, J.E.5    Waters, A.F.6    Gingeras, T.R.7
  • 67
    • 0035151431 scopus 로고    scopus 로고
    • Grouping together highly diverged PD-(D/E) XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles
    • Bujnicki, J. M. and Rychlewski, L. (2001) Grouping together highly diverged PD-(D/E) XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles. J. Mol. Microbiol. Biotechnol., 3, 69-72.
    • (2001) J. Mol. Microbiol. Biotechnol. , vol.3 , pp. 69-72
    • Bujnicki, J.M.1    Rychlewski, L.2
  • 68
    • 0029048413 scopus 로고
    • Structure of Bam HI endonuclease bound to DNA: Partial folding and unfolding on DNA binding
    • Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I. and Aggarwal, A. K. (1995) Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science, 269, 656-663.
    • (1995) Science , vol.269 , pp. 656-663
    • Newman, M.1    Strzelecka, T.2    Dorner, L.F.3    Schildkraut, I.4    Aggarwal, A.K.5
  • 69
    • 0033981010 scopus 로고    scopus 로고
    • Understanding the immutability of restriction enzymes: Crystal structure of BglII and its DNA substrate at 1.5 A resolution
    • Lukacs, C. M., Kucera, R., Schildkraut, I. and Aggarwal, A. K. (2000) Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Nat. Struct. Biol., 7, 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
  • 70
    • 0033579567 scopus 로고    scopus 로고
    • Reactions of type II restriction endonucleases with 8-base pair recognition sites
    • Bilcock, D. T., Daniels, L. E., Bath, A. J. and Halford, S. E. (1999) Reactions of type II restriction endonucleases with 8-base pair recognition sites. J. Biol. Chem., 274, 36379-36386.
    • (1999) J. Biol. Chem. , vol.274 , pp. 36379-36386
    • Bilcock, D.T.1    Daniels, L.E.2    Bath, A.J.3    Halford, S.E.4
  • 71
    • 0029067358 scopus 로고
    • Cloning and characterization of the unusual restriction-modification system comprising two restriction endonucleases and one methyltransferase
    • Stankevicius, K., Povilionis, P., Lubys, A., Menkevicius, S. and Janulaitis, A. (1995) Cloning and characterization of the unusual restriction-modification system comprising two restriction endonucleases and one methyltransferase. Gene, 157, 49-53.
    • (1995) Gene , vol.157 , pp. 49-53
    • Stankevicius, K.1    Povilionis, P.2    Lubys, A.3    Menkevicius, S.4    Janulaitis, A.5
  • 73
    • 0033202956 scopus 로고    scopus 로고
    • Site-directed mutagenesis of restriction endonuclease HindIII
    • Dahai, T., Ando, S., Takasaki, Y. and Tadano, J. (1999) Site-directed mutagenesis of restriction endonuclease HindIII. Biosci. Biotechnol. Biochem., 63, 1703-1707.
    • (1999) Biosci. Biotechnol. Biochem. , vol.63 , pp. 1703-1707
    • Dahai, T.1    Ando, S.2    Takasaki, Y.3    Tadano, J.4
  • 74
    • 14044252836 scopus 로고    scopus 로고
    • Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA
    • Hashimoto, H., Shimizu, T., Imasaki, T., Kato, M., Shichijo, N., Kita, K. and Sato, M. (2005) Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA. J. Biol. Chem., 280, 5605-5610.
    • (2005) J. Biol. Chem. , vol.280 , pp. 5605-5610
    • Hashimoto, H.1    Shimizu, T.2    Imasaki, T.3    Kato, M.4    Shichijo, N.5    Kita, K.6    Sato, M.7
  • 76
    • 35748982414 scopus 로고    scopus 로고
    • Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease
    • Sapienza, P. J., Rosenberg, J. M. and Jen-Jacobson, L. (2007) Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease. Structure, 15, 1368-1382.
    • (2007) Structure , vol.15 , pp. 1368-1382
    • Sapienza, P.J.1    Rosenberg, J.M.2    Jen-Jacobson, L.3
  • 77
    • 0027008370 scopus 로고
    • Structure and evolution of the XcyI restriction-modification system
    • Withers, B. E., Ambroso, L. A. and Dunbar, J. C. (1992) Structure and evolution of the XcyI restriction-modification system. Nucleic Acids Res., 20, 6267-6273.
    • (1992) Nucleic Acids Res. , vol.20 , pp. 6267-6273
    • Withers, B.E.1    Ambroso, L.A.2    Dunbar, J.C.3
  • 78
    • 0035096078 scopus 로고    scopus 로고
    • Restriction enzyme BsoBI-DNA complex: A tunnel for recognition of degenerate DNA sequences and potential histidine catalysis
    • van der Woerd, M. J., Pelletier, J. J., Xu, S. and Friedman, A. M. (2001) Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure, 9, 133-144.
    • (2001) Structure , vol.9 , pp. 133-144
    • Van Der Woerd, M.J.1    Pelletier, J.J.2    Xu, S.3    Friedman, A.M.4
  • 79
    • 57049101786 scopus 로고    scopus 로고
    • Early interrogation and recognition of DNA sequence by indirect readout
    • Little, E. J., Babic, A. C. and Horton, N. C. (2008) Early interrogation and recognition of DNA sequence by indirect readout. Structure, 16, 1828-1837.
    • (2008) Structure , vol.16 , pp. 1828-1837
    • Little, E.J.1    Babic, A.C.2    Horton, N.C.3
  • 80
    • 0024509697 scopus 로고
    • Nucleotide sequence and genetic organization of the NgoPII restriction-modification system of Neisseria gonorrhoeae
    • Sullivan, K. M. and Saunders, J. R. (1989) Nucleotide sequence and genetic organization of the NgoPII restriction-modification system of Neisseria gonorrhoeae. Mol. Gen. Genet., 216, 380-387.
    • (1989) Mol. Gen. Genet. , vol.216 , pp. 380-387
    • Sullivan, K.M.1    Saunders, J.R.2
  • 81
    • 0030781097 scopus 로고    scopus 로고
    • The Tsp45I restriction-modification system is plasmid-borne within its thermophilic host
    • Wayne, J., Holden, M. and Xu, S. Y. (1997) The Tsp45I restriction-modification system is plasmid-borne within its thermophilic host. Gene, 202, 83-88.
    • (1997) Gene , vol.202 , pp. 83-88
    • Wayne, J.1    Holden, M.2    Xu, S.Y.3
  • 82
    • 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. (2004) An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure, 12, 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
  • 83
    • 0033229820 scopus 로고    scopus 로고
    • Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution
    • Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V. and Huber, R. (1999) Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution. EMBO J., 18, 5805-5816.
    • (1999) EMBO J. , vol.18 , pp. 5805-5816
    • Deibert, M.1    Grazulis, S.2    Janulaitis, A.3    Siksnys, V.4    Huber, R.5
  • 85
    • 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
  • 86
    • 0029995002 scopus 로고    scopus 로고
    • Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution
    • Bozic, D., Grazulis, S., Siksnys, V. and Huber, R. (1996) Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution. J. Mol. Biol., 255, 176-186.
    • (1996) J. Mol. Biol. , vol.255 , pp. 176-186
    • Bozic, D.1    Grazulis, S.2    Siksnys, V.3    Huber, R.4
  • 87
    • 0032519309 scopus 로고    scopus 로고
    • Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes
    • Stankevicius, K., Lubys, A., Timinskas, A., Vaitkevicius, D. and Janulaitis, A. (1998) Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes. Nucleic Acids Res., 26, 1084-1091.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1084-1091
    • Stankevicius, K.1    Lubys, A.2    Timinskas, A.3    Vaitkevicius, D.4    Janulaitis, A.5
  • 88
    • 84954358674 scopus 로고    scopus 로고
    • Structural analysis of the heterodimeric type IIS restriction endonuclease R. BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit
    • Kachalova, G. S., Rogulin, E. A., Yunusova, A. K., Artyukh, R. I., Perevyazova, T. A., Matvienko, N. I., Zheleznaya, L. A. and Bartunik, H. D. (2008) Structural analysis of the heterodimeric type IIS restriction endonuclease R. BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit. J. Mol. Biol., 384, 489-502.
    • (2008) J. Mol. Biol. , vol.384 , pp. 489-502
    • Kachalova, G.S.1    Rogulin, E.A.2    Yunusova, A.K.3    Artyukh, R.I.4    Perevyazova, T.A.5    Matvienko, N.I.6    Zheleznaya, L.A.7    Bartunik, H.D.8
  • 89
    • 33646547959 scopus 로고    scopus 로고
    • A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system
    • O'Driscoll, J., Heiter, D. F., Wilson, G. G., Fitzgerald, G. F., Roberts, R. and van Sinderen, D. (2006) A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system. BMC Microbiol., 6, 40.
    • (2006) BMC Microbiol. , vol.6 , pp. 40
    • O'Driscoll, J.1    Heiter, D.F.2    Wilson, G.G.3    Fitzgerald, G.F.4    Roberts, R.5    Van Sinderen, D.6
  • 90
    • 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. (2006) The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture. Structure, 14, 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
  • 91
    • 14244254584 scopus 로고    scopus 로고
    • Specificity changes in the evolution of type II restriction endonucleases: A biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences
    • Pingoud, V., Sudina, A., Geyer, H., Bujnicki, J. M., Lurz, R., Luder, G., Morgan, R., Kubareva, E. and Pingoud, A. (2005) Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences. J. Biol. Chem., 280, 4289-4298.
    • (2005) J. Biol. Chem. , vol.280 , pp. 4289-4298
    • Pingoud, V.1    Sudina, A.2    Geyer, H.3    Bujnicki, J.M.4    Lurz, R.5    Luder, G.6    Morgan, R.7    Kubareva, E.8    Pingoud, A.9
  • 93
    • 17144381324 scopus 로고    scopus 로고
    • Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI
    • Yang, Z., Horton, J. R., Maunus, R., Wilson, G. G., Roberts, R. J. and Cheng, X. (2005) Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucleic Acids Res., 33, 1892-1901.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 1892-1901
    • Yang, Z.1    Horton, J.R.2    Maunus, R.3    Wilson, G.G.4    Roberts, R.J.5    Cheng, X.6
  • 94
    • 41449117713 scopus 로고    scopus 로고
    • Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding
    • Lambert, A. R., Sussman, D., Shen, B., Maunus, R., Nix, J., Samuelson, J., Xu, S. Y. and Stoddard, B. L. (2008) Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure, 16, 558-569.
    • (2008) Structure , vol.16 , pp. 558-569
    • Lambert, A.R.1    Sussman, D.2    Shen, B.3    Maunus, R.4    Nix, J.5    Samuelson, J.6    Xu, S.Y.7    Stoddard, B.L.8
  • 95
    • 13844316471 scopus 로고    scopus 로고
    • Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: A case study of restriction endonucleases Bsp6I and PvuII
    • Pawlak, S. D., Radlinska, M., Chmiel, A. A., Bujnicki, J. M. and Skowronek, K. J. (2005) Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII. Nucleic Acids Res., 33, 661-671.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 661-671
    • Pawlak, S.D.1    Radlinska, M.2    Chmiel, A.A.3    Bujnicki, J.M.4    Skowronek, K.J.5
  • 96
    • 44849104035 scopus 로고    scopus 로고
    • The BsaHI restriction-modification system: Cloning, sequencing and analysis of conserved motifs
    • Neely, R. K. and Roberts, R. J. (2008) The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs. BMC Mol. Biol., 9, 48.
    • (2008) BMC Mol. Biol. , vol.9 , pp. 48
    • Neely, R.K.1    Roberts, R.J.2
  • 97
    • 0032484137 scopus 로고    scopus 로고
    • Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage
    • Cao, W. and Barany, F. (1998) Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage. J. Biol. Chem., 273, 33002-33010.
    • (1998) J. Biol. Chem. , vol.273 , pp. 33002-33010
    • Cao, W.1    Barany, F.2
  • 98
    • 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. (2005) A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J., 24, 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
  • 100
  • 102
    • 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
  • 103
    • 24144454859 scopus 로고    scopus 로고
    • Characterization of the Type III restriction endonuclease PstII from Providencia stuartii
    • Sears, A., Peakman, L. J., Wilson, G. G. and Szczelkun, M. D. (2005) Characterization of the Type III restriction endonuclease PstII from Providencia stuartii. Nucleic Acids Res., 33, 4775-4787.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 4775-4787
    • Sears, A.1    Peakman, L.J.2    Wilson, G.G.3    Szczelkun, M.D.4
  • 104
    • 80054053723 scopus 로고    scopus 로고
    • Characterization and crystal structure of the type IIG restriction endonuclease RM. BpuSI
    • Shen, B. W., Xu, D., Chan, S. H., Zheng, Y., Zhu, Z., Xu, S. Y. and Stoddard, B. L. (2011) Characterization and crystal structure of the type IIG restriction endonuclease RM. BpuSI. Nucleic Acids Res., 39, 8223-8236.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 8223-8236
    • Shen, B.W.1    Xu, D.2    Chan, S.H.3    Zheng, Y.4    Zhu, Z.5    Xu, S.Y.6    Stoddard, B.L.7
  • 105
    • 0035906281 scopus 로고    scopus 로고
    • Identification of a PD-(D/E) XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs
    • Bujnicki, J. M. and Rychlewski, L. (2001) Identification of a PD-(D/E) XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. Gene, 267, 183-191.
    • (2001) Gene , vol.267 , pp. 183-191
    • Bujnicki, J.M.1    Rychlewski, L.2
  • 107
    • 0033529916 scopus 로고    scopus 로고
    • A Holliday junction resolvase from Pyrococcus furiosus: Functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea
    • Komori, K., Sakae, S., Shinagawa, H., Morikawa, K. and Ishino, Y. (1999) A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. Proc. Natl Acad. Sci. USA, 96, 8873-8878.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 8873-8878
    • Komori, K.1    Sakae, S.2    Shinagawa, H.3    Morikawa, K.4    Ishino, Y.5
  • 108
    • 0141707818 scopus 로고    scopus 로고
    • The endogenous Mus81-Eme1 complex resolves Holliday junctions by a nick and counternick mechanism
    • Gaillard, P. H., Noguchi, E., Shanahan, P. and Russell, P. (2003) The endogenous Mus81-Eme1 complex resolves Holliday junctions by a nick and counternick mechanism. Mol. Cell, 12, 747-759.
    • (2003) Mol. Cell , vol.12 , pp. 747-759
    • Gaillard, P.H.1    Noguchi, E.2    Shanahan, P.3    Russell, P.4
  • 109
    • 52649098554 scopus 로고    scopus 로고
    • The RecU Holliday junction resolvase acts at early stages of homologous recombination
    • Canas, C., Carrasco, B., Ayora, S. and Alonso, J. C. (2008) The RecU Holliday junction resolvase acts at early stages of homologous recombination. Nucleic Acids Res., 36, 5242-5249.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5242-5249
    • Canas, C.1    Carrasco, B.2    Ayora, S.3    Alonso, J.C.4
  • 110
    • 34948815680 scopus 로고    scopus 로고
    • The structural basis of Holliday junction resolution by T7 endonuclease I
    • Hadden, J. M., Declais, A. C., Carr, S. B., Lilley, D. M. and Phillips, S. E. (2007) The structural basis of Holliday junction resolution by T7 endonuclease I. Nature, 449, 621-624.
    • (2007) Nature , vol.449 , pp. 621-624
    • Hadden, J.M.1    Declais, A.C.2    Carr, S.B.3    Lilley, D.M.4    Phillips, S.E.5
  • 111
    • 33846321147 scopus 로고    scopus 로고
    • Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold
    • Song, J. and Markley, J. L. (2007) Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold. J. Mol. Biol., 366, 155-164.
    • (2007) J. Mol. Biol. , vol.366 , pp. 155-164
    • Song, J.1    Markley, J.L.2
  • 112
    • 0033544707 scopus 로고    scopus 로고
    • Recognition of a TG mismatch: The crystal structure of very short patch repair endonuclease in complex with a DNA duplex
    • Tsutakawa, S. E., Jingami, H. and Morikawa, K. (1999) Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell, 99, 615-623.
    • (1999) Cell , vol.99 , pp. 615-623
    • Tsutakawa, S.E.1    Jingami, H.2    Morikawa, K.3
  • 113
    • 83755205429 scopus 로고    scopus 로고
    • Activity, specificity and structure of I-Bth0305I: A representative of a new homing endonuclease family
    • Taylor, G. K., Heiter, D. F., Pietrokovski, S. and Stoddard, B. L. (2011) Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family. Nucleic Acids Res., 39, 9705-9719.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 9705-9719
    • Taylor, G.K.1    Heiter, D.F.2    Pietrokovski, S.3    Stoddard, B.L.4
  • 114
    • 4243123147 scopus 로고    scopus 로고
    • The carboxy-terminal portion of TnsC activates the Tn7 transposase through a specific interaction with TnsA
    • Ronning, D. R., Li, Y., Perez, Z. N., Ross, P. D., Hickman, A. B., Craig, N. L. and Dyda, F. (2004) The carboxy-terminal portion of TnsC activates the Tn7 transposase through a specific interaction with TnsA. EMBO J., 23, 2972-2981.
    • (2004) EMBO J. , vol.23 , pp. 2972-2981
    • Ronning, D.R.1    Li, Y.2    Perez, Z.N.3    Ross, P.D.4    Hickman, A.B.5    Craig, N.L.6    Dyda, F.7
  • 115
    • 0030896473 scopus 로고    scopus 로고
    • Cell-type specificity of the Anabaena fdxN-element rearrangement requires xisH and xisI
    • Ramaswamy, K. S., Carrasco, C. D., Fatma, T. and Golden, J. W. (1997) Cell-type specificity of the Anabaena fdxN-element rearrangement requires xisH and xisI. Mol. Microbiol., 23, 1241-1249.
    • (1997) Mol. Microbiol. , vol.23 , pp. 1241-1249
    • Ramaswamy, K.S.1    Carrasco, C.D.2    Fatma, T.3    Golden, J.W.4
  • 118
    • 0032491378 scopus 로고    scopus 로고
    • Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme
    • Yu, M., Souaya, J. and Julin, D. A. (1998) Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme. J. Mol. Biol., 283, 797-808.
    • (1998) J. Mol. Biol. , vol.283 , pp. 797-808
    • Yu, M.1    Souaya, J.2    Julin, D.A.3
  • 119
    • 79961050090 scopus 로고    scopus 로고
    • Crystal structures of lambda exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity
    • Zhang, J., McCabe, K. A. and Bell, C. E. (2011) Crystal structures of lambda exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity. Proc. Natl Acad. Sci. USA, 108, 11872-11877.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 11872-11877
    • Zhang, J.1    McCabe, K.A.2    Bell, C.E.3
  • 120
    • 65149086817 scopus 로고    scopus 로고
    • Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks
    • Zhang, J., Xing, X., Herr, A. B. and Bell, C. E. (2009) Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks. Structure, 17, 690-702.
    • (2009) Structure , vol.17 , pp. 690-702
    • Zhang, J.1    Xing, X.2    Herr, A.B.3    Bell, C.E.4
  • 121
    • 77749334630 scopus 로고    scopus 로고
    • Yeast exonuclease 5 is essential for mitochondrial genome maintenance
    • Burgers, P. M., Stith, C. M., Yoder, B. L. and Sparks, J. L. (2010) Yeast exonuclease 5 is essential for mitochondrial genome maintenance. Mol. Cell Biol., 30, 1457-1466.
    • (2010) Mol. Cell Biol. , vol.30 , pp. 1457-1466
    • Burgers, P.M.1    Stith, C.M.2    Yoder, B.L.3    Sparks, J.L.4
  • 122
    • 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. (2007) The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif. EMBO J., 26, 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
  • 125
    • 0024503186 scopus 로고
    • The primary structure of the lymphocytic choriomeningitis virus L gene encodes a putative RNA polymerase
    • Salvato, M., Shimomaye, E. and Oldstone, M. B. (1989) The primary structure of the lymphocytic choriomeningitis virus L gene encodes a putative RNA polymerase. Virology, 169, 377-384.
    • (1989) Virology , vol.169 , pp. 377-384
    • Salvato, M.1    Shimomaye, E.2    Oldstone, M.B.3
  • 127
    • 23844548251 scopus 로고    scopus 로고
    • Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1
    • Tsodikov, O. V., Enzlin, J. H., Scharer, O. D. and Ellenberger, T. (2005) Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1. Proc. Natl Acad. Sci. USA, 102, 11236-11241.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 11236-11241
    • Tsodikov, O.V.1    Enzlin, J.H.2    Scharer, O.D.3    Ellenberger, T.4
  • 128
    • 0032033128 scopus 로고    scopus 로고
    • Plant homologue of human excision repair gene ERCC1 points to conservation of DNA repair mechanisms
    • Xu, H., Swoboda, I., Bhalla, P. L., Sijbers, A. M., Zhao, C., Ong, E. K., Hoeijmakers, J. H. and Singh, M. B. (1998) Plant homologue of human excision repair gene ERCC1 points to conservation of DNA repair mechanisms. Plant J., 13, 823-829.
    • (1998) Plant J. , vol.13 , pp. 823-829
    • Xu, H.1    Swoboda, I.2    Bhalla, P.L.3    Sijbers, A.M.4    Zhao, C.5    Ong, E.K.6    Hoeijmakers, J.H.7    Singh, M.B.8
  • 129
    • 78149353044 scopus 로고    scopus 로고
    • Bunyaviridae RNA polymerases (L-protein) have an N-terminal, influenza-like endonuclease domain, essential for viral cap-dependent transcription
    • Reguera, J., Weber, F. and Cusack, S. (2010) Bunyaviridae RNA polymerases (L-protein) have an N-terminal, influenza-like endonuclease domain, essential for viral cap-dependent transcription. PLoS Pathog., 6, e1001101.
    • (2010) PLoS Pathog. , vol.6
    • Reguera, J.1    Weber, F.2    Cusack, S.3
  • 130
    • 69449096816 scopus 로고    scopus 로고
    • Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center
    • Zhao, C., Lou, Z., Guo, Y., Ma, M., Chen, Y., Liang, S., Zhang, L., Chen, S., Li, X., Liu, Y. et al. (2009) Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center. J. Virol., 83, 9024-9030.
    • (2009) J. Virol. , vol.83 , pp. 9024-9030
    • Zhao, C.1    Lou, Z.2    Guo, Y.3    Ma, M.4    Chen, Y.5    Liang, S.6    Zhang, L.7    Chen, S.8    Li, X.9    Liu, Y.10
  • 131
    • 0029838373 scopus 로고    scopus 로고
    • The PB1 subunit alone can catalyze cRNA synthesis, and the PA subunit in addition to the PB1 subunit is required for viral RNA synthesis in replication of the influenza virus genome
    • Nakagawa, Y., Oda, K. and Nakada, S. (1996) The PB1 subunit alone can catalyze cRNA synthesis, and the PA subunit in addition to the PB1 subunit is required for viral RNA synthesis in replication of the influenza virus genome. J. Virol., 70, 6390-6394.
    • (1996) J. Virol. , vol.70 , pp. 6390-6394
    • Nakagawa, Y.1    Oda, K.2    Nakada, S.3
  • 132
    • 77952731322 scopus 로고    scopus 로고
    • The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E) XK nuclease superfamily
    • Menon, S. K., Eilers, B. J., Young, M. J. and Lawrence, C. M. (2010) The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E) XK nuclease superfamily. J. Virol., 84, 5890-5897.
    • (2010) J. Virol. , vol.84 , pp. 5890-5897
    • Menon, S.K.1    Eilers, B.J.2    Young, M.J.3    Lawrence, C.M.4
  • 133
    • 33749150994 scopus 로고    scopus 로고
    • Snf2 family ATPases and DExx box helicases: Differences and unifying concepts from high-resolution crystal structures
    • Durr, H., Flaus, A., Owen-Hughes, T. and Hopfner, K. P. (2006) Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures. Nucleic Acids Res., 34, 4160-4167.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4160-4167
    • Durr, H.1    Flaus, A.2    Owen-Hughes, T.3    Hopfner, K.P.4
  • 134
  • 135
    • 77949557756 scopus 로고    scopus 로고
    • Dna2 on the road to Okazaki fragment processing and genome stability in eukaryotes
    • Kang, Y. H., Lee, C. H. and Seo, Y. S. (2010) Dna2 on the road to Okazaki fragment processing and genome stability in eukaryotes. Crit. Rev. Biochem. Mol. Biol., 45, 71-96.
    • (2010) Crit. Rev. Biochem. Mol. Biol. , vol.45 , pp. 71-96
    • Kang, Y.H.1    Lee, C.H.2    Seo, Y.S.3
  • 136
    • 0033941545 scopus 로고    scopus 로고
    • Genetic analyses of Schizosaccharomyces pombe dna2 (+) reveal that dna2 plays an essential role in Okazaki fragment metabolism
    • Kang, H. Y., Choi, E., Bae, S. H., Lee, K. H., Gim, B. S., Kim, H. D., Park, C., MacNeill, S. A. and Seo, Y. S. (2000) Genetic analyses of Schizosaccharomyces pombe dna2 (+) reveal that dna2 plays an essential role in Okazaki fragment metabolism. Genetics, 155, 1055-1067.
    • (2000) Genetics , vol.155 , pp. 1055-1067
    • Kang, H.Y.1    Choi, E.2    Bae, S.H.3    Lee, K.H.4    Gim, B.S.5    Kim, H.D.6    Park, C.7    MacNeill, S.A.8    Seo, Y.S.9
  • 137
    • 79955999320 scopus 로고    scopus 로고
    • Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint
    • Budd, M. E., Antoshechkin, I. A., Reis, C., Wold, B. J. and Campbell, J. L. (2011) Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint. Cell Cycle, 10, 1690-1698.
    • (2011) Cell Cycle , vol.10 , pp. 1690-1698
    • Budd, M.E.1    Antoshechkin, I.A.2    Reis, C.3    Wold, B.J.4    Campbell, J.L.5
  • 138
    • 0030272028 scopus 로고    scopus 로고
    • Characterization and sequence of the Escherichia coli panBCD gene cluster
    • Merkel, W. K. and Nichols, B. P. (1996) Characterization and sequence of the Escherichia coli panBCD gene cluster. FEMS Microbiol. Lett., 143, 247-252.
    • (1996) FEMS Microbiol. Lett. , vol.143 , pp. 247-252
    • Merkel, W.K.1    Nichols, B.P.2
  • 139
    • 33745904994 scopus 로고    scopus 로고
    • An unstable competence-induced protein, CoiA, promotes processing of donor DNA after uptake during genetic transformation in Streptococcus pneumoniae
    • Desai, B. V. and Morrison, D. A. (2006) An unstable competence-induced protein, CoiA, promotes processing of donor DNA after uptake during genetic transformation in Streptococcus pneumoniae. J. Bacteriol., 188, 5177-5186.
    • (2006) J. Bacteriol. , vol.188 , pp. 5177-5186
    • Desai, B.V.1    Morrison, D.A.2
  • 140
    • 55449098768 scopus 로고    scopus 로고
    • Intersection of RNA processing and the type II fatty acid synthesis pathway in yeast mitochondria
    • Schonauer, M. S., Kastaniotis, A. J., Hiltunen, J. K. and Dieckmann, C. L. (2008) Intersection of RNA processing and the type II fatty acid synthesis pathway in yeast mitochondria. Mol. Cell Biol., 28, 6646-6657.
    • (2008) Mol. Cell Biol. , vol.28 , pp. 6646-6657
    • Schonauer, M.S.1    Kastaniotis, A.J.2    Hiltunen, J.K.3    Dieckmann, C.L.4
  • 141
    • 74549130263 scopus 로고    scopus 로고
    • Int6 and Moe1 interact with Cdc48 to regulate ERAD and proper chromosome segregation
    • Otero, J. H., Suo, J., Gordon, C. and Chang, E. C. (2010) Int6 and Moe1 interact with Cdc48 to regulate ERAD and proper chromosome segregation. Cell Cycle, 9, 147-161.
    • (2010) Cell Cycle , vol.9 , pp. 147-161
    • Otero, J.H.1    Suo, J.2    Gordon, C.3    Chang, E.C.4
  • 145
    • 77952578298 scopus 로고    scopus 로고
    • Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae
    • Thrash, J. C., Cho, J. C., Vergin, K. L., Morris, R. M. and Giovannoni, S. J. (2010) Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae. J. Bacteriol., 192, 2938-2939.
    • (2010) J. Bacteriol. , vol.192 , pp. 2938-2939
    • Thrash, J.C.1    Cho, J.C.2    Vergin, K.L.3    Morris, R.M.4    Giovannoni, S.J.5
  • 146
    • 25444522883 scopus 로고    scopus 로고
    • The PD-(D/E) XK superfamily revisited: Identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
    • Kosinski, J., Feder, M. and Bujnicki, J. M. (2005) The PD-(D/E) XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. BMC Bioinformatics, 6, 172.
    • (2005) BMC Bioinformatics , vol.6 , pp. 172
    • Kosinski, J.1    Feder, M.2    Bujnicki, J.M.3
  • 147
    • 0035228022 scopus 로고    scopus 로고
    • Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA
    • Takeda, K., Akimoto, C. and Kawamukai, M. (2001) Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA. Biosci. Biotechnol. Biochem., 65, 213-217.
    • (2001) Biosci. Biotechnol. Biochem. , vol.65 , pp. 213-217
    • Takeda, K.1    Akimoto, C.2    Kawamukai, M.3
  • 148
    • 67651232707 scopus 로고    scopus 로고
    • The conserved UL24 family of human alpha, beta and gamma herpesviruses induces cell cycle arrest and inactivation of the cyclinB/cdc2 complex
    • Nascimento, R., Dias, J. D. and Parkhouse, R. M. (2009) The conserved UL24 family of human alpha, beta and gamma herpesviruses induces cell cycle arrest and inactivation of the cyclinB/cdc2 complex. Arch. Virol., 154, 1143-1149.
    • (2009) Arch. Virol. , vol.154 , pp. 1143-1149
    • Nascimento, R.1    Dias, J.D.2    Parkhouse, R.M.3
  • 149
    • 34248504598 scopus 로고    scopus 로고
    • Involvement of UL24 in herpes-simplex-virus-1-induced dispersal of nucleolin
    • Lymberopoulos, M. H. and Pearson, A. (2007) Involvement of UL24 in herpes-simplex-virus-1-induced dispersal of nucleolin. Virology, 363, 397-409.
    • (2007) Virology , vol.363 , pp. 397-409
    • Lymberopoulos, M.H.1    Pearson, A.2
  • 150
    • 72849129184 scopus 로고    scopus 로고
    • Conserved residues in the UL24 protein of herpes simplex virus 1 are important for dispersal of the nucleolar protein nucleolin
    • Bertrand, L., Leiva-Torres, G. A., Hyjazie, H. and Pearson, A. (2010) Conserved residues in the UL24 protein of herpes simplex virus 1 are important for dispersal of the nucleolar protein nucleolin. J. Virol., 84, 109-118.
    • (2010) J. Virol. , vol.84 , pp. 109-118
    • Bertrand, L.1    Leiva-Torres, G.A.2    Hyjazie, H.3    Pearson, A.4
  • 152
    • 36849089086 scopus 로고    scopus 로고
    • A novel class of bacteria-induced small RNAs in Arabidopsis
    • Katiyar-Agarwal, S., Gao, S., Vivian-Smith, A. and Jin, H. (2007) A novel class of bacteria-induced small RNAs in Arabidopsis. Genes Dev., 21, 3123-3134.
    • (2007) Genes Dev. , vol.21 , pp. 3123-3134
    • Katiyar-Agarwal, S.1    Gao, S.2    Vivian-Smith, A.3    Jin, H.4
  • 153
    • 35448980826 scopus 로고    scopus 로고
    • Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E) XK nuclease motif
    • Guzzo, C. R., Nagem, R. A., Barbosa, J. A. and Farah, C. S. (2007) Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E) XK nuclease motif. Proteins, 69, 644-651.
    • (2007) Proteins , vol.69 , pp. 644-651
    • Guzzo, C.R.1    Nagem, R.A.2    Barbosa, J.A.3    Farah, C.S.4
  • 154
    • 0031897138 scopus 로고    scopus 로고
    • A gene, yaeQ, that suppresses reduced operon expression caused by mutations in the transcription elongation gene rfaH in Escherichia coli and Salmonella typhimurium
    • Wong, K. R., Hughes, C. and Koronakis, V. (1998) A gene, yaeQ, that suppresses reduced operon expression caused by mutations in the transcription elongation gene rfaH in Escherichia coli and Salmonella typhimurium. Mol. Gen. Genet., 257, 693-696.
    • (1998) Mol. Gen. Genet. , vol.257 , pp. 693-696
    • Wong, K.R.1    Hughes, C.2    Koronakis, V.3
  • 155
    • 13244296852 scopus 로고    scopus 로고
    • Virulence regulators RfaH and YaeQ do not operate in the same pathway
    • Vicari, D. and Artsimovitch, I. (2004) Virulence regulators RfaH and YaeQ do not operate in the same pathway. Mol. Genet. Genomics, 272, 489-496.
    • (2004) Mol. Genet. Genomics , vol.272 , pp. 489-496
    • Vicari, D.1    Artsimovitch, I.2
  • 156
    • 0034776053 scopus 로고    scopus 로고
    • Complete nucleotide sequence and characterization of pUA140, a cryptic plasmid from Streptococcus mutans
    • Zou, X., Caufield, P. W., Li, Y. and Qi, F. (2001) Complete nucleotide sequence and characterization of pUA140, a cryptic plasmid from Streptococcus mutans. Plasmid, 46, 77-85.
    • (2001) Plasmid , vol.46 , pp. 77-85
    • Zou, X.1    Caufield, P.W.2    Li, Y.3    Qi, F.4
  • 157
    • 0035110751 scopus 로고    scopus 로고
    • Two atypical mobilization proteins are involved in plasmid CloDF13 relaxation
    • Nunez, B. and De La Cruz, F. (2001) Two atypical mobilization proteins
    • (2001) Mol. Microbiol. , vol.39 , pp. 1088-1099
    • Nunez, B.1    De La Cruz, F.2
  • 159
    • 29344450201 scopus 로고    scopus 로고
    • Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA
    • Yamamoto, T., Matsuda, T., Inoue, T., Matsumura, H., Morikawa, M., Kanaya, S. and Kai, Y. (2006) Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA. Protein Sci., 15, 152-161.
    • (2006) Protein Sci. , vol.15 , pp. 152-161
    • Yamamoto, T.1    Matsuda, T.2    Inoue, T.3    Matsumura, H.4    Morikawa, M.5    Kanaya, S.6    Kai, Y.7
  • 160
    • 78650045540 scopus 로고    scopus 로고
    • The phage-host arms race: Shaping the evolution of microbes
    • Stern, A. and Sorek, R. (2011) The phage-host arms race: shaping the evolution of microbes. Bioessays, 33, 43-51.
    • (2011) Bioessays , vol.33 , pp. 43-51
    • Stern, A.1    Sorek, R.2
  • 162
    • 17444377949 scopus 로고    scopus 로고
    • Structural drift: A possible path to protein fold change
    • Krishna, S. S. and Grishin, N. V. (2005) Structural drift: a possible path to protein fold change. Bioinformatics, 21, 1308-1310.
    • (2005) Bioinformatics , vol.21 , pp. 1308-1310
    • Krishna, S.S.1    Grishin, N.V.2
  • 163
    • 67650497792 scopus 로고    scopus 로고
    • Nature of the protein universe
    • Levitt, M. (2009) Nature of the protein universe. Proc. Natl Acad. Sci. USA, 106, 11079-11084.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 11079-11084
    • Levitt, M.1


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