메뉴 건너뛰기




Volumn 32, Issue 4, 1998, Pages 414-424

Recognition of single-stranded DNA by nuclease P1: High resolution crystal structures of complexes with substrate analogs

Author keywords

Catalytic mechanism; P1 nuclease; Substrate recognition; Thiophosphorylated oligonucleotides; X ray crystallography

Indexed keywords

BACTERIAL ENZYME; NUCLEASE; NUCLEASE S1; OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

EID: 0031850427     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980901)32:4<414::AID-PROT2>3.0.CO;2-G     Document Type: Article
Times cited : (107)

References (37)
  • 1
    • 0016155198 scopus 로고
    • Identity of phosphodiesterase and phosphomonoesterase activities with nuclease P1
    • Fujimoto, M., Kuninaka, A., Yoshino, H. Identity of phosphodiesterase and phosphomonoesterase activities with nuclease P1. Agr. Biol. Chem. 38:785-790, 1974.
    • (1974) Agr. Biol. Chem. , vol.38 , pp. 785-790
    • Fujimoto, M.1    Kuninaka, A.2    Yoshino, H.3
  • 3
    • 0016286446 scopus 로고
    • Mode of action of nuclease P1 on nucleic acids and its specificity for synthetic phosphodiesters
    • Fujimoto, M., Fujiyama, K., Kuninaka, A., Yoshino, H. Mode of action of nuclease P1 on nucleic acids and its specificity for synthetic phosphodiesters. Agr. Biol. Chem. 38:2141-2147, 1974.
    • (1974) Agr. Biol. Chem. , vol.38 , pp. 2141-2147
    • Fujimoto, M.1    Fujiyama, K.2    Kuninaka, A.3    Yoshino, H.4
  • 4
    • 0016646157 scopus 로고
    • Some physical and chemical properties of nuclease P1
    • Fujimoto, M., Kuninaka, A., Yoshino, H. Some physical and chemical properties of nuclease P1. Agr. Biol. Chem. 39: 1991-1997, 1975.
    • (1975) Agr. Biol. Chem. , vol.39 , pp. 1991-1997
    • Fujimoto, M.1    Kuninaka, A.2    Yoshino, H.3
  • 5
    • 0020536591 scopus 로고
    • Synthesis and configurational analysis of a dinucleoside phosphate isotopically chiral at phosphorus. Stereochemical course of Penicillium citrinum nuclease P1 reaction
    • Potter, B.V.L., Conolly, B.A., Eckstein, F. Synthesis and configurational analysis of a dinucleoside phosphate isotopically chiral at phosphorus. Stereochemical course of Penicillium citrinum nuclease P1 reaction. Biochemistry 22:1369-1377, 1983.
    • (1983) Biochemistry , vol.22 , pp. 1369-1377
    • Potter, B.V.L.1    Conolly, B.A.2    Eckstein, F.3
  • 6
    • 0024341026 scopus 로고
    • Selective hydrolysis by exo- and endonucleases of phosphodiester bonds adjacent to an apurinic site
    • Weinfeld, M., Liuzzi, M., Paterson, M.C. Selective hydrolysis by exo-and endonucleases of phosphodiester bonds adjacent to an apurinic site. Nucleic Acids Res. 17:3735-3745, 1989.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 3735-3745
    • Weinfeld, M.1    Liuzzi, M.2    Paterson, M.C.3
  • 7
    • 0027205006 scopus 로고
    • Influence of nucleic acid base aromaticity on substrate reactivity with enzymes acting on single-stranded DNA
    • Weinfeld, M., Soderlind, K.J.M., Buchko, G.W. Influence of nucleic acid base aromaticity on substrate reactivity with enzymes acting on single-stranded DNA. Nucleic Acids Res. 21:621-626, 1993.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 621-626
    • Weinfeld, M.1    Soderlind, K.J.M.2    Buchko, G.W.3
  • 9
    • 0025093863 scopus 로고
    • Crystallisation and preliminary crystallographic analysis of P1 nuclease from Penicillium citrinum
    • Lahm, A., Volbeda, A., Suck, D. Crystallisation and preliminary crystallographic analysis of P1 nuclease from Penicillium citrinum. J. Mol. Biol. 215:207-210, 1990.
    • (1990) J. Mol. Biol. , vol.215 , pp. 207-210
    • Lahm, A.1    Volbeda, A.2    Suck, D.3
  • 10
    • 0025763145 scopus 로고
    • Crystal structure of Penicillium citrinum P1 nuclease at 2.8 Å resolution
    • Volbeda, A., Lahm, A., Sakiyama, F., Suck, D. Crystal structure of Penicillium citrinum P1 nuclease at 2.8 Å resolution. EMBO J. 10:1607-1618, 1991.
    • (1991) EMBO J. , vol.10 , pp. 1607-1618
    • Volbeda, A.1    Lahm, A.2    Sakiyama, F.3    Suck, D.4
  • 11
    • 0024976936 scopus 로고
    • High-resolution (1.5 Å) of phospholipase C from Bacillus cereus
    • Hough, E., Hansen, L.K., Birknes, B. et al. High-resolution (1.5 Å) of phospholipase C from Bacillus cereus. Nature 338:357-360, 1989.
    • (1989) Nature , vol.338 , pp. 357-360
    • Hough, E.1    Hansen, L.K.2    Birknes, B.3
  • 12
    • 0021891882 scopus 로고
    • Nucleoside phosphorothioates
    • Eckstein, F. Nucleoside phosphorothioates. Ann. Rev. Biochem. 54:367-402, 1985.
    • (1985) Ann. Rev. Biochem. , vol.54 , pp. 367-402
    • Eckstein, F.1
  • 14
    • 0027303379 scopus 로고
    • New perspective on zinc biochemistry: Cocatalytic sites in multi-zinc enzymes
    • Vallee, B.L., Auld, D.S. New perspective on zinc biochemistry: Cocatalytic sites in multi-zinc enzymes. Biochemistry 32:6493-6500, 1993.
    • (1993) Biochemistry , vol.32 , pp. 6493-6500
    • Vallee, B.L.1    Auld, D.S.2
  • 15
    • 0028173920 scopus 로고
    • A proposal for the catalytic mechanism in phospholipase C based on interaction energy and distance geometry calculations
    • Sundell, S., Hansen, S., Hough, E. A proposal for the catalytic mechanism in phospholipase C based on interaction energy and distance geometry calculations. Protein Eng. 7:571-577, 1994.
    • (1994) Protein Eng. , vol.7 , pp. 571-577
    • Sundell, S.1    Hansen, S.2    Hough, E.3
  • 16
    • 0026019625 scopus 로고
    • Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism
    • Beese, L.S., Steitz, T.A. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism. EMBO J. 10:25-33, 1991.
    • (1991) EMBO J. , vol.10 , pp. 25-33
    • Beese, L.S.1    Steitz, T.A.2
  • 17
    • 0027184481 scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • Steitz, T.A., Steitz, J.A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci., U.S.A. 90:6498-6502, 1993.
    • (1993) Proc. Natl. Acad. Sci., U.S.A. , vol.90 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 18
    • 0025313293 scopus 로고
    • Deoxynucleoside phosphorodithioates. Preparation by a triester method
    • Dahl, B., Bjergårde, K., Nielsen, J., Dahl, O. Deoxynucleoside phosphorodithioates. Preparation by a triester method. Tetrahedron Lett. 31:3489-3492, 1990.
    • (1990) Tetrahedron Lett. , vol.31 , pp. 3489-3492
    • Dahl, B.1    Bjergårde, K.2    Nielsen, J.3    Dahl, O.4
  • 19
    • 85046526624 scopus 로고
    • Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector
    • Kabsch, W. Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Crystallogr. 21:916-924, 1988.
    • (1988) J. Appl. Crystallogr. , vol.21 , pp. 916-924
    • Kabsch, W.1
  • 20
    • 84920325457 scopus 로고
    • AMoRe: An automated package for molecular replacement
    • Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A50:157-163, 1994.
    • (1994) Acta Crystallogr. , vol.A50 , pp. 157-163
    • Navaza, J.1
  • 22
    • 79952608525 scopus 로고
    • Accurate bond and angle parameters for X-ray protein structure refinement
    • Engh, R.A., Huber, R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A47:392-400, 1991.
    • (1991) Acta Crystallogr. , vol.A47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 23
    • 0026597444 scopus 로고
    • Free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger, A.T. Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355: 472-475, 1992.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 24
    • 3543041448 scopus 로고    scopus 로고
    • Roussel, A., Cambillau, C. TURBO-FRODO, CNRS-LCCMB, Marseille, 1992
    • Roussel, A., Cambillau, C. TURBO-FRODO, CNRS-LCCMB, Marseille, 1992.
  • 25
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R.A., McArthur, M.W., Moss, D.S., Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291, 1993.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    McArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 27
    • 0031090688 scopus 로고    scopus 로고
    • Common fold, common function, common origin?
    • Suck, D. Common fold, common function, common origin? Nat. Struct. Biol. 4:161-165, 1997.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 161-165
    • Suck, D.1
  • 28
    • 0031030449 scopus 로고    scopus 로고
    • Structure of the single-stranded-DNA-binding domain of replication protein a bound to DNA
    • Bochkarev, A., Pfuetzner, R.A., Edwards, A.M., Frappier, L. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385:176-181, 1997.
    • (1997) Nature , vol.385 , pp. 176-181
    • Bochkarev, A.1    Pfuetzner, R.A.2    Edwards, A.M.3    Frappier, L.4
  • 30
    • 0001431264 scopus 로고    scopus 로고
    • Binuclear metallohydrolases
    • Wilcox, D.E. Binuclear metallohydrolases. Chem. Rev. 96:2435-2458, 1996.
    • (1996) Chem. Rev. , vol.96 , pp. 2435-2458
    • Wilcox, D.E.1
  • 31
    • 0001233207 scopus 로고    scopus 로고
    • Enzymatische Acyl- und Phosphoryltransferreaktionen unter Beteiligung von zwei Metallionen
    • Sträter, N., Lipscomb, W.N., Klabunde, T., Krebs, B. Enzymatische Acyl-und Phosphoryltransferreaktionen unter Beteiligung von zwei Metallionen. Angew. Chem. 108:2158-2191, 1996.
    • (1996) Angew. Chem. , vol.108 , pp. 2158-2191
    • Sträter, N.1    Lipscomb, W.N.2    Klabunde, T.3    Krebs, B.4
  • 32
    • 0027379581 scopus 로고
    • Crystal structure of phospholipase C from Bacillus cereus complexed with a substrate analog
    • Hansen, S., Hough, E., Svensson, L.A., Wong, Y.L., Martin, S.F. Crystal structure of phospholipase C from Bacillus cereus complexed with a substrate analog. J. Mol. Biol. 234:179-187, 1993.
    • (1993) J. Mol. Biol. , vol.234 , pp. 179-187
    • Hansen, S.1    Hough, E.2    Svensson, L.A.3    Wong, Y.L.4    Martin, S.F.5
  • 33
    • 0025777694 scopus 로고
    • Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis
    • Kim, E.E., Wyckoff, H.W. Reaction mechanism of alkaline phosphatase based on crystal structures. Two-metal ion catalysis. J. Mol. Biol. 218:449-464, 1991.
    • (1991) J. Mol. Biol. , vol.218 , pp. 449-464
    • Kim, E.E.1    Wyckoff, H.W.2
  • 34
    • 3543032374 scopus 로고
    • Fungal and mitochondrial nucleases
    • New York: Cold Spring Harbor Laboratory Press
    • Linn, S.M., Lloyd, R.S., Roberts, R.J. (eds.). Fungal and mitochondrial nucleases. In: "Nucleases." 2nd edit. New York: Cold Spring Harbor Laboratory Press, 1993:171-207.
    • (1993) "Nucleases." 2nd Edit. , pp. 171-207
    • Linn, S.M.1    Lloyd, R.S.2    Roberts, R.J.3
  • 35
    • 0026643811 scopus 로고
    • Active site characterization of S1 nuclease
    • Gite, S., Reddy, G., Shankar, V. Active site characterization of S1 nuclease. Biochem. J. 285:489-494, 1992.
    • (1992) Biochem. J. , vol.285 , pp. 489-494
    • Gite, S.1    Reddy, G.2    Shankar, V.3
  • 36
    • 0015924086 scopus 로고
    • Purification and further properties of single-strand specific nuclease for Aspergillus oryzae
    • Vogt, V.M. Purification and further properties of single-strand specific nuclease for Aspergillus oryzae. Eur. J. Biochem. 33:192-200, 1973.
    • (1973) Eur. J. Biochem. , vol.33 , pp. 192-200
    • Vogt, V.M.1
  • 37
    • 0018846634 scopus 로고
    • Purification and properties of S1 nuclease from Aspergillus
    • Grossman, L., Moldave, K. (eds.). New York: Academic Press
    • Vogt, V.M. Purification and properties of S1 nuclease from Aspergillus. In: "Methods in Enzymology." Vol. 65. Grossman, L., Moldave, K. (eds.). New York: Academic Press, 1980:248-255.
    • (1980) Methods in Enzymology , vol.65 , pp. 248-255
    • Vogt, V.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.