메뉴 건너뛰기




Volumn 6, Issue 12, 1999, Pages 901-908

Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment

Author keywords

3' 5' exonuclease; Europium (III); Lanthanide (III); Two metal ion mechanism; X ray crystallography

Indexed keywords


EID: 0033485840     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(00)80009-5     Document Type: Article
Times cited : (36)

References (41)
  • 1
    • 0024281443 scopus 로고
    • Genetic and crystallographic studies of the 3′, 5′-exonucleolytic site of DNA polymerase I
    • Derbyshire, V., et al., & Steitz, T.A. (1988). Genetic and crystallographic studies of the 3′, 5′-exonucleolytic site of DNA polymerase I. Science 240, 199-201.
    • (1988) Science , vol.240 , pp. 199-201
    • Derbyshire, V.1    Steitz, T.A.2
  • 2
    • 0026085471 scopus 로고
    • The 3′-5′ exonuclease of DNA polymerase I of Escherichia coli: Contribution of each amino acid at the active site to the reaction
    • Derbyshire, V., Grindley, N.D.F. & Joyce, C.M. (1991). The 3′-5′ exonuclease of DNA polymerase I of Escherichia coli: Contribution of each amino acid at the active site to the reaction. EMBO J. 10, 17-24.
    • (1991) EMBO J. , vol.10 , pp. 17-24
    • Derbyshire, V.1    Grindley, N.D.F.2    Joyce, C.M.3
  • 4
    • 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. (1991). 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) EMBO J. , vol.10 , pp. 25-33
    • Beese, L.S.1    Steitz, T.A.2
  • 5
    • 0032571245 scopus 로고    scopus 로고
    • Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates
    • Brautigam, C.A. & Steitz, T.A. (1998). Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J. Mol. Biol. 277, 363-377.
    • (1998) J. Mol. Biol. , vol.277 , pp. 363-377
    • Brautigam, C.A.1    Steitz, T.A.2
  • 6
    • 0001431264 scopus 로고    scopus 로고
    • Binuclear metallohydrolases
    • Wilcox, D.E. (1996). Binuclear metallohydrolases. Chem. Rev. 96, 2435-2458.
    • (1996) Chem. Rev. , vol.96 , pp. 2435-2458
    • Wilcox, D.E.1
  • 7
    • 0027411261 scopus 로고
    • DNA- and RNA-dependent DNA polymerases
    • Steitz, T.A. (1993). DNA- and RNA-dependent DNA polymerases. Curr. Opin. Struct. Biol. 3, 31-38.
    • (1993) Curr. Opin. Struct. Biol. , vol.3 , pp. 31-38
    • Steitz, T.A.1
  • 8
    • 0028049441 scopus 로고
    • Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP
    • Pelletier, H., Sawaya, M.R., Kumar, A., Wilson, S.H. & Kraut, J. (1994). Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 264, 1891-1903.
    • (1994) Science , vol.264 , pp. 1891-1903
    • Pelletier, H.1    Sawaya, M.R.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 9
    • 0032425080 scopus 로고    scopus 로고
    • The mechanism of action of T7 DNA polymerase
    • Doubli, S. & Ellenberger, T. (1998). The mechanism of action of T7 DNA polymerase. Curr. Opin. Struct. Biol. 8, 704-712.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 704-712
    • Doubli, S.1    Ellenberger, T.2
  • 10
    • 0032005866 scopus 로고    scopus 로고
    • Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
    • Brautigam, C.A. & Steitz, T.A. (1998). Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 8, 54-63.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 54-63
    • Brautigam, C.A.1    Steitz, T.A.2
  • 11
    • 0032412405 scopus 로고    scopus 로고
    • The structure, catalytic mechanism and regulation of adenylyl cyclase
    • Tesmer, J.J.G. & Sprang, S.R. (1998). The structure, catalytic mechanism and regulation of adenylyl cyclase. Curr. Opin. Struct. Biol. 8, 713-719.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 713-719
    • Tesmer, J.J.G.1    Sprang, S.R.2
  • 13
    • 0025777694 scopus 로고
    • Reaction mechanism of alkaline phosphatase based on crystal structures
    • Kim, E.E. & Wyckoff, H.W. (1991). Reaction mechanism of alkaline phosphatase based on crystal structures. J. Mol. Biol. 218, 449-464.
    • (1991) J. Mol. Biol. , vol.218 , pp. 449-464
    • Kim, E.E.1    Wyckoff, H.W.2
  • 14
    • 0025908083 scopus 로고
    • Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase
    • Davies, J.F., Hostomska, Z., Hostomsky, Z., Jordan, S.R. & Matthews, D.A. (1991). Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase. Science 252, 88-95.
    • (1991) Science , vol.252 , pp. 88-95
    • Davies, J.F.1    Hostomska, Z.2    Hostomsky, Z.3    Jordan, S.R.4    Matthews, D.A.5
  • 15
    • 0028105959 scopus 로고
    • Structural studies of metal binding by inositol monophosphatase: Evidence for two-metal ion catalysis
    • Bone, R., Frank, L., Springer, J.P. & Atack, J.R. (1994). Structural studies of metal binding by inositol monophosphatase: Evidence for two-metal ion catalysis. Biochemistry 33, 9468-9476.
    • (1994) Biochemistry , vol.33 , pp. 9468-9476
    • Bone, R.1    Frank, L.2    Springer, J.P.3    Atack, J.R.4
  • 16
    • 0028234802 scopus 로고
    • Mechanism of inositol monophosphatase, the putative target of lithium therapy
    • Pollack, S.J., et al., & Broughton, H.B. (1994). Mechanism of inositol monophosphatase, the putative target of lithium therapy. Proc. Natl Acad. Sci. USA 91, 5766-5770.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 5766-5770
    • Pollack, S.J.1    Broughton, H.B.2
  • 17
    • 0028946336 scopus 로고
    • Structure and mechanism of inositol monophosphatase
    • Atack, J.R., Broughton, H.B. & Pollack, S.J. (1995). Structure and mechanism of inositol monophosphatase. FEBS Lett. 361, 1-7.
    • (1995) FEBS Lett. , vol.361 , pp. 1-7
    • Atack, J.R.1    Broughton, H.B.2    Pollack, S.J.3
  • 18
    • 0027184481 scopus 로고
    • A general two-metal-ion mechanism for catalytic RNA
    • Steitz, T.A. & Steitz, J.A. (1993). A general two-metal-ion mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA 90, 6498-6502.
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 6498-6502
    • Steitz, T.A.1    Steitz, J.A.2
  • 19
    • 0001063348 scopus 로고
    • The deoxyribonucleases of Escherichia coli: IV. An exonuclease activity present in purified preparations of deoxyribonucleic acid polymerase
    • Lehman, I.R. & Richardson, C.C. (1964). The deoxyribonucleases of Escherichia coli: IV. An exonuclease activity present in purified preparations of deoxyribonucleic acid polymerase. J. Biol. Chem. 239, 233-241.
    • (1964) J. Biol. Chem. , vol.239 , pp. 233-241
    • Lehman, I.R.1    Richardson, C.C.2
  • 20
    • 0024989773 scopus 로고
    • Metal binding to DNA polymerase I, its large fragment, and two 3′, 5′-exonuclease mutants of the large fragment
    • Mullen, G.P., Serpersu, E.H., Ferrin, L.J., Loeb, L.A. & Mildvan, A.S. (1990). Metal binding to DNA polymerase I, its large fragment, and two 3′, 5′-exonuclease mutants of the large fragment. J. Biol. Chem. 265, 14327-14334.
    • (1990) J. Biol. Chem. , vol.265 , pp. 14327-14334
    • Mullen, G.P.1    Serpersu, E.H.2    Ferrin, L.J.3    Loeb, L.A.4    Mildvan, A.S.5
  • 21
    • 0026351220 scopus 로고
    • Role of divalent cations in the 3′, 5′-exonuclease reaction of DNA polymerase I
    • Han, H., Rifkind, J.M. & Mildvan, A.S. (1991). Role of divalent cations in the 3′, 5′-exonuclease reaction of DNA polymerase I. Biochemistry 30, 11104-11108.
    • (1991) Biochemistry , vol.30 , pp. 11104-11108
    • Han, H.1    Rifkind, J.M.2    Mildvan, A.S.3
  • 23
    • 0030133381 scopus 로고    scopus 로고
    • Elucidation of the metal-binding properties of the Klenow fragment of Escherichia coli and bacteriophage T4 DNA polymerase by lanthanide (III) luminescence spectroscopy
    • Frey, M.W., Frey, S.T., de W. Horrocks, W, Jr., Kaboord, B.F. & Benkovic, S.J. (1996). Elucidation of the metal-binding properties of the Klenow fragment of Escherichia coli and bacteriophage T4 DNA polymerase by lanthanide (III) luminescence spectroscopy. Chem. Biol. 3, 393-403.
    • (1996) Chem. Biol. , vol.3 , pp. 393-403
    • Frey, M.W.1    Frey, S.T.2    De W. Horrocks W., Jr.3    Kaboord, B.F.4    Benkovic, S.J.5
  • 24
    • 37049075459 scopus 로고
    • Unprecedentedly fast hydrolysis of the RNA dinucleoside monophosphates ApA and UpU by rare earth metal ions
    • Komiyama, M., Matsumura, K. & Matsumoto, Y. (1992). Unprecedentedly fast hydrolysis of the RNA dinucleoside monophosphates ApA and UpU by rare earth metal ions. J. Chem. Soc., Chem. Commun. 640-641.
    • (1992) J. Chem. Soc., Chem. Commun. , pp. 640-641
    • Komiyama, M.1    Matsumura, K.2    Matsumoto, Y.3
  • 25
    • 33845561094 scopus 로고
    • Lanthanide ion probes of structure in biology. Laser-induced luminescence decay constants provide a direct measure of the number of metal-coordinated water molecules
    • de W. Horrocks, W., Jr. & Sudnick, D.R. (1979). Lanthanide ion probes of structure in biology. Laser-induced luminescence decay constants provide a direct measure of the number of metal-coordinated water molecules. J. Am. Chem. Soc. 101, 334-340.
    • (1979) J. Am. Chem. Soc. , vol.101 , pp. 334-340
    • De W. Horrocks W., Jr.1    Sudnick, D.R.2
  • 26
    • 0014940831 scopus 로고
    • Rare earth metal ions as probes of calcium ion binding sites in proteins. Neodymium (III) acceleration of the activation of trypsinogen
    • Darnall, D.W. & Birnbaum, E.R. (1970). Rare earth metal ions as probes of calcium ion binding sites in proteins. Neodymium (III) acceleration of the activation of trypsinogen. J. Biol. Chem. 245, 6484-6486.
    • (1970) J. Biol. Chem. , vol.245 , pp. 6484-6486
    • Darnall, D.W.1    Birnbaum, E.R.2
  • 27
    • 0015237767 scopus 로고
    • Rare earth metal ions as substitutes for the calcium ion in Bacillus subtilis amylase
    • Smolka, G.E., Birnbaum, E.R. & Darnall, D.W. (1971). Rare earth metal ions as substitutes for the calcium ion in Bacillus subtilis amylase. Biochemistry 10, 4556-4561.
    • (1971) Biochemistry , vol.10 , pp. 4556-4561
    • Smolka, G.E.1    Birnbaum, E.R.2    Darnall, D.W.3
  • 28
    • 0015902368 scopus 로고
    • Lanthanide ions activate α-amylase
    • Darnall, D.W. & Birnbaum E.R. (1973). Lanthanide ions activate α-amylase. Biochemistry 12, 3489-3491.
    • (1973) Biochemistry , vol.12 , pp. 3489-3491
    • Darnall, D.W.1    Birnbaum, E.R.2
  • 29
    • 0033547832 scopus 로고    scopus 로고
    • Structures of normal single-stranded DNA and deoxyribo-3′-S-phosphorothiolates bound to the 3′-5′ exonucleolytic active site of DNA polymerase I from Escherichia coli
    • Brautigam, C.A., Sun, S., Piccirilli, J.A. & Steitz, T.A. (1999). Structures of normal single-stranded DNA and deoxyribo-3′-S-phosphorothiolates bound to the 3′-5′ exonucleolytic active site of DNA polymerase I from Escherichia coli. Biochemistry 38, 696-704.
    • (1999) Biochemistry , vol.38 , pp. 696-704
    • Brautigam, C.A.1    Sun, S.2    Piccirilli, J.A.3    Steitz, T.A.4
  • 30
    • 0029666424 scopus 로고    scopus 로고
    • 2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions
    • 2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Biochemistry 35, 8110-8119.
    • (1996) Biochemistry , vol.35 , pp. 8110-8119
    • Wang, J.1    Yu, P.2    Lin, T.C.3    Konigsberg, W.H.4    Steitz, T.A.5
  • 31
    • 0016378745 scopus 로고
    • Binding of lanthanide ions to thermolysin
    • Matthews, B.W. & Weaver, L.H. (1974). Binding of lanthanide ions to thermolysin. Biochemistry 13, 1719-1725.
    • (1974) Biochemistry , vol.13 , pp. 1719-1725
    • Matthews, B.W.1    Weaver, L.H.2
  • 32
    • 0026493674 scopus 로고
    • Structrure of inositol monophosphatase, the putative target of lithium therapy
    • Bone, R., Springer, J.P. & Atack, J.R. (1992). Structrure of inositol monophosphatase, the putative target of lithium therapy. Proc. Natl Acad. Sci. USA 89, 10031-10035.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10031-10035
    • Bone, R.1    Springer, J.P.2    Atack, J.R.3
  • 34
    • 0021111944 scopus 로고
    • Crystallization and 7 Å resolution electron density map of the large fragment of Escherichia coli DNA polymerase I
    • Brick, P., Ollis, D. & Steitz, T.A. (1983). Crystallization and 7 Å resolution electron density map of the large fragment of Escherichia coli DNA polymerase I. J. Mol. Biol. 166, 453-456.
    • (1983) J. Mol. Biol. , vol.166 , pp. 453-456
    • Brick, P.1    Ollis, D.2    Steitz, T.A.3
  • 35
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-325.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-325
    • Otwinowski, Z.1    Minor, W.2
  • 36
  • 37
    • 84944812409 scopus 로고
    • Improved Fourier coefficients for maps using phases from partial structures with errors
    • Read, R.J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 140-149.
    • (1986) Acta Crystallogr. A , vol.42 , pp. 140-149
    • Read, R.J.1
  • 39
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, Number 4 (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 760-763
  • 40
    • 84945096204 scopus 로고
    • Model bias in macromolecular crystal structures
    • Hodel, A., Kim, S.-H. & Brünger, A.T. (1992). Model bias in macromolecular crystal structures. Acta Crystollogr. A 48, 851-859.
    • (1992) Acta Crystollogr. A , vol.48 , pp. 851-859
    • Hodel, A.1    Kim, S.-H.2    Brünger, A.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.