메뉴 건너뛰기




Volumn 99, Issue 6, 1999, Pages 615-623

Recognition of a TG mismatch: The crystal structure of very short patch repair endonuclease in complex with a DNA duplex

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENDONUCLEASE; MAGNESIUM ION;

EID: 0033544707     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81550-0     Document Type: Article
Times cited : (95)

References (48)
  • 1
    • 0032212134 scopus 로고    scopus 로고
    • NMR solution structure of a DNA dodecamer containing single GT mismatches
    • Allawi, H., and SantaLucia, J. (1998). NMR solution structure of a DNA dodecamer containing single GT mismatches. Nucleic Acids Res. 26, 4925-4934.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4925-4934
    • Allawi, H.1    Santalucia, J.2
  • 2
    • 0031827294 scopus 로고    scopus 로고
    • Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct
    • Barrett, T.E., Savva, R., Barlow, T., Brown, T., Jiricny, J., and Pearl, L.H. (1998). Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct. Nat. Struct. Biol. 5, 697-701.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 697-701
    • Barrett, T.E.1    Savva, R.2    Barlow, T.3    Brown, T.4    Jiricny, J.5    Pearl, L.H.6
  • 3
    • 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., and 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
  • 4
    • 0026597444 scopus 로고
    • Free R value: A novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger, A.T. (1992). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 6
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • CCP4
    • CCP4 (1994). The CCP4 suite: programs for protein crystallography.Acta Crystallogr. D 50, 760-763.
    • (1994) Acta Crystallogr. , vol.50 , pp. 760-763
  • 7
    • 0032522139 scopus 로고    scopus 로고
    • DNA bending: The prevalence of kinkiness and the virtues of normality
    • Dickerson, R.E. (1998). DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26, 1906-1926.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1906-1926
    • Dickerson, R.E.1
  • 8
    • 0032519335 scopus 로고    scopus 로고
    • The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA
    • Drotschmann, K., Aronshtam, A., Fritz, H.J., and Marinus, M.G.(1998). The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA. Nucleic Acids Res. 26, 948-953.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 948-953
    • Drotschmann, K.1    Aronshtam, A.2    Fritz, H.J.3    Marinus, M.G.4
  • 9
    • 0024675587 scopus 로고
    • Genetic requirements for hyperrecombination by very short patch mismatch repair: Involvement of Escherichia coli DNA polymerase I
    • Dzidic, S., and Radman, M. (1989). Genetic requirements for hyperrecombination by very short patch mismatch repair: involvement of Escherichia coli DNA polymerase I. Mol. Gen. Genet. 217, 254-256.
    • (1989) Mol. Gen. Genet. , vol.217 , pp. 254-256
    • Dzidic, S.1    Radman, M.2
  • 10
    • 0032474760 scopus 로고    scopus 로고
    • DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-Ppol
    • Flick, K.E., Jurica, M.S., Monnat, R.J., Jr., and Stoddard, B.L. (1998).DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-Ppol. Nature 394, 96-101.
    • (1998) Nature , vol.394 , pp. 96-101
    • Flick, K.E.1    Jurica, M.S.2    Monnat R.J., Jr.3    Stoddard, B.L.4
  • 12
    • 0028854033 scopus 로고
    • Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome
    • Gläsner, W., Merkl, R., Schellenberger, V., and Fritz, H.J. (1995).Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome.J. Mol. Biol. 245, 1-7.
    • (1995) J. Mol. Biol. , vol.245 , pp. 1-7
    • Gläsner, W.1    Merkl, R.2    Schellenberger, V.3    Fritz, H.J.4
  • 13
    • 0030728449 scopus 로고    scopus 로고
    • The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites
    • German, M.A., Morera, S., Rothwell, D.G., de La Fortelle, E., Mol, C.D., Tainer, J.A., Hickson, I.D., and Freemont, P.S. (1997). The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J. 16, 6548-6558.
    • (1997) EMBO J. , vol.16 , pp. 6548-6558
    • German, M.A.1    Morera, S.2    Rothwell, D.G.3    De La Fortelle, E.4    Mol, C.D.5    Tainer, J.A.6    Hickson, I.D.7    Freemont, P.S.8
  • 14
    • 0025816853 scopus 로고
    • The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G: The effect of base pair reversals
    • Grzeskowiak, K., Yanagi, K., Prive, G.G., and Dickerson, R.E. (1991).The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G: the effect of base pair reversals. J. Biol.Chem. 266, 8861-8883.
    • (1991) J. Biol.chem. , vol.266 , pp. 8861-8883
    • Grzeskowiak, K.1    Yanagi, K.2    Prive, G.G.3    Dickerson, R.E.4
  • 15
    • 0031763884 scopus 로고    scopus 로고
    • MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily
    • Guan, Y., Manuel, R.C., Arvai, A.S., Parikh, S.S., Mol, C.D., Miller,J.H., Lloyd, S., and Tainer, J.A. (1998). MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat. Struct. Biol. 5, 1058-1064.
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 1058-1064
    • Guan, Y.1    Manuel, R.C.2    Arvai, A.S.3    Parikh, S.S.4    Mol, C.D.5    Lloyd, S.6    Tainer, J.A.7
  • 16
    • 0026094872 scopus 로고
    • The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease
    • Hennecke, F., Kolmar, H., Bründl, K., and Fritz, H.J. (1991). The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease. Nature 353, 776-778.
    • (1991) Nature , vol.353 , pp. 776-778
    • Hennecke, F.1    Kolmar, H.2    Bründl, K.3    Fritz, H.J.4
  • 17
    • 0033529716 scopus 로고    scopus 로고
    • Structure of the DNA repair enzyme endonuclease IV and its DNA complex: Double-nucleotide flipping at abasic sites and three-metal-ion catalysis
    • Hosfield, D.J., Guan, Y., Haas, B.J., Cunningham, R.P., and Tainer,J.A. (1999). Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98, 397-408.
    • (1999) Cell , vol.98 , pp. 397-408
    • Hosfield, D.J.1    Guan, Y.2    Haas, B.J.3    Cunningham, R.P.4    Tainer, J.A.5
  • 18
    • 0023053739 scopus 로고
    • Refined crystal structure of an octanucleotide duplex with GT mismatched base-pairs
    • Hunter, W.N., Kneale, G., Brown, T., Rabinovich, D., and Kennard,O. (1986). Refined crystal structure of an octanucleotide duplex with GT mismatched base-pairs. J. Mol. Biol. 190, 605-618.
    • (1986) J. Mol. Biol. , vol.190 , pp. 605-618
    • Hunter, W.N.1    Kneale, G.2    Brown, T.3    Rabinovich, D.4    Kennard, O.5
  • 19
    • 0023664744 scopus 로고
    • The structure of guanosine-thymidine mismatches in B-DNA at 2.5 Å resolution
    • Hunter, W.N., Brown, T., Kneale, G., Anand, N.N., Rabinovich, D.,and Kennard, O. (1987). The structure of guanosine-thymidine mismatches in B-DNA at 2.5 Å resolution. J. Biol. Chem. 262, 9962-9970.
    • (1987) J. Biol. Chem. , vol.262 , pp. 9962-9970
    • Hunter, W.N.1    Brown, T.2    Kneale, G.3    Anand, N.N.4    Rabinovich, D.5    Kennard, O.6
  • 20
    • 0023644569 scopus 로고
    • Mismatch repair of deaminated 5-methyl-cytosine
    • Jones, M., Wagner, R., and Radman, M. (1987). Mismatch repair of deaminated 5-methyl-cytosine. J. Mol. Biol. 194, 155-159.
    • (1987) J. Mol. Biol. , vol.194 , pp. 155-159
    • Jones, M.1    Wagner, R.2    Radman, M.3
  • 21
    • 0027483012 scopus 로고
    • Co-crystal structure of TBP recognizing the minor groove of a TATA element
    • Kim, J.L., Nikolov, D.B., and Burley, S.K. (1993a). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature365, 520-527.
    • (1993) Nature , vol.365 , pp. 520-527
    • Kim, J.L.1    Nikolov, D.B.2    Burley, S.K.3
  • 22
    • 0027504913 scopus 로고
    • Crystal structure of a yeast TBP/TATA-box complex
    • Kim, Y., Geiger, J.H., Hahn, S., and Sigler, P.B. (1993b). Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520.
    • (1993) Nature , vol.365 , pp. 512-520
    • Kim, Y.1    Geiger, J.H.2    Hahn, S.3    Sigler, P.B.4
  • 23
    • 0022429756 scopus 로고
    • GT base-pairs in a DNA helix: The crystal structure of d(G-G-G-G-T-C-C-C)
    • Kneale, G., Brown, T., Kennard, O., and Rabinovich, D. (1985). GT base-pairs in a DNA helix: the crystal structure of d(G-G-G-G-T-C-C-C). J. Mol. Biol. 186, 805-814.
    • (1985) J. Mol. Biol. , vol.186 , pp. 805-814
    • Kneale, G.1    Brown, T.2    Kennard, O.3    Rabinovich, D.4
  • 24
    • 0000243829 scopus 로고
    • PROCHECK-a program to check the stereochemical quality of protein structures
    • Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M.(1993). PROCHECK-a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-290.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-290
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 25
    • 0020565834 scopus 로고
    • Specific mismatch correction in bacteriophage lambda crosses by very short patch repair
    • Lieb, M. (1983). Specific mismatch correction in bacteriophage lambda crosses by very short patch repair. Mol. Gen. Genet. 191,118-125.
    • (1983) Mol. Gen. Genet. , vol.191 , pp. 118-125
    • Lieb, M.1
  • 26
    • 0023448889 scopus 로고
    • Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites
    • Lieb, M. (1987). Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites. J. Bacteriol. 169,5241-5246.
    • (1987) J. Bacteriol. , vol.169 , pp. 5241-5246
    • Lieb, M.1
  • 27
    • 0029925165 scopus 로고    scopus 로고
    • Very short patch repair: Reducing the cost of cytosine methylation
    • Lieb, M., and Bhagwat, A.S. (1996). Very short patch repair: reducing the cost of cytosine methylation. Mol. Microbiol. 20, 467-473.
    • (1996) Mol. Microbiol. , vol.20 , pp. 467-473
    • Lieb, M.1    Bhagwat, A.S.2
  • 28
    • 0029131298 scopus 로고
    • Structural basis for DNA bending by the architectural transcription factor LEF-1
    • Love, J.J., Li, X., Case, D.A., Giese, K., Grosschedl, R., and Wright,P.E. (1995). Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature 376, 791-795.
    • (1995) Nature , vol.376 , pp. 791-795
    • Love, J.J.1    Li, X.2    Case, D.A.3    Giese, K.4    Grosschedl, R.5    Wright, P.E.6
  • 29
    • 0033591238 scopus 로고    scopus 로고
    • The active site of Serratia endonuclease contains a conserved magnesium-water cluster
    • Miller, M.D., Cai, J., and Krause, K.L. (1999). The active site of Serratia endonuclease contains a conserved magnesium-water cluster.J. Mol. Biol. 288, 975-987.
    • (1999) J. Mol. Biol. , vol.288 , pp. 975-987
    • Miller, M.D.1    Cai, J.2    Krause, K.L.3
  • 30
    • 0028923440 scopus 로고
    • Structure and function of the multifunctional DNA-repair enzyme exonuclease III
    • Mol, C.D., Kuo, C.F., Thayer, M.M., Cunningham, R.P., and Tainer,J.A. (1995). Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374, 381-386.
    • (1995) Nature , vol.374 , pp. 381-386
    • Mol, C.D.1    Kuo, C.F.2    Thayer, M.M.3    Cunningham, R.P.4    Tainer, J.A.5
  • 31
    • 84920325457 scopus 로고
    • AMoRe: An automated package for molecular replacement
    • Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157-163.
    • (1994) Acta Crystallogr. , vol.50 , pp. 157-163
    • Navaza, J.1
  • 32
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls, A., Sharp, K.A., and Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 33
    • 0033578010 scopus 로고    scopus 로고
    • Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins
    • Ohndorf, U.M., Rould, M.A., He, Q., Pabo, C.O., and Lippard, S.J.(1999). Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins. Nature 399, 708-712.
    • (1999) Nature , vol.399 , pp. 708-712
    • Ohndorf, U.M.1    Rould, M.A.2    He, Q.3    Pabo, C.O.4    Lippard, S.J.5
  • 34
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • J.Charles, W. Carter, and R.M. Sweet, eds. (New York: Academic Press)
    • Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology, J.Charles, W. Carter, and R.M. Sweet, eds. (New York: Academic Press), pp. 307-325.
    • (1997) Methods in Enzymology , pp. 307-325
    • Otwinowski, Z.1    Minor, W.2
  • 35
    • 0032167424 scopus 로고    scopus 로고
    • Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylasewith DNA
    • Parikh, S.S., Mol, C.D., Slupphaug, G, Bharati, S., Krokan, H.E., and Tainer, J.A. (1998). Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylasewith DNA. EMBO J. 17, 5214-5226.
    • (1998) EMBO J. , vol.17 , pp. 5214-5226
    • Parikh, S.S.1    Mol, C.D.2    Slupphaug, G.3    Bharati, S.4    Krokan, H.E.5    Tainer, J.A.6
  • 36
    • 0030911133 scopus 로고    scopus 로고
    • Recognition and cleavage of DNA by type-II restriction endonucleases
    • Pingoud, A., and Jeltsch, A. (1997). Recognition and cleavage ofDNA by type-II restriction endonucleases. Eur. J. Biochem. 246,1-22.
    • (1997) Eur. J. Biochem. , vol.246 , pp. 1-22
    • Pingoud, A.1    Jeltsch, A.2
  • 37
    • 0000803295 scopus 로고    scopus 로고
    • Dam-directed DNA mismatch repair
    • J.A.Nickoloff and M.F. Hoekstra, eds. (Totowa, NJ: Humana Press)
    • Rasmussen, L.J., Samson, L., and Marinus, M.G. (1998). Dam-directed DNA mismatch repair. In DNA Damage and Repair, J.A. Nickoloff and M.F. Hoekstra, eds. (Totowa, NJ: Humana Press), pp. 205-228.
    • (1998) DNA Damage and Repair , pp. 205-228
    • Rasmussen, L.J.1    Samson, L.2    Marinus, M.G.3
  • 38
    • 0030451819 scopus 로고    scopus 로고
    • Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
    • Rice, P.A., Yang, S., Mizuuchi, K., and Nash, H.A. (1996). Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.Cell 87, 1295-1306.
    • (1996) Cell , vol.87 , pp. 1295-1306
    • Rice, P.A.1    Yang, S.2    Mizuuchi, K.3    Nash, H.A.4
  • 41
    • 0028173030 scopus 로고
    • Crystal structure of Lacl member, PurR, bound to DNA: Minor groove binding by alpha helices
    • Schumacher, M.A., Choi, K.Y., Zalkin, H., and Brennan, R.G. (1994).Crystal structure of Lacl member, PurR, bound to DNA: minor groove binding by alpha helices. Science 266, 763-770.
    • (1994) Science , vol.266 , pp. 763-770
    • Schumacher, M.A.1    Choi, K.Y.2    Zalkin, H.3    Brennan, R.G.4
  • 42
    • 0029904839 scopus 로고    scopus 로고
    • A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
    • Slupphaug, G, Mol, C.D., Kavli, B., Arvai, A.S., Krokan, H.E., and Tainer, J.A. (1996). A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 384,87-92.
    • (1996) Nature , vol.384 , pp. 87-92
    • Slupphaug, G.1    Mol, C.D.2    Kavli, B.3    Arvai, A.S.4    Krokan, H.E.5    Tainer, J.A.6
  • 43
    • 0025327968 scopus 로고
    • A generequired for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene
    • Sohail, A., Lieb, M., Dar, M., and Bhagwat, A.S. (1990). A generequired for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene. J. Bacteriol. 172, 4214-4221.
    • (1990) J. Bacteriol. , vol.172 , pp. 4214-4221
    • Sohail, A.1    Lieb, M.2    Dar, M.3    Bhagwat, A.S.4
  • 44
    • 0030831985 scopus 로고    scopus 로고
    • Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster
    • Swaminathan, K., Flynn, P., Reece, R.J., and Marmorstein, R. (1997).Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster. Nat. Struct. Biol. 4, 751-759.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 751-759
    • Swaminathan, K.1    Flynn, P.2    Reece, R.J.3    Marmorstein, R.4
  • 46
    • 0029075461 scopus 로고
    • Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex
    • Werner, M.H., Huth, J.R., Gronenborn, A.M., and Clore, G.M. (1995).Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell 81, 705-714.
    • (1995) Cell , vol.81 , pp. 705-714
    • Werner, M.H.1    Huth, J.R.2    Gronenborn, A.M.3    Clore, G.M.4
  • 47
    • 0030046809 scopus 로고    scopus 로고
    • Intercalation, DNA kinking, and the control of transcription
    • Werner, M.H., Gronenborn, A.M., and Clore, G.M. (1996). Intercalation, DNA kinking, and the control of transcription. Science 271,778-784.
    • (1996) Science , vol.271 , pp. 778-784
    • Werner, M.H.1    Gronenborn, A.M.2    Clore, G.M.3
  • 48
    • 0026447731 scopus 로고
    • X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 Å resolution
    • Weston, S.A., Lahm, A., and Suck, D. (1992). X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 Å resolution. J. Mol. Biol.226, 1237-1256.
    • (1992) J. Mol. Biol. , vol.226 , pp. 1237-1256
    • Weston, S.A.1    Lahm, A.2    Suck, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.