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Volumn 287, Issue 2, 1999, Pages 331-346

Protein mimicry of DNA from crystal structures of the Uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli Uracil-DNA glycosylase

Author keywords

DNA glycosylase; DNA repair; Enzyme inhibitor complex; Protein mimicry of nucleic acids; Protein structure

Indexed keywords

DNA; ENZYME INHIBITOR; INHIBITOR PROTEIN; MUTANT PROTEIN; PROTEIN; URACIL DNA GLYCOSYLTRANSFERASE;

EID: 0033605817     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2605     Document Type: Article
Times cited : (117)

References (53)
  • 2
    • 0026574664 scopus 로고
    • Characterization of the Escherichia coli uracil-DNA glycosylase inhibitor-protein complex
    • Bennett S. E., Mosbaugh D. W. Characterization of the Escherichia coli uracil-DNA glycosylase inhibitor-protein complex. J. Biol. Chem. 268:1992;22512-22521.
    • (1992) J. Biol. Chem. , vol.268 , pp. 22512-22521
    • Bennett, S.E.1    Mosbaugh, D.W.2
  • 3
    • 0027761910 scopus 로고
    • Kinetics of the uracil-DNA glycosylase/inhibitor protein association. Ung interaction with Ugi, nucleic acids, and uracil compounds
    • Bennett S. E., Schimerlik M. I., Mosbaugh D. W. Kinetics of the uracil-DNA glycosylase/inhibitor protein association. Ung interaction with Ugi, nucleic acids, and uracil compounds. J. Biol. Chem. 268:1993;26879-26885.
    • (1993) J. Biol. Chem. , vol.268 , pp. 26879-26885
    • Bennett, S.E.1    Schimerlik, M.I.2    Mosbaugh, D.W.3
  • 4
    • 0027993592 scopus 로고
    • UV-catalyzed cross-linking of Escherichia coli uracil-DNA glycosylase to DNA
    • Bennett S. E., Jensen O. N., Barofsky D. F., Mosbaugh D. W. UV-catalyzed cross-linking of Escherichia coli uracil-DNA glycosylase to DNA. J. Biol. Chem. 269:1994;21870-21879.
    • (1994) J. Biol. Chem. , vol.269 , pp. 21870-21879
    • Bennett, S.E.1    Jensen, O.N.2    Barofsky, D.F.3    Mosbaugh, D.W.4
  • 5
    • 0029079249 scopus 로고
    • Processivity of Escherichia coli and rat liver mitochondrial uracil-DNA glycosylase is affected by NaCl concentration
    • Bennett S. E., Sanderson R. J., Mosbaugh D. W. Processivity of Escherichia coli and rat liver mitochondrial uracil-DNA glycosylase is affected by NaCl concentration. Biochemistry. 34:1995;6109-6119.
    • (1995) Biochemistry , vol.34 , pp. 6109-6119
    • Bennett, S.E.1    Sanderson, R.J.2    Mosbaugh, D.W.3
  • 6
    • 0030045003 scopus 로고    scopus 로고
    • Structure and mechanism of DNA topoisomerase II
    • Berger J. M., Gamblin S. J., Harrison S. C., Wang J. C. Structure and mechanism of DNA topoisomerase II. Nature. 379:1996;225-232.
    • (1996) Nature , vol.379 , pp. 225-232
    • Berger, J.M.1    Gamblin, S.J.2    Harrison, S.C.3    Wang, J.C.4
  • 7
    • 0032511137 scopus 로고    scopus 로고
    • Multiple open forms of ribose-binding protein trace the path of its conformational change
    • Bjorkman A. J., Mowbray S. L. Multiple open forms of ribose-binding protein trace the path of its conformational change. J. Mol. Biol. 279:1998;651-664.
    • (1998) J. Mol. Biol. , vol.279 , pp. 651-664
    • Bjorkman, A.J.1    Mowbray, S.L.2
  • 9
    • 0001897686 scopus 로고
    • Assessment of phase accuracy by cross validation: The free R value. Methods and applications
    • Brünger A. T. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallog. sect. D. 49:1993;24-36.
    • (1993) Acta Crystallog. Sect. D , vol.49 , pp. 24-36
    • Brünger, A.T.1
  • 10
    • 0019170435 scopus 로고
    • Inhibitor of uracil-DNA glycosylase induced by bacteriophage PBS2. Purification and preliminary characterization
    • Cone R., Bonura T., Friedberg E. C. Inhibitor of uracil-DNA glycosylase induced by bacteriophage PBS2. Purification and preliminary characterization. J. Biol. Chem. 255:1980;10354-10358.
    • (1980) J. Biol. Chem. , vol.255 , pp. 10354-10358
    • Cone, R.1    Bonura, T.2    Friedberg, E.C.3
  • 11
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly M. L. Analytical molecular surface calculation. J. Appl. Crystallog. 16:1993a;548-558.
    • (1993) J. Appl. Crystallog. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 12
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science. 221:1993b;709-713.
    • (1993) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 13
    • 0020461949 scopus 로고
    • Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli
    • Duncan B. K., Weiss B. Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli. J. Bacteriol. 151:1982;750-755.
    • (1982) J. Bacteriol. , vol.151 , pp. 750-755
    • Duncan, B.K.1    Weiss, B.2
  • 14
    • 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 Crystallog. sect. A. 47:1991;392-400.
    • (1991) Acta Crystallog. Sect. a , vol.47 , pp. 392-400
    • Engh, R.A.1    Huber, R.2
  • 15
    • 0026567907 scopus 로고
    • Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
    • Eriksson A. E., Baase W. A., Zhang X., Heinz D. W., Blaber M., Baldwin E. P., Matthews B. W. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 255:1992;178-183.
    • (1992) Science , vol.255 , pp. 178-183
    • Eriksson, A.E.1    Baase, W.A.2    Zhang, X.3    Heinz, D.W.4    Blaber, M.5    Baldwin, E.P.6    Matthews, B.W.7
  • 16
    • 0016782046 scopus 로고
    • N-Glycosidase activity in extracts of Bacillus subtilis and its inhibition after infection with bacteriophage PBS2
    • Friedberg E. C., Ganeson A. K., Minton K. N-Glycosidase activity in extracts of Bacillus subtilis and its inhibition after infection with bacteriophage PBS2. J. Virol. 16:1975;315-321.
    • (1975) J. Virol. , vol.16 , pp. 315-321
    • Friedberg, E.C.1    Ganeson, A.K.2    Minton, K.3
  • 18
    • 0026016867 scopus 로고
    • Refined crystal structure of β-lactamase from Staphylococcus aureus PC1 at 2.0 Å resolution
    • Herzberg O. Refined crystal structure of β-lactamase from Staphylococcus aureus PC1 at 2.0 Å resolution. J. Mol. Biol. 217:1991;701-719.
    • (1991) J. Mol. Biol. , vol.217 , pp. 701-719
    • Herzberg, O.1
  • 19
    • 0019864721 scopus 로고
    • Specificity of the bacteriophage PBS2 induced inhibitor of uracil-DNA glycosylase
    • Karran P., Cone R., Friedberg E. C. Specificity of the bacteriophage PBS2 induced inhibitor of uracil-DNA glycosylase. Biochemistry. 20:1981;6092-6096.
    • (1981) Biochemistry , vol.20 , pp. 6092-6096
    • Karran, P.1    Cone, R.2    Friedberg, E.C.3
  • 21
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of protein cavities
    • Kleywegt G. J., Jones T. A. Detection, delineation, measurement and display of protein cavities. Acta Crystallog. sect. D. 50:1994;178-185.
    • (1994) Acta Crystallog. Sect. D , vol.50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 23
    • 0028115776 scopus 로고
    • Three-dimensional structure of the 67 K N-terminal fragment of E. coli DNA topoisomerase I
    • Lima C. D., Wang J. C., Mondragon A. Three-dimensional structure of the 67 K N-terminal fragment of E. coli DNA topoisomerase I. Nature. 367:1994;138-146.
    • (1994) Nature , vol.367 , pp. 138-146
    • Lima, C.D.1    Wang, J.C.2    Mondragon, A.3
  • 24
    • 0017392934 scopus 로고
    • DNA N-glycosidase: Properties of uracil-DNA glycosidase from Escherichia coli
    • Lindahl T., Ljungquist S., Siegert W., Nyberg B., Sperens B. DNA N-glycosidase: properties of uracil-DNA glycosidase from Escherichia coli. J. Biol. Chem. 252:1977;3286-3294.
    • (1977) J. Biol. Chem. , vol.252 , pp. 3286-3294
    • Lindahl, T.1    Ljungquist, S.2    Siegert, W.3    Nyberg, B.4    Sperens, B.5
  • 26
    • 0030875780 scopus 로고    scopus 로고
    • Site-directed mutagenesis and characterization of uracil-DNA glycosylase inhibitor protein: Role of specific carboxylic amino acids in complex formation with Escherichia coli uracil-DNA glycosylase
    • Lundquist A. J., Beger R. D., Bennett S. E., Bolton P. H., Mosbaugh D. W. Site-directed mutagenesis and characterization of uracil-DNA glycosylase inhibitor protein: role of specific carboxylic amino acids in complex formation with Escherichia coli uracil-DNA glycosylase. J. Biol. Chem. 272:1997;21408-21419.
    • (1997) J. Biol. Chem. , vol.272 , pp. 21408-21419
    • Lundquist, A.J.1    Beger, R.D.2    Bennett, S.E.3    Bolton, P.H.4    Mosbaugh, D.W.5
  • 27
    • 0002705842 scopus 로고
    • A visual protein crystallographic software system for X11/Xview
    • McRee D. E. A visual protein crystallographic software system for X11/Xview. J. Mol. Graph. 10:1992;44-46.
    • (1992) J. Mol. Graph. , vol.10 , pp. 44-46
    • McRee, D.E.1
  • 28
    • 0028934537 scopus 로고
    • Crystal structure and mutation analysis of human uracil-DNA glycosylase: Structural basis for specificity and catalysis
    • Mol C., Arvai A. S., Slupphaug G., Kavli B., Alseth I., Krokan H. E., Tainer J. A. Crystal structure and mutation analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 80:1995a;869-878.
    • (1995) Cell , vol.80 , pp. 869-878
    • Mol, C.1    Arvai, A.S.2    Slupphaug, G.3    Kavli, B.4    Alseth, I.5    Krokan, H.E.6    Tainer, J.A.7
  • 29
    • 0029084487 scopus 로고
    • Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: Protein mimicry of DNA
    • Mol C. D., Arvai A. S., Sanderson R. J., Slupphaug G., Kavli B., Krokan H. E., Mosbaugh D. W., Tainer J. A. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA. Cell. 82:1995b;701-708.
    • (1995) Cell , vol.82 , pp. 701-708
    • Mol, C.D.1    Arvai, A.S.2    Sanderson, R.J.3    Slupphaug, G.4    Kavli, B.5    Krokan, H.E.6    Mosbaugh, D.W.7    Tainer, J.A.8
  • 31
    • 0027112289 scopus 로고
    • 1.7 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli
    • Mowbray S. L., Cole L. B. 1.7 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli. J. Mol. Biol. 225:1992;155-175.
    • (1992) J. Mol. Biol. , vol.225 , pp. 155-175
    • Mowbray, S.L.1    Cole, L.B.2
  • 32
    • 84920325457 scopus 로고
    • AMoRe: An automated package for molecular replacement
    • Navaza L. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
    • (1994) Acta Crystallog. Sect. a , vol.50 , pp. 157-163
    • Navaza, L.1
  • 34
    • 0003976860 scopus 로고
    • Data collection and processing
    • L. Sawyer, N. Isaacs, & S. Bailey. Warrington: Science and Engineering Research Council
    • Otwinowski Z. Data collection and processing. Sawyer L., Isaacs N., Bailey S. Proceedings of the CCP4 Study Weekend. 1993;56-62 Science and Engineering Research Council, Warrington.
    • (1993) Proceedings of the CCP4 Study Weekend , pp. 56-62
    • Otwinowski, Z.1
  • 35
    • 0032167424 scopus 로고    scopus 로고
    • Base-excision repair initiation revealed by crystal structures and DNA-binding kinetics of human uracil-DNA glycosylase bound to DNA
    • Parikh S. S., Mol C. D., Slupphaug G., Bharati S., Krokan H. E., Tainer J. A. Base-excision repair initiation revealed by crystal structures and DNA-binding kinetics of human uracil-DNA glycosylase bound to DNA. EMBO J. 17:1998;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
    • 0021205810 scopus 로고
    • Novel stereospecificity of the L -arabinose-binding protein
    • Quiocho F. A., Vyas N. K. Novel stereospecificity of the L -arabinose-binding protein. Nature. 310:1984;381-386.
    • (1984) Nature , vol.310 , pp. 381-386
    • Quiocho, F.A.1    Vyas, N.K.2
  • 37
    • 0029799887 scopus 로고    scopus 로고
    • Identification of specific carboxyl groups on uracil-DNA glycosylase inhibitor protein that are required for activity
    • Sanderson R. J., Mosbaugh D. W. Identification of specific carboxyl groups on uracil-DNA glycosylase inhibitor protein that are required for activity. J. Biol. Chem. 271:1996;29170-29181.
    • (1996) J. Biol. Chem. , vol.271 , pp. 29170-29181
    • Sanderson, R.J.1    Mosbaugh, D.W.2
  • 38
    • 0029086874 scopus 로고
    • Cloning and expression of the uracil-DNA glycosylase inhibitor (UGI) from bacteriophage PBS-1 and crystallization of a uracil-DNA glycosylase-UGI complex
    • Savva R., Pearl L. H. Cloning and expression of the uracil-DNA glycosylase inhibitor (UGI) from bacteriophage PBS-1 and crystallization of a uracil-DNA glycosylase-UGI complex. Proteins: Struct. Funct. Genet. 22:1995a;287-289.
    • (1995) Proteins: Struct. Funct. Genet. , vol.22 , pp. 287-289
    • Savva, R.1    Pearl, L.H.2
  • 39
    • 0029115366 scopus 로고
    • Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex
    • Savva R., Pearl L. H. Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex. Nature Struct. Biol. 2:1995b;752-757.
    • (1995) Nature Struct. Biol. , vol.2 , pp. 752-757
    • Savva, R.1    Pearl, L.H.2
  • 40
    • 0028959237 scopus 로고
    • The structural basis of specific base-excision repair by uracil-DNA glycosylase
    • Savva R., McAuley-Hecht K., Brown T., Pearl L. The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature. 373:1995;487-493.
    • (1995) Nature , vol.373 , pp. 487-493
    • Savva, R.1    McAuley-Hecht, K.2    Brown, T.3    Pearl, L.4
  • 42
    • 0033551258 scopus 로고    scopus 로고
    • Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: Effect on DNA-binding, uracil inhibition and catalysis
    • Shroyer M., Bennett S. E., Putnam C. D., Tainer J. A., Mosbaugh D. W. Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: effect on DNA-binding, uracil inhibition and catalysis. Biochemistry. 1999.
    • (1999) Biochemistry
    • Shroyer, M.1    Bennett, S.E.2    Putnam, C.D.3    Tainer, J.A.4    Mosbaugh, D.W.5
  • 43
    • 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., Tainer J. A. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 384:1996;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
  • 44
    • 0033579953 scopus 로고    scopus 로고
    • Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
    • Stivers J. T., Pankiewicz K. W., Watanabe K. A. Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry. 38:1999;952-963.
    • (1999) Biochemistry , vol.38 , pp. 952-963
    • Stivers, J.T.1    Pankiewicz, K.W.2    Watanabe, K.A.3
  • 45
    • 0000933459 scopus 로고
    • Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage forBacillus subtilis
    • Takahashi I., Marmur J. Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage forBacillus subtilis. Nature. 197:1963;794-795.
    • (1963) Nature , vol.197 , pp. 794-795
    • Takahashi, I.1    Marmur, J.2
  • 46
    • 0019332581 scopus 로고
    • Covalent bonds between protein and DNA
    • Tse Y. C., Kirkegaard K., Wang J. C. Covalent bonds between protein and DNA. J. Biol. Chem. 255:1980;5560-5565.
    • (1980) J. Biol. Chem. , vol.255 , pp. 5560-5565
    • Tse, Y.C.1    Kirkegaard, K.2    Wang, J.C.3
  • 47
    • 0025732374 scopus 로고
    • Specificities and kinetics of uracil excision from uracil-containing DNA oligomers by Escherichia coli uracil DNA glycosylase
    • Varshney U., van de Sande J. H. Specificities and kinetics of uracil excision from uracil-containing DNA oligomers by Escherichia coli uracil DNA glycosylase. Biochemistry. 30:1991;4055-4061.
    • (1991) Biochemistry , vol.30 , pp. 4055-4061
    • Varshney, U.1    Van De Sande, J.H.2
  • 48
    • 0026495424 scopus 로고
    • Uracil-DNA glycosylases preferentially excise mispaired uracil
    • Verri A., Mazzarello P., Spadari S., Focher F. Uracil-DNA glycosylases preferentially excise mispaired uracil. Biochem. J. 287:1992;1007-1010.
    • (1992) Biochem. J. , vol.287 , pp. 1007-1010
    • Verri, A.1    Mazzarello, P.2    Spadari, S.3    Focher, F.4
  • 49
    • 0024473670 scopus 로고
    • Restriction analysis of PBS 1-related phages
    • Vieria G., de Lencastre H., Archer L. Restriction analysis of PBS 1-related phages. Arch. Virol. 106:1989;121-126.
    • (1989) Arch. Virol. , vol.106 , pp. 121-126
    • Vieria, G.1    De Lencastre, H.2    Archer, L.3
  • 50
    • 0023972380 scopus 로고
    • Uracil-DNA glycosylase inhibitor of bacteriophage PBS2: Cloning and effects of expression of the inhibitor gene inEscherichia coli
    • Wang Z., Mosbaugh D. W. Uracil-DNA glycosylase inhibitor of bacteriophage PBS2: cloning and effects of expression of the inhibitor gene inEscherichia coli. J. Bacteriol. 170:1988;1082-1091.
    • (1988) J. Bacteriol. , vol.170 , pp. 1082-1091
    • Wang, Z.1    Mosbaugh, D.W.2
  • 51
    • 0024587232 scopus 로고
    • Uracil-DNA glycosylase inhibitor gene of bacteriophage PBS2 encodes a binding protein specific for uracil-DNA glycosylase
    • Wang Z., Mosbaugh D. W. Uracil-DNA glycosylase inhibitor gene of bacteriophage PBS2 encodes a binding protein specific for uracil-DNA glycosylase. J. Biol. Chem. 264:1989;1163-1171.
    • (1989) J. Biol. Chem. , vol.264 , pp. 1163-1171
    • Wang, Z.1    Mosbaugh, D.W.2
  • 52
    • 0025726472 scopus 로고
    • Overproduction and characterization of uracil-DNA glycosylase inhibitor of bacteriophage PBS2
    • Wang Z., Smith D. G., Mosbaugh D. W. Overproduction and characterization of uracil-DNA glycosylase inhibitor of bacteriophage PBS2. Gene. 99:1991;31-37.
    • (1991) Gene , vol.99 , pp. 31-37
    • Wang, Z.1    Smith, D.G.2    Mosbaugh, D.W.3
  • 53
    • 0025334495 scopus 로고
    • A mollicute (mycoplasma) DNA repair enzyme: Purification and characterization of uracil-DNA glycosylase
    • Williams M. V., Pollack J. D. A mollicute (mycoplasma) DNA repair enzyme: purification and characterization of uracil-DNA glycosylase. J. Bacteriol. 172:1990;2979-2985.
    • (1990) J. Bacteriol. , vol.172 , pp. 2979-2985
    • Williams, M.V.1    Pollack, J.D.2


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