메뉴 건너뛰기




Volumn 4, Issue 1, 1996, Pages 97-107

Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site

Author keywords

Active site; Alpha beta protein; Biocatalyst; Nucleoside; X ray crystallography

Indexed keywords

GLYCOSYLTRANSFERASE; NUCLEOSIDE DEOXYRIBOSYLTRANSFERASE; PURINE DERIVATIVE; PYRIMIDINE DERIVATIVE;

EID: 0029643856     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(96)00013-5     Document Type: Article
Times cited : (49)

References (49)
  • 1
    • 0026033819 scopus 로고
    • Nucleoside deoxyribosyltransferase activity and inosine phosphorylase activity in lactic acid bacteria
    • Chawdhri, R.F., Hutchinson, D.W. & Richards, A. O'L. (1991). Nucleoside deoxyribosyltransferase activity and inosine phosphorylase activity in lactic acid bacteria. Arch. Microbiol. 155, 409-411.
    • (1991) Arch. Microbiol. , vol.155 , pp. 409-411
    • Chawdhri, R.F.1    Hutchinson, D.W.2    Richards, A.O'L.3
  • 2
    • 2142785551 scopus 로고
    • The enzymically catalyzed transfer of the deoxyribosyl group from one purine or pyrimidine to another
    • MacNutt, W.S. (1952). The enzymically catalyzed transfer of the deoxyribosyl group from one purine or pyrimidine to another. Biochem. J. 50, 384-397.
    • (1952) Biochem. J. , vol.50 , pp. 384-397
    • MacNutt, W.S.1
  • 3
    • 0025917139 scopus 로고
    • Lyase activity of nucleoside-2′-deoxyribosyltransferase: Transient generation of ribal and its use in the synthesis of 2′-deoxynucleosides
    • Smar, M., Short, S. & Wertenden, R. (1991). Lyase activity of nucleoside-2′-deoxyribosyltransferase: transient generation of ribal and its use in the synthesis of 2′-deoxynucleosides. Biochemistry 30, 7908-7912.
    • (1991) Biochemistry , vol.30 , pp. 7908-7912
    • Smar, M.1    Short, S.2    Wertenden, R.3
  • 4
    • 0015220189 scopus 로고
    • Trans-N-deoxyribosylase from Lactobacillus helveticus
    • Uerkvitz, W. (1971). Trans-N-deoxyribosylase from Lactobacillus helveticus. Eur. J. Biochem. 23, 387-395.
    • (1971) Eur. J. Biochem. , vol.23 , pp. 387-395
    • Uerkvitz, W.1
  • 5
    • 0025891793 scopus 로고
    • The purine-2-deoxyribonucleosidase from Crithidia luculiae: Purification and trans-N-deoxyribosylase activity
    • Steenkamp, D. (1991). The purine-2-deoxyribonucleosidase from Crithidia luculiae: purification and trans-N-deoxyribosylase activity. Eur. J. Biochem. 197, 431-439.
    • (1991) Eur. J. Biochem. , vol.197 , pp. 431-439
    • Steenkamp, D.1
  • 6
    • 0026794954 scopus 로고
    • Substrate specificity of the purine-2′-deoxyribonucleosidase of Crithidia luculiae
    • Steenkamp, D.J. & Halbich, J.F. (1992). Substrate specificity of the purine-2′-deoxyribonucleosidase of Crithidia luculiae. Biochem. J. 287, 125-129.
    • (1992) Biochem. J. , vol.287 , pp. 125-129
    • Steenkamp, D.J.1    Halbich, J.F.2
  • 7
    • 0029034947 scopus 로고
    • Identification of the active site nucleophile in nucleoside 2′-deoxyribosyltransferase as glutamic acid 98
    • Porter, D.J., Merrill, B.M. & Short, S.A. (1995). Identification of the active site nucleophile in nucleoside 2′-deoxyribosyltransferase as glutamic acid 98. J. Biol. Chem. 270, 15551-15556.
    • (1995) J. Biol. Chem. , vol.270 , pp. 15551-15556
    • Porter, D.J.1    Merrill, B.M.2    Short, S.A.3
  • 8
    • 0025270735 scopus 로고
    • Crystallization and preliminary X-ray investigation of recombinant Lactobacillus leichmannii nucleoside deoxyribosyltransferase
    • Cook, W.J., Short, S.A. & Ealick, S.E. (1989). Crystallization and preliminary X-ray investigation of recombinant Lactobacillus leichmannii nucleoside deoxyribosyltransferase. J. Biol. Chem. 265, 2682-2683.
    • (1989) J. Biol. Chem. , vol.265 , pp. 2682-2683
    • Cook, W.J.1    Short, S.A.2    Ealick, S.E.3
  • 9
    • 73649199749 scopus 로고
    • Purification, kinetics, and repression control of bacterial trans-N-deoxyribosylase
    • Beck, W.S. & Levin, M. (1963). Purification, kinetics, and repression control of bacterial trans-N-deoxyribosylase. J. Biol. Chem. 238, 702-709.
    • (1963) J. Biol. Chem. , vol.238 , pp. 702-709
    • Beck, W.S.1    Levin, M.2
  • 10
    • 0016204167 scopus 로고
    • Deoxyribosyl transfer catalysis with trans-N-deoxyribosylase
    • Danzin, C. & Cardinaud, R. (1974). Deoxyribosyl transfer catalysis with trans-N-deoxyribosylase. Eur. J. Biochem. 48, 255-262.
    • (1974) Eur. J. Biochem. , vol.48 , pp. 255-262
    • Danzin, C.1    Cardinaud, R.2
  • 11
    • 77956922394 scopus 로고
    • Glycosidases and Glycosyltransferases
    • Sigman, D.S., ed, Academic Press, New York
    • Mooser, G. (1992). Glycosidases and Glycosyltransferases. In The Enzymes, Vol. 20. (Sigman, D.S., ed), pp. 187-233, Academic Press, New York.
    • (1992) The Enzymes , vol.20 , pp. 187-233
    • Mooser, G.1
  • 13
    • 0023680555 scopus 로고
    • Synthesis of 2′,3′-dideoxynucleosides by enzymatic transglycosylation
    • Carson, D. & Wasson, D. (1988). Synthesis of 2′,3′-dideoxynucleosides by enzymatic transglycosylation. Biochem. Biophys. Res. Commun. 155, 829-834.
    • (1988) Biochem. Biophys. Res. Commun. , vol.155 , pp. 829-834
    • Carson, D.1    Wasson, D.2
  • 15
    • 0025570249 scopus 로고
    • New approaches to the synthesis of antiviral nucleosides
    • Hutchinson, D.W. (1990), New approaches to the synthesis of antiviral nucleosides. Trends Biotechnol. 8, 348-353.
    • (1990) Trends Biotechnol. , vol.8 , pp. 348-353
    • Hutchinson, D.W.1
  • 16
    • 0026555473 scopus 로고
    • The enzymatic synthesis of antiviral agents
    • Hanrahan, J.R. & Hutchinson, D.W. (1992). The enzymatic synthesis of antiviral agents. J. Biotech. 23, 193-210.
    • (1992) J. Biotech. , vol.23 , pp. 193-210
    • Hanrahan, J.R.1    Hutchinson, D.W.2
  • 17
    • 0019357107 scopus 로고
    • Analogs of 2′-deoxyadenosine: Facile enzyme preparation and growth inhibitory effects on human cell lines
    • Huang, M., Hatfield, K., Roetker, A., Montgomery, J. & Blakely, R. (1981). Analogs of 2′-deoxyadenosine: facile enzyme preparation and growth inhibitory effects on human cell lines. Biochem. Pharmacol. 30, 2663-2671.
    • (1981) Biochem. Pharmacol. , vol.30 , pp. 2663-2671
    • Huang, M.1    Hatfield, K.2    Roetker, A.3    Montgomery, J.4    Blakely, R.5
  • 18
    • 0029069647 scopus 로고
    • 2-amino-9-(3-azido-2,3-dideoxy-β-D-erythro-pentofuranosyl)-6- substituted-purines: Synthesis and anti-HIV activity
    • in press
    • Freeman, G.A., Shaver, S.R., Rideout, J.L. & Short, S.A. (1995). 2-amino-9-(3-azido-2,3-dideoxy-β-D-erythro-pentofuranosyl)-6-substituted- purines: synthesis and anti-HIV activity. Bioorg. Med. Chem. Lett. 3, in press.
    • (1995) Bioorg. Med. Chem. Lett. , vol.3
    • Freeman, G.A.1    Shaver, S.R.2    Rideout, J.L.3    Short, S.A.4
  • 19
    • 0029010378 scopus 로고
    • Nucleoside 2-deoxyribosyltransferase. Pre-steady state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98
    • Porter, D.J.T. & Short, S.A. (1995). Nucleoside 2-deoxyribosyltransferase. Pre-steady state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98. J. Biol. Chem. 270, 15557-15562.
    • (1995) J. Biol. Chem. , vol.270 , pp. 15557-15562
    • Porter, D.J.T.1    Short, S.A.2
  • 21
    • 0024562159 scopus 로고
    • Three-dimensional structure of CheY, the response regulator of bacterial chemotaxis
    • Stock, A.M., Mottonen, J.M., Stock, J.B. & Schutt, C.E. (1989). Three-dimensional structure of CheY, the response regulator of bacterial chemotaxis. Nature 337, 745-749.
    • (1989) Nature , vol.337 , pp. 745-749
    • Stock, A.M.1    Mottonen, J.M.2    Stock, J.B.3    Schutt, C.E.4
  • 22
    • 0026434561 scopus 로고
    • Atomic structure of adenosine deaminase completed with a transition-state analog: Understanding catalysis and immunodeficiency mutations
    • Wilson, O.K., Rudolph, F.B. & Quiocho, F.A. (1991). Atomic structure of adenosine deaminase completed with a transition-state analog: understanding catalysis and immunodeficiency mutations. Science 252, 1278-1284.
    • (1991) Science , vol.252 , pp. 1278-1284
    • Wilson, O.K.1    Rudolph, F.B.2    Quiocho, F.A.3
  • 23
    • 0028057520 scopus 로고
    • Cytidine deaminase. The 2.3 å crystal structure of an enzyme:transition state complex
    • Betts, L., Xiang, S., Short, S.A., Wolfenden, R. & Carter, C.W., Jr. (1994). Cytidine deaminase. The 2.3 å crystal structure of an enzyme:transition state complex. J. Mol. Biol. 235, 635-656.
    • (1994) J. Mol. Biol. , vol.235 , pp. 635-656
    • Betts, L.1    Xiang, S.2    Short, S.A.3    Wolfenden, R.4    Carter Jr., C.W.5
  • 24
    • 0025021597 scopus 로고
    • Three-dimensional structure of human erythrocitic purine nucleoside phosphorylase at 3.2 Å resolution
    • Ealick, S.E., et al., & Bugg, O.E. (1990). Three-dimensional structure of human erythrocitic purine nucleoside phosphorylase at 3.2 Å resolution. J. Biol. Chem. 265, 1812-1820.
    • (1990) J. Biol. Chem. , vol.265 , pp. 1812-1820
    • Ealick, S.E.1    Bugg, O.E.2
  • 25
    • 0025160874 scopus 로고
    • Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 Å resolution
    • Walter, M.R., et al., & Ealick, S.E. (1990). Three-dimensional structure of thymidine phosphorylase from Escherichia coli at 2.8 Å resolution. J. Biol. Chem. 265, 14016-14022.
    • (1990) J. Biol. Chem. , vol.265 , pp. 14016-14022
    • Walter, M.R.1    Ealick, S.E.2
  • 26
    • 0029027433 scopus 로고
    • Atomic structure at 2.5 Å resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice
    • Morgunova, E.Y., et al., & Debabov, V.G. (1995). Atomic structure at 2.5 Å resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice. FEBS Lett. 367, 183-187.
    • (1995) FEBS Lett. , vol.367 , pp. 183-187
    • Morgunova, E.Y.1    Debabov, V.G.2
  • 27
    • 0028281205 scopus 로고
    • Crystal structure of orotate phosphoribosyltransferase
    • Scapin, G., Grubmeyer, C. & Sacchettini, J.C. (1994). Crystal structure of orotate phosphoribosyltransferase. Biochemistry 33, 1287-1294.
    • (1994) Biochemistry , vol.33 , pp. 1287-1294
    • Scapin, G.1    Grubmeyer, C.2    Sacchettini, J.C.3
  • 28
    • 0028083309 scopus 로고
    • The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase with bound GMP
    • Eads, J.C., Scapin, G., Xu, Y., Grubmeyer, C. & Sacchettini, J.C. (1994). The crystal structure of human hypoxanthine-guanine phosphoribosyltransferase with bound GMP. Cell 78, 325-334.
    • (1994) Cell , vol.78 , pp. 325-334
    • Eads, J.C.1    Scapin, G.2    Xu, Y.3    Grubmeyer, C.4    Sacchettini, J.C.5
  • 29
    • 0028762844 scopus 로고
    • Structure of the allosteric regulatory enzyme of purine biosynthesis
    • Smith, J.L., et al., & Satow, Y. (1994). Structure of the allosteric regulatory enzyme of purine biosynthesis. Science 264, 1427-1433.
    • (1994) Science , vol.264 , pp. 1427-1433
    • Smith, J.L.1    Satow, Y.2
  • 30
    • 0026727881 scopus 로고
    • X-ray structure of nucleoside diphosphate kinase
    • Dumas, C., et al., & Janin, J. (1992). X-ray structure of nucleoside diphosphate kinase. EMBO J. 11, 3202-3208.
    • (1992) EMBO J. , vol.11 , pp. 3202-3208
    • Dumas, C.1    Janin, J.2
  • 31
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
    • Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 32
    • 0025277191 scopus 로고
    • The classification and origins of protein folding patterns
    • Chothia, C. & Finkelstein, A. (1990). The classification and origins of protein folding patterns. Annu. Rev. Biochem. 59, 1007-1039.
    • (1990) Annu. Rev. Biochem. , vol.59 , pp. 1007-1039
    • Chothia, C.1    Finkelstein, A.2
  • 33
    • 0002548426 scopus 로고
    • Structures and conformational properties of bases, furanose sugars, and phosphate groups
    • Cantor, C.R., ed, Springer-Verlag New York, Inc., New York
    • Saenger, W. (1984). Structures and conformational properties of bases, furanose sugars, and phosphate groups. In Principles of Nucleic Acid Structure, (Cantor, C.R., ed), pp. 51-104, Springer-Verlag New York, Inc., New York.
    • (1984) Principles of Nucleic Acid Structure , pp. 51-104
    • Saenger, W.1
  • 34
    • 0019053306 scopus 로고
    • Relation between structure and function of α/β proteins
    • Branden, C. (1980). Relation between structure and function of α/β proteins. Q. Rev. Biophys. 13, 317-338.
    • (1980) Q. Rev. Biophys. , vol.13 , pp. 317-338
    • Branden, C.1
  • 35
    • 0020596786 scopus 로고
    • Formation of 3-(2′-deoxyribofuranosyl) and 9-(2′-deoxyribofuranosyl) nucleosides of 8-substituted purines by nucleoside deoxyribosyltransferase
    • Huang, M., Montgomery, J.A., Thorpe, M.C., Stewart, E.L., Secrist, J.A. & Blakely, R.L. (1983). Formation of 3-(2′-deoxyribofuranosyl) and 9-(2′-deoxyribofuranosyl) nucleosides of 8-substituted purines by nucleoside deoxyribosyltransferase. Arch. Biochem. Biophys. 222, 183-144.
    • (1983) Arch. Biochem. Biophys. , vol.222 , pp. 183-1144
    • Huang, M.1    Montgomery, J.A.2    Thorpe, M.C.3    Stewart, E.L.4    Secrist, J.A.5    Blakely, R.L.6
  • 36
    • 0022326269 scopus 로고
    • Software for a diffractometer with multiwire area detector
    • Howard, A.J., Nielsen, C. & Xuong, N.H. (1985). Software for a diffractometer with multiwire area detector. Methods Enzymol. 114, 452-472.
    • (1985) Methods Enzymol. , vol.114 , pp. 452-472
    • Howard, A.J.1    Nielsen, C.2    Xuong, N.H.3
  • 37
    • 0000134034 scopus 로고
    • Strategy for data collection from protein crystals using a multiwire counter area detector diffractometer
    • Xuong, N.B., Nielsen, C., Hamlin, R. & Anderson, D. (1985). Strategy for data collection from protein crystals using a multiwire counter area detector diffractometer, J. Appl. Cryst. 18, 342-350.
    • (1985) J. Appl. Cryst. , vol.18 , pp. 342-350
    • Xuong, N.B.1    Nielsen, C.2    Hamlin, R.3    Anderson, D.4
  • 38
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews, B.W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
    • (1968) J. Mol. Biol. , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 39
    • 0022325950 scopus 로고
    • Resolution of phase ambiguity in macromolecular crystallography
    • Wang, B.C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 155, 90-112.
    • (1985) Methods Enzymol. , vol.155 , pp. 90-112
    • Wang, B.C.1
  • 40
    • 0022333120 scopus 로고
    • Interactive computer graphics: FRODO
    • Jones, T.A. (1985). Interactive computer graphics: FRODO. Methods Enzymol. 115, 157-171.
    • (1985) Methods Enzymol. , vol.115 , pp. 157-171
    • Jones, T.A.1
  • 41
    • 0002301187 scopus 로고
    • Incorporation of fast Fourier transforms to speed least squares refinement of protein structures
    • Finzel, B.C. (1987). Incorporation of fast Fourier transforms to speed least squares refinement of protein structures. J. Appl. Cryst. 20, 53-55.
    • (1987) J. Appl. Cryst. , vol.20 , pp. 53-55
    • Finzel, B.C.1
  • 43
    • 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
  • 45
    • 0000082544 scopus 로고
    • CHAIN - A crystallographic modeling program
    • Sack, J. (1988). CHAIN - a crystallographic modeling program. J. Mol. Graph. 6, 244-245.
    • (1988) J. Mol. Graph. , vol.6 , pp. 244-245
    • Sack, J.1
  • 46
    • 0017411710 scopus 로고
    • The protein data bank: A computer-based archival file for macromolecular structures
    • Berstein, F.C., et al., & Tasumi, M. (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
    • (1977) J. Mol. Biol. , vol.112 , pp. 535-542
    • Berstein, F.C.1    Tasumi, M.2
  • 47
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
    • (1991) J. Appl. Cryst. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 48
    • 0000449348 scopus 로고
    • Ribbon models of macromolecules
    • Carson, M. (1987). Ribbon models of macromolecules. J. Mol. Graphics 5, 103-106.
    • (1987) J. Mol. Graphics , vol.5 , pp. 103-106
    • Carson, M.1
  • 49
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
    • (1993) J. Appl. Cryst. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.