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Volumn 19, Issue 15, 2000, Pages 3849-3856

Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism

Author keywords

( )8 barrel; 2 dehydro 3 deoxygalactarate (DDG) aldolase; Aldolase; Domain swapping; X ray crystallography

Indexed keywords

ANION; CARBON; FRUCTOSE BISPHOSPHATE ALDOLASE; METAL; PHOSPHATE; PROTON; SELENIUM;

EID: 0034254465     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/19.15.3849     Document Type: Article
Times cited : (51)

References (32)
  • 1
    • 0000913086 scopus 로고
    • A fast algorithm for rendering space-filling molecule pictures
    • Bacon, D.J. and Anderson, W.F. (1988) A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph., 6, 219-220.
    • (1988) J. Mol. Graph. , vol.6 , pp. 219-220
    • Bacon, D.J.1    Anderson, W.F.2
  • 2
    • 0031457319 scopus 로고    scopus 로고
    • Immune versus natural selection: Antibody aldolases with enzymic rates but broader scope
    • Barbas, C.F., III et al. (1997) Immune versus natural selection: antibody aldolases with enzymic rates but broader scope. Science, 278, 2085-2092.
    • (1997) Science , vol.278 , pp. 2085-2092
    • Barbas C.F. III1
  • 3
    • 0028865843 scopus 로고
    • 3D domain swapping: A mechanism for oligomer assembly
    • Bennett, M.J., Schlunegger, M.P. and Eisenberg, D. (1995) 3D domain swapping: a mechanism for oligomer assembly. Protein Sci., 4, 2455-2468.
    • (1995) Protein Sci. , vol.4 , pp. 2455-2468
    • Bennett, M.J.1    Schlunegger, M.P.2    Eisenberg, D.3
  • 5
    • 13044294024 scopus 로고    scopus 로고
    • Rhombohedral crystals of 2-dehydro-3-deoxy galactarate aldolase from Escherichia coli
    • Blackwell, N.C., Cullis, P.M., Cooper, R.A. and Izard, T. (1999) Rhombohedral crystals of 2-dehydro-3-deoxy galactarate aldolase from Escherichia coli. Acta Cryslallogr. D, 55, 1368-1369.
    • (1999) Acta Cryslallogr. D , vol.55 , pp. 1368-1369
    • Blackwell, N.C.1    Cullis, P.M.2    Cooper, R.A.3    Izard, T.4
  • 6
    • 0029761259 scopus 로고    scopus 로고
    • Novel active site in Escherichia coli fructose-1,6-bisphosphate aldolase
    • Blom, N.S., Tetreault, S., Coulombe, R. and Sygusch, J. (1996) Novel active site in Escherichia coli fructose-1,6-bisphosphate aldolase. Nature Struct. Biol., 3, 856-862.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 856-862
    • Blom, N.S.1    Tetreault, S.2    Coulombe, R.3    Sygusch, J.4
  • 7
    • 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
  • 8
    • 0023140814 scopus 로고
    • Crystallographic R-factor refinement by molecular dynamics
    • Brünger, A.T., Kuriyan, J. and Karplus, M. (1988) Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
    • (1988) Science , vol.235 , pp. 458-460
    • Brünger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 9
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography & NMR system: A new software suite for macromolecular structure determination
    • Brünger, A.T. et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D, 54, 905-921.
    • (1998) Acta Crystallogr. D , vol.54 , pp. 905-921
    • Brünger, A.T.1
  • 10
    • 0029064088 scopus 로고
    • High-level biosynthetic substitution of methionine in proteins by its analogues 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli
    • Budisa, N., Steipe, B., Demange, P., Eckerskorn, C., Kellermann, J. and Huber, R. (1995) High-level biosynthetic substitution of methionine in proteins by its analogues 2-aminohexanoic acid, selenomethionine, telluromethionine and ethionine in Escherichia coli. Eur. J. Biochem., 230, 788-796.
    • (1995) Eur. J. Biochem. , vol.230 , pp. 788-796
    • Budisa, N.1    Steipe, B.2    Demange, P.3    Eckerskorn, C.4    Kellermann, J.5    Huber, R.6
  • 11
    • 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
  • 12
    • 0030589053 scopus 로고    scopus 로고
    • The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding site embedded in a familiar fold
    • Cooper, S.J., Leonard, G.A., McSweeney, S.M., Thompson, A.W., Naismith, J.H., Qamar, S., Plater, A., Berry, A. and Hunter, W.N. (1996) The crystal structure of a class II fructose-1,6-bisphosphate aldolase shows a novel binuclear metal-binding site embedded in a familiar fold. Structure, 4, 1303-1315.
    • (1996) Structure , vol.4 , pp. 1303-1315
    • Cooper, S.J.1    Leonard, G.A.2    McSweeney, S.M.3    Thompson, A.W.4    Naismith, J.H.5    Qamar, S.6    Plater, A.7    Berry, A.8    Hunter, W.N.9
  • 13
    • 0027275542 scopus 로고
    • The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli
    • Dreyer, M.K. and Schulz, G.E. (1993) The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli. J. Mol. Biol., 231, 549-553.
    • (1993) J. Mol. Biol. , vol.231 , pp. 549-553
    • Dreyer, M.K.1    Schulz, G.E.2
  • 15
    • 0009586434 scopus 로고
    • 2-Keto-3-deoxy-D-glucarate aldolase
    • Fish, D.C. and Blumenthal, H.J. (1966) 2-keto-3-deoxy-D-glucarate aldolase. Methods Enzymol., 9, 529-534.
    • (1966) Methods Enzymol. , vol.9 , pp. 529-534
    • Fish, D.C.1    Blumenthal, H.J.2
  • 16
    • 77956895467 scopus 로고
    • Aldolases
    • Academic Press, New York, NY
    • Horecker, B.L., Tsolas, O. and Lai, C.Y. (1972) Aldolases. In The Enzymes, 3rd edn, Vol. 7. Academic Press, New York, NY, pp. 213-258.
    • (1972) The Enzymes, 3rd Edn , vol.7 , pp. 213-258
    • Horecker, B.L.1    Tsolas, O.2    Lai, C.Y.3
  • 18
    • 0032514651 scopus 로고    scopus 로고
    • Evolution of enzymatic activities in the enolase superfamily: Characterization of the D-glucarate/galactarate catabolic pathway in Escherichia coli
    • Hubbard, B.K., Koch, M., Palmer, D.R.J., Babbitt, P.C. and Gerlt, J.A. (1998) Evolution of enzymatic activities in the enolase superfamily: characterization of the D-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry, 37, 14369-14375.
    • (1998) Biochemistry , vol.37 , pp. 14369-14375
    • Hubbard, B.K.1    Koch, M.2    Palmer, D.R.J.3    Babbitt, P.C.4    Gerlt, J.A.5
  • 19
    • 0028773463 scopus 로고
    • Three-dimensional structure of N-acetylneuraminate lyase from Escherichia coli
    • Izard, T., Lawrence, M.C., Malby, R.L., Lilley, G.G. and Colman, P.M. (1994) Three-dimensional structure of N-acetylneuraminate lyase from Escherichia coli. Structure, 2, 361-369.
    • (1994) Structure , vol.2 , pp. 361-369
    • Izard, T.1    Lawrence, M.C.2    Malby, R.L.3    Lilley, G.G.4    Colman, P.M.5
  • 20
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones, T.A., Zou, J.-Y., Cowan, S.W. and Kjeldgaard, M, (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A, 47, 110-119.
    • (1991) Acta Crystallogr. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.-Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 21
    • 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. Crystallogr., 24, 946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 22
    • 0028057108 scopus 로고
    • Raster3D version 2.0 - A program for photorealistic molecular graphics
    • Merritt, E.A. and Murphy, M.E.P. (1994) Raster3D version 2.0 - a program for photorealistic molecular graphics. Acta Crystallogr. D, 50, 869-873.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 869-873
    • Merritt, E.A.1    Murphy, M.E.P.2
  • 24
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 25
    • 0009593417 scopus 로고
    • Does substrate rather than protein provide the catalyst for an α-proton abstraction in aldolase?
    • Periana, R.A., Motiu-DeGrood, R., Chiang, Y. and Hupe, D.J. (1980) Does substrate rather than protein provide the catalyst for an α-proton abstraction in aldolase? J. Am. Chem. Soc., 102, 3923-3927.
    • (1980) J. Am. Chem. Soc. , vol.102 , pp. 3923-3927
    • Periana, R.A.1    Motiu-DeGrood, R.2    Chiang, Y.3    Hupe, D.J.4
  • 27
    • 0030070065 scopus 로고    scopus 로고
    • Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of E.coli
    • Qamar, S., Marsh, K. and Berry, A. (1996) Identification of arginine 331 as an important active site residue in the class II fructose-1,6-bisphosphate aldolase of E.coli. Protein Sci., 5, 154-161.
    • (1996) Protein Sci. , vol.5 , pp. 154-161
    • Qamar, S.1    Marsh, K.2    Berry, A.3
  • 29
    • 0030465630 scopus 로고    scopus 로고
    • Bayesian weighting for macromolecular crystallographic refinement
    • Terwilliger, T.C. and Berendzen, J. (1996) Bayesian weighting for macromolecular crystallographic refinement. Acta Cryatallogr. D, 52, 743-748.
    • (1996) Acta Cryatallogr. D , vol.52 , pp. 743-748
    • Terwilliger, T.C.1    Berendzen, J.2
  • 30
    • 0025303335 scopus 로고
    • Zinc coordination, function and structure of zinc enzymes and other proteins
    • Vallee, B.L. and Auld, D.S. (1990) Zinc coordination, function and structure of zinc enzymes and other proteins. Biochemistry, 29, 5647-5659.
    • (1990) Biochemistry , vol.29 , pp. 5647-5659
    • Vallee, B.L.1    Auld, D.S.2
  • 31
    • 0029590066 scopus 로고
    • Efficient aldolase catalytic antibodies that use the enamine mechanism of natural enzymes
    • Wagner, J., Lerner, R.A. and Barbas, C.F., III (1995) Efficient aldolase catalytic antibodies that use the enamine mechanism of natural enzymes. Science, 270, 1797-1800.
    • (1995) Science , vol.270 , pp. 1797-1800
    • Wagner, J.1    Lerner, R.A.2    Barbas C.F. III3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.