Crystal Structure Of The Alcohol Dehydrogenase From The Hyperthermophilic Archaeon Sulfolobus Solfataricus At 1. 85 Angstrom Resolution(435 views) Esposito L, Sica F, Raia CA, Giordano A, Rossi M, Mazzarella L, Zagari A
Istituto Di Biostrutture E Bioimmagini, CNR, Via Mezzocannone 6, I-80134 Napoli, Italy
Dipartimento Di Chimica, Università degli Studi Di Napoli Federico II, Via Cinthia, I-80126 Napoli, Italy
Istituto Di Biochimica Delle Proteine Ed Enzimologia, CNR, Via Marconi 10, I-80125 Napoli, Italy
CEINGE, Biotecnologie Avanzate Scarl, Napoli, Italy
References: Persson, B., Krook, M., Jörnvall, H., Characteristics of short-chain alcohol dehydrogenases and related enzymes (1991) Eur. J. Biochem., 200, pp. 537-54
Jörnvall, H., Höög, J.-O., Nomenclature of alcohol dehydrogenases (1995) Alcohol Alcohol., 30, pp. 153-161
Inoue, T., Sunagawa, M., Mori, A., Imai, C., Fukuda, M., Takagi, M., Yano, K., Cloning and sequencing of the gene encoding the 72-kDa dehydrogenase subunit of alcohol dehydrogenase from Acetobacter aceti (1989) J. Bacteriol., 171, pp. 3115-3122
Eklund, H., Nordström, B., Zeppezauer, E., Söderlund, G., Ohlsson, I., Boiwe, T., Three-dimensional structure of horse liver alcohol dehydrogenase at 2.4 Å resolution (1976) J. Mol. Biol., 102, pp. 27-59
Eklund, H., Samma, J.P., Wallen, L., Brändén, C.-I., Åkeson, Å., Jones, T.A., Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 Å resolution (1981) J. Mol. Biol., 146, pp. 561-587
Eklund, H., Brändén, C.-I., Alcohol dehydrogenase (1987) Biological Macromolecules and Assemblies, 3, pp. 73-142. , Wiley-Interscience, New York
Meijers, R., Morris, R.J., Adolph, H.W., Merli, A., Lamzin, V.S., Cedergren-Zeppezauer, E.S., On the enzymatic activation of NADH (2001) J. Biol. Chem., 276, pp. 9316-9321
Niederhut, M.S., Gibbons, B.J., Perez-Miller, S., Hurley, T.D., Three-dimensional structures of the three human class I alcohol dehydrogenases (2001) Protein Sci., 10, pp. 697-706
Yang, Z.N., Bosron, W.F., Hurley, T.D., Structure of human χχ alcohol dehydrogenase: A glutathione-dependent formaldehyde dehydrogenase (1997) J. Mol. Biol., 265, pp. 330-343
Xie, P., Parsons, S.H., Speckhard, D.C., Bosron, W.F., Hurley, T.D., X-ray structure of human class IV σσ alcohol dehydrogenase. Structural basis for substrate specificity (1997) J. Biol. Chem., 272, pp. 18558-18563
Svensson, S., Höög, J.-O., Schneider, G., Sandalova, T., Crystal structures of mouse class II alcohol dehydrogenase reveal determinants of substrate specificity and catalytic efficiency (2000) J. Mol. Biol., 302, pp. 441-453
Ramaswamy, S., El Ahmad, M., Danielsson, O., Jörnvall, H., Eklund, H., Crystal structure of cod liver class I alcohol dehydrogenase: Substrate pocket and structurally variable segments (1996) Protein Sci., 5, pp. 663-671
Korkhin, Y., Kalb, A.J., Peretz, M., Bogin, O., Burstein, Y., Frolow, F., NADP-dependent bacterial alcohol dehydrogenases: Crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii (1998) J. Mol. Biol., 278, pp. 967-981
Rella, R., Raia, C.A., Pensa, M., Pisani, F.M., Gambacorta, A., De Rosa, M., Rossi, M., A novel archaebacterial NAD+-dependent alcohol dehydrogenase. Purification and properties (1987) Eur. J. Biochem., 167, pp. 475-479
Brown, J.R., Doolittle, W.F., Archaea and the prokaryote-to-eukaryote transition (1997) Microbiol. Mol. Biol. Rev., 61, pp. 456-502
Adams, M.W.W., Enzymes and proteins from organisms that grow near and above 100°C (1993) Annu. Rev. Microbiol., 47, pp. 627-658
Ammendola, S., Raia, C.A., Caruso, C., Camardella, L., D'Auria, S., De Rosa, M., Rossi, M., Thermostable NAD(+)-dependent alcohol dehydrogenase from Sulfolobus solfataricus: Gene and protein sequence determination and relationship to other alcohol dehydrogenases (1992) Biochemistry, 31, pp. 12514-12523
Raia, C.A., D'Auria, S., Rossi, M., NAD+ dependent alcohol dehydrogenase from Sulfolobus solfataricus: Structural and functional features (1994) Biocatalysis, 11, pp. 143-150
Cannio, R., Fiorentino, G., Carpinelli, P., Rossi, M., Bartolucci, S., Cloning and overexpression in Escherichia coli of the genes encoding NAD-dependent alcohol dehydrogenase from two Sulfolobus species (1996) J. Bacteriol., 178, pp. 301-305
Raia, C.A., Giordano, A., Rossi, M., Alcohol dehydrogenase from Sulfolobus solfataricus (2001) Methods Enzymol., 331, pp. 176-195
Banfield, M.J., Salvucci, M.E., Baker, E.N., Smith, C.A., Crystal structure of the NADP(H)-dependent ketose reductase from Bemisia argentifolii at 2.3 Å resolution (2001) J. Mol. Biol., 306, pp. 239-250
Colonna-Cesari, F., Perahia, D., Karplus, M., Eklund, H., Brändén, C.-I., Tapia, O., Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode (1986) J. Biol. Chem., 261, pp. 15273-15280
Ramaswamy, S., Dynamics in alcohol dehydrogenase elucidated from crystallographic investigations (1999) Advan. Exp. Med. Biol., 463, pp. 275-284
Kleifeld, O., Frenkel, A., Bogin, O., Eisenstein, M., Brumfeld, V., Burstein, Y., Sagi, I., Spectroscopic studies of inhibited alcohol dehydrogenase from Thermoanaerobacter brockii: Proposed structure for the catalytic intermediate state (2000) Biochemistry, 39, pp. 7702-7711
Vetriani, C., Maeder, D.L., Tolliday, N., Yip, K.S.-P., Stillman, T.J., Britton, K.L., Protein thermostability above 100°C: A key role for ionic interactions (1998) Proc. Natl. Acad. Sci. USA, 95, pp. 12300-12305
Elcock, A.H., The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins (1998) J. Mol. Biol., 284, pp. 489-502
Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kuntsleve, R.W., Crystallography and NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallog. Sect. D, 54, pp. 905-921
Sun, H.W., Plapp, B.V., Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family (1992) J. Mol. Evol., 34, pp. 522-535
Ganzhorn, A.J., Plapp, B.V., Carboxyl groups near the active site zinc contribute to catalysis in yeast alcohol dehydrogenase (1988) J. Biol. Chem., 263, pp. 5446-5454
Al-Karadaghi, S., Cedergren-Zeppezauer, E.S., Hoevmoller, S., Petratos, K., Terry, H., Wilson, K.S., Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 Å resolution (1994) Acta Crystallog. Sect. D, 50, pp. 793-807
Ryde, U., On the role of Glu-68 in alcohol dehydrogenase (1995) Protein Sci., 4, pp. 1124-1132
Kannan, N., Vishveshwara, S., Aromatic clusters: A determinant of thermal stability of thermophilic proteins (2000) Protein Eng., 13, pp. 753-761
Stone, C.L., Li, T.K., Bosron, W.F., Stereospecific oxidation of secondary alcohols by human alcohol dehydrogenases (1989) J. Biol. Chem., 264, pp. 11112-11116
LeBrun, L.A., Plapp, B.V., Control of coenzyme binding to horse liver alcohol dehydrogenase (1999) Biochemistry, 38, pp. 12387-12393
Magonet, E., Hayen, P., Delforge, D., Delaive, E., Remacle, J., Importance of the structural zinc atom for the stability of yeast alcohol dehydrogenase (1992) Biochem. J., 287, pp. 361-365
Vallee, B.L., Auld, D.S., Zinc coordination, function, structure of zinc enzymes and other proteins (1990) Biochemistry, 29, pp. 5648-5659
John, J., Crennell, S.J., Hough, D.W., Danson, M.J., Taylor, G.L., The crystal structure of glucose dehydrogenase from Thermoplasma acidophilum (1994) Structure, 2, pp. 385-393
Ammendola, S., Raucci, G., Incani, O., Mele, A., Tramontano, A., Wallace, A., Replacing the glutamate ligand in the structural zinc site of Sulfolobus solfataricus alcohol dehydrogenase with a cysteine decreases thermostability (1995) Protein Eng., 8, pp. 31-37
Jeloková, J., Karlsson, C., Estonius, M., Jörnvall, H., Höög, J.-O., Features of structural zinc in mammalian alcohol dehydrogenase. Site-directed mutagenesis of the zinc ligands (1994) Eur. J. Biochem., 225, pp. 1015-1019
Giordano, A., Cannio, R., La Cara, F., Bartolucci, S., Rossi, M., Raia, C.A., Asn249Tyr substitution at the coenzyme binding domain activates Sulfolobus solfataricus alcohol dehydrogenase and increases its thermal stability (1999) Biochemistry, 38, pp. 3043-3054
Pearl, L.H., Demasi, D., Hemmings, A.M., Sica, F., Mazzarella, L., Raia, C.A., Crystallization and preliminary X-ray analysis of an NAD+-dependent alcohol dehydrogenase from the extreme thermophilic archaebacterium Sulfolobus solfataricus (1993) J. Mol. Biol., 229, pp. 782-784
Otwinowski, Z., Minor, W., Processing of X-ray diffraction data collected in oscillation mode (1997) Methods Enzymol., 276, pp. 307-326
Terwilliger, T.C., Berendzen, J., Automated MAD and MIR structure solution (1999) Acta Crystallog. Sect. D, 55, pp. 849-861
Cowtan, K.D., Zhang, K.Y., Density modification for macromolecular phase improvement (1999) Prog. Biophys. Mol. Biol., 72, pp. 245-270
Perrakis, A., Sixma, T.K., Wilson, K.S., Lamzin, V.S., wARP: Improvement and extension of crystallographic phase by weighted averaging of multiple-refined dummy atomic models (1997) Acta Crystallog. Sect. D, 53, pp. 448-455
Jones, T.A., Zou, J.Y., Cowan, S.W., Kjeldgaard, M., Improved methods for building protein models in electron density maps and the location of errors in these models (1991) Acta Crystallog. Sect. A, 47, pp. 110-119
Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 283-291
Kraulis, P.J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures (1991) J. Appl. Crystallog., 24, pp. 945-949
Holm, L., Sander, C., Alignment of three-dimensional protein structures: Network server for database searching (1996) Methods Enzymol., 266, pp. 653-662
Esnouf, R.M., An extensively modified version of MolScript that includes greatly enhanced coloring capabilities (1997) J. Mol. Graph. Model., 15, pp. 132-134
J rnvall, H., H g, J. -O., Nomenclature of alcohol dehydrogenases (1995) Alcohol Alcohol., 30, pp. 153-161
Eklund, H., Br nd n, C. -I., Alcohol dehydrogenase (1987) Biological Macromolecules and Assemblies, 3, pp. 73-142. , Wiley-Interscience, New York
Niederhut, M. S., Gibbons, B. J., Perez-Miller, S., Hurley, T. D., Three-dimensional structures of the three human class I alcohol dehydrogenases (2001) Protein Sci., 10, pp. 697-706
Yang, Z. N., Bosron, W. F., Hurley, T. D., Structure of human alcohol dehydrogenase: A glutathione-dependent formaldehyde dehydrogenase (1997) J. Mol. Biol., 265, pp. 330-343
Svensson, S., H g, J. -O., Schneider, G., Sandalova, T., Crystal structures of mouse class II alcohol dehydrogenase reveal determinants of substrate specificity and catalytic efficiency (2000) J. Mol. Biol., 302, pp. 441-453
Brown, J. R., Doolittle, W. F., Archaea and the prokaryote-to-eukaryote transition (1997) Microbiol. Mol. Biol. Rev., 61, pp. 456-502
Adams, M. W. W., Enzymes and proteins from organisms that grow near and above 100 C (1993) Annu. Rev. Microbiol., 47, pp. 627-658
Raia, C. A., D'Auria, S., Rossi, M., NAD+ dependent alcohol dehydrogenase from Sulfolobus solfataricus: Structural and functional features (1994) Biocatalysis, 11, pp. 143-150
Raia, C. A., Giordano, A., Rossi, M., Alcohol dehydrogenase from Sulfolobus solfataricus (2001) Methods Enzymol., 331, pp. 176-195
Banfield, M. J., Salvucci, M. E., Baker, E. N., Smith, C. A., Crystal structure of the NADP (H) -dependent ketose reductase from Bemisia argentifolii at 2. 3 resolution (2001) J. Mol. Biol., 306, pp. 239-250
Elcock, A. H., The stability of salt bridges at high temperatures: Implications for hyperthermophilic proteins (1998) J. Mol. Biol., 284, pp. 489-502
Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kuntsleve, R. W., Crystallography and NMR system: A new software suite for macromolecular structure determination (1998) Acta Crystallog. Sect. D, 54, pp. 905-921
Sun, H. W., Plapp, B. V., Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family (1992) J. Mol. Evol., 34, pp. 522-535
Ganzhorn, A. J., Plapp, B. V., Carboxyl groups near the active site zinc contribute to catalysis in yeast alcohol dehydrogenase (1988) J. Biol. Chem., 263, pp. 5446-5454
Stone, C. L., Li, T. K., Bosron, W. F., Stereospecific oxidation of secondary alcohols by human alcohol dehydrogenases (1989) J. Biol. Chem., 264, pp. 11112-11116
LeBrun, L. A., Plapp, B. V., Control of coenzyme binding to horse liver alcohol dehydrogenase (1999) Biochemistry, 38, pp. 12387-12393
Vallee, B. L., Auld, D. S., Zinc coordination, function, structure of zinc enzymes and other proteins (1990) Biochemistry, 29, pp. 5648-5659
Jelokov, J., Karlsson, C., Estonius, M., J rnvall, H., H g, J. -O., Features of structural zinc in mammalian alcohol dehydrogenase. Site-directed mutagenesis of the zinc ligands (1994) Eur. J. Biochem., 225, pp. 1015-1019
Pearl, L. H., Demasi, D., Hemmings, A. M., Sica, F., Mazzarella, L., Raia, C. A., Crystallization and preliminary X-ray analysis of an NAD+-dependent alcohol dehydrogenase from the extreme thermophilic archaebacterium Sulfolobus solfataricus (1993) J. Mol. Biol., 229, pp. 782-784
Terwilliger, T. C., Berendzen, J., Automated MAD and MIR structure solution (1999) Acta Crystallog. Sect. D, 55, pp. 849-861
Cowtan, K. D., Zhang, K. Y., Density modification for macromolecular phase improvement (1999) Prog. Biophys. Mol. Biol., 72, pp. 245-270
Jones, T. A., Zou, J. Y., Cowan, S. W., Kjeldgaard, M., Improved methods for building protein models in electron density maps and the location of errors in these models (1991) Acta Crystallog. Sect. A, 47, pp. 110-119
Laskowski, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M., PROCHECK: A program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallog., 26, pp. 283-291
Kraulis, P. J., MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures (1991) J. Appl. Crystallog., 24, pp. 945-949
Merritt, E. A., Bacon, D. J., Raster3D: Photo-realistic molecular graphics (1997) Methods Enzymol., 277, pp. 505-524
Esnouf, R. M., An extensively modified version of MolScript that includes greatly enhanced coloring capabilities (1997) J. Mol. Graph. Model., 15, pp. 132-134
Crystal Structure Of The Alcohol Dehydrogenase From The Hyperthermophilic Archaeon Sulfolobus Solfataricus At 1. 85 Angstrom Resolution
The crystal structure of a medium-chain NAD (H) -dependent alcohol dehydrogenase (ADH) from an archaeon has been solved by multiwavelength anomalous diffraction, using a selenomethionine-substituted enzyme. The protein (SsADH), extracted from the hyperthermophilic organism Sulfolobus solfataricus, is a homo-tetramer with a crystallographic 222 symmetry. Despite the low level of sequence identity, the overall fold of the monomer is similar to that of the other homologous ADHs of known structure. However, a significant difference is the orientation of the catalytic domain relative to the coenzyme-binding domain that results in a larger interdomain cleft. At the bottom of this cleft, the catalytic zinc ion is coordinated tetrahedrally and lacks the zinc-bound water molecule that is usually found in ADH apoform structures. The fourth coordination position is indeed occupied by a Glu residue, as found in bacterial tetrameric ADHs. Other differences are found in the architecture of the substrate pocket whose entrance is more restricted than in other ADHs. SsADH is the first tetrameric DAH X-ray structure containing a second zinc ion playing a structural role. This latter metal ion shows a peculiar coordination, with a glutamic acid residue replacing one of the four cysteine ligands that are highly conserved throughout the structural zinc-containing dimeric ADHs. (C) 2002 Elsevier Science Ltd. All rights reserved
Crystal Structure Of The Alcohol Dehydrogenase From The Hyperthermophilic Archaeon Sulfolobus Solfataricus At 1. 85 Angstrom Resolution