Structure of yeast triosephosphate isomerase at 1.9-A resolution.

The structure of yeast triosephosphate isomerase (TIM) has been solved at 3.0-A resolution and refined at 1.9-A resolution to an R factor of 21.0%. The final model consists of all non-hydrogen atoms in the polypeptide chain and 119 water molecules, a number of which are found in the interior of the protein. The structure of the active site clearly indicates that the carboxylate of the catalytic base, Glu 165, is involved in a hydrogen-bonding interaction with the hydroxyl of Ser 96. In addition, the interactions of the other active site residues, Lys 12 and His 95, are also discussed. For the first time in any TIM structure, the "flexible loop" has well-defined density; the conformation of the loop in this structure is stabilized by a crystal contact. Analysis of the subunit interface of this dimeric enzyme hints at the source of the specificity of one subunit for another and allows us to estimate an association constant of 10(14)-10(16) M-1 for the two monomers. The analysis also suggests that the interface may be a particularly good target for drug design. The conserved positions (20%) among sequences from 13 sources ranging on the evolutionary scale from Escherichia coli to humans reveal the intense pressure to maintain the active site structure.

[1]  M. Sternberg,et al.  An analysis of the three-dimensional structure of chicken triose phosphate isomerase. , 1977, Biochemical Society transactions.

[2]  M. Vijayan,et al.  The determination and refinement of heavy‐atom parameters in protein heavy‐atom derivatives. Some model calculations using acentric reflexions , 1971 .

[3]  G. Petsko,et al.  Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5Å resolution: using amino acid sequence data , 1975, Nature.

[4]  L. Maquat,et al.  Human triosephosphate isomerase cDNA and protein structure. Studies of triosephosphate isomerase deficiency in man. , 1985, The Journal of biological chemistry.

[5]  P J Artymiuk,et al.  Human triose-phosphate isomerase deficiency: a single amino acid substitution results in a thermolabile enzyme. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[6]  R.D.B. Fraser,et al.  An improved method for calculating the contribution of solvent to the X‐ray diffraction pattern of biological molecules , 1978 .

[7]  Robert M. Stroud,et al.  The accuracy of refined protein structures: comparison of two independently refined models of bovine trypsin , 1978 .

[8]  F. Crick,et al.  The treatment of errors in the isomorphous replacement method , 1959 .

[9]  J. Harris,et al.  Triose phosphate isomerase from the coelacanth. An approach to the rapid determination of an amino acid sequence with small amounts of material. , 1974, The Biochemical journal.

[10]  J. Knowles,et al.  Active site of triosephosphate isomerase: in vitro mutagenesis and characterization of an altered enzyme. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[11]  G. Petsko,et al.  Crystallography and site-directed mutagenesis of yeast triosephosphate isomerase: what can we learn about catalysis from a "simple" enzyme? , 1987, Cold Spring Harbor symposia on quantitative biology.

[12]  M. Hatada,et al.  Structure of 2-keto-3-deoxy-6-phosphogluconate aldolase at 2 . 8 A resolution. , 1978, Journal of molecular biology.

[13]  D I Stuart,et al.  Crystal structure of cat muscle pyruvate kinase at a resolution of 2.6 A. , 1979, Journal of molecular biology.

[14]  W. Lim,et al.  Triosephosphate isomerase catalysis is diffusion controlled , 1988 .

[15]  G. Petsko,et al.  The 3.0 A crystal structure of xylose isomerase from Streptomyces olivochromogenes. , 1987, Protein engineering.

[16]  M. Allaire,et al.  Molecular architecture of rabbit skeletal muscle aldolase at 2.7-A resolution. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[17]  S. Old,et al.  Nucleotide sequence of the triosephosphate isomerase gene from Macaca mulatta. , 1988, Nucleic acids research.

[18]  T. A. Jones,et al.  Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.

[19]  D W Banner,et al.  On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase. , 1981, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[20]  G A Petsko,et al.  Subunit interface of triosephosphate isomerase: site-directed mutagenesis and characterization of the altered enzyme. , 1987, Biochemistry.

[21]  G. Schneider,et al.  Three‐dimensional structure of ribulose‐1,5‐bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum at 2.9 Å resolution , 1986, The EMBO journal.

[22]  E. W. Czerwinski,et al.  Local scaling: a method to reduce systematic errors in isomorphous replacement and anomalous scattering measurements , 1975 .

[23]  Y. Matsuura,et al.  Structure and possible catalytic residues of Taka-amylase A. , 1982, Journal of biochemistry.

[24]  F. C. Hartman,et al.  Crystallization of yeast triose phosphate isomerase from polyethylene glycol. Protein crystal formation following phase separation. , 1981, The Journal of biological chemistry.

[25]  G. Petsko,et al.  Control of oligomeric enzyme thermostability by protein engineering. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[26]  B. Matthews.  The extension of the isomorphous replacement method to include anomalous scattering measurements , 1966 .

[27]  Alan R. Fersht,et al.  Stabilization of protein structure by interaction of α-helix dipole with a charged side chain , 1988, Nature.

[28]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[29]  P. Borst,et al.  Characterization of the gene for the microbody (glycosomal) triosephosphate isomerase of Trypanosoma brucei. , 1986, The EMBO journal.

[30]  J. Knowles,et al.  Triosephosphate isomerase: energetics of the reaction catalyzed by the yeast enzyme expressed in Escherichia coli. , 1988, Biochemistry.

[31]  J. Knowles,et al.  Perfection in enzyme catalysis: the energetics of triosephosphate isomerase , 1977 .

[32]  F. Payan,et al.  Three dimensional structure of porcine pancreatic alpha‐amylase at 2.9 A resolution. Role of calcium in structure and activity. , 1987, The EMBO journal.

[33]  V. Luzzati,et al.  Traitement statistique des erreurs dans la determination des structures cristallines , 1952 .

[34]  S. G. Waley,et al.  The active centre of rabbit muscle triose phosphate isomerase. The site that is labelled by glycidol phosphate. , 1971, The Biochemical journal.

[35]  W. J. Albery,et al.  Efficiency and evolution of enzyme catalysis. , 1977, Angewandte Chemie.

[36]  D. J. Steenkamp,et al.  Three-dimensional structure of the iron-sulfur flavoprotein trimethylamine dehydrogenase at 2.4-A resolution. , 1986, The Journal of biological chemistry.

[37]  Y. Lindqvist,et al.  Structure of glycolate oxidase from spinach. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[38]  F. S. Mathews,et al.  Three-dimensional structure of flavocytochrome b2 from baker's yeast at 3.0-A resolution. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[39]  S J Wodak,et al.  Structural principles of parallel beta-barrels in proteins. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[40]  R. Offord,et al.  Active-site labelling of triose phosphate isomerase. The reaction of bromohydroxyacetone phosphate with a unique glutamic acid residue and the migration of the label to tyrosine. , 1972, The Biochemical journal.

[41]  J. Knowles,et al.  Critical ionization states in the reaction catalyzed by triosephosphate isomerase. , 1978, Biochemistry.

[42]  Boguslaw Stec,et al.  Crystal structure of enolase indicates that enolase and pyruvate kinase evolved from a common ancestor , 1988, Nature.

[43]  K. H. Kalk,et al.  Structure determination of the glycosomal triosephosphate isomerase from Trypanosoma brucei brucei at 2.4 A resolution. , 1987, Journal of molecular biology.

[44]  P. Russell,et al.  Transcription of the triose-phosphate-isomerase gene of Schizosaccharomyces pombe initiates from a start point different from that in Saccharomyces cerevisiae. , 1985, Gene.

[45]  J. Harris,et al.  Primary structure of triosephosphate isomerase from Bacillus stearothermophilus. , 1980, European journal of biochemistry.

[46]  P. Corran,et al.  The amino acid sequence of rabbit muscle triose phosphate isomerase. , 1975, The Biochemical journal.

[47]  R. W. Gracy,et al.  Primary structure of human triosephosphate isomerase. , 1984, The Journal of biological chemistry.

[48]  H L Carrell,et al.  Comparison of backbone structures of glucose isomerase from Streptomyces and Arthrobacter. , 1988, Protein engineering.

[49]  T. Jardetzky,et al.  Three-dimensional structure of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[50]  J. Richard.  Acid-base catalysis of the elimination and isomerization reactions of triose phosphates , 1984 .

[51]  H. Berendsen,et al.  The α-helix dipole and the properties of proteins , 1978, Nature.

[52]  Walter Gilbert,et al.  The triosephosphate isomerase gene from maize introns antedate the plant-animal divergence , 1986, Cell.

[53]  M. Parker,et al.  Nucleotide sequence of the triosephosphate isomerase gene from Aspergillus nidulans: Implications for a differential loss of introns , 1986, Cell.

[54]  R. Wolfenden,et al.  Transition State Analogues for Enzyme Catalysis , 1969, Nature.

[55]  P. Y. Chou,et al.  β-turns in proteins☆ , 1977 .

[56]  M. Karplus,et al.  Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.

[57]  W. Gilbert,et al.  Chicken triosephosphate isomerase complements an Escherichia coli deficiency. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[58]  F. C. Hartman.  Haloacetol phosphates. Characterization of the active site of rabbit muscle triose phosphate isomerase. , 1971, Biochemistry.

[59]  B. W. Mathews,et al.  The determination of the position of anomalously scattering heavy atom groups in protein crystals , 1966 .

[60]  G. Petsko,et al.  Triosephosphate isomerase: removal of a putatively electrophilic histidine residue results in a subtle change in catalytic mechanism. , 1988, Biochemistry.

[61]  W. Lim,et al.  Triosephosphate isomerase catalysis is diffusion controlled. Appendix: Analysis of triose phosphate equilibria in aqueous solution by 31P NMR. , 1988, Biochemistry.

[62]  F. S. Mathews,et al.  A semi-empirical method of absorption correction , 1968 .

[63]  J. Knowles,et al.  Free-energy profile of the reaction catalyzed by triosephosphate isomerase. , 1976, Biochemistry.

[64]  Leonard J. Banaszak,et al.  Polypeptide conformation of cytoplasmic malate dehydrogenase from an electron density map at 3.0 Å resolution , 1972 .

[65]  M S Chapman,et al.  Tertiary structure of plant RuBisCO: domains and their contacts. , 1988, Science.