Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties.

The purification and characterization of triose-phosphate isomerase from the psychrophilic bacterium Vibrio marinus (vTIM) is described. Crystal structures of the vTIM-sulfate complex and the vTIM-2-phosphoglycolate complex (at a 2.7-A resolution) are also presented. The optimal growth temperature of Vibrio marinus is 15 degrees C. Stability studies show that vTIM is an unstable protein with a half-life of only 10 min at 25 degrees C. The vTIM sequence is most closely related to the sequence of Escherichia coli TIM (eTIM) (66% identity), and several unique structural features described for eTIM are also seen in vTIM, but eTIM is considerably more stable. The Td values of vTIM and eTIM, determined by calorimetric studies, are 41 and 54 degrees C, respectively. Amino acid sequence comparison reveals that vTIM has an alanine in loop 8 (at position 238), whereas all other TIM sequences known to date have a serine. The vTIM mutant A238S was produced and characterized. Compared with wild type, the catalytic efficiency of the A238S mutant is somewhat reduced, and its stability is considerably increased.

[1]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[2]  R. Abagyan,et al.  Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop. , 1997, Protein engineering.

[3]  G Vriend,et al.  Refined 1.83 A structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex. , 1991, Journal of molecular biology.

[4]  B. Matthews,et al.  Studies on protein stability with T4 lysozyme. , 1995, Advances in protein chemistry.

[5]  N. Thanki,et al.  Active site properties of monomeric triosephosphate isomerase (monoTIM) as deduced from mutational and structural studies , 1996, Protein science : a publication of the Protein Society.

[6]  F. Studier,et al.  Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. , 1986, Journal of molecular biology.

[7]  M. Noble,et al.  Structures of the “open” and “closed” state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: Implications for the reaction mechanism , 1993, Proteins.

[8]  Michael L. Connolly,et al.  Computation of molecular volume , 1985 .

[9]  M. Noble,et al.  The crystal structure of the “open” and the “closed” conformation of the flexible loop of trypanosomal triosephosphate isomerase , 1991, Proteins.

[10]  J. Martial,et al.  Crystal structure of recombinant triosephosphate isomerase from bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three‐dimensional structures points to the importance of hydrophobic interactions , 1995, Protein science : a publication of the Protein Society.

[11]  J. Knowles,et al.  Enzyme catalysis: not different, just better , 1991, Nature.

[12]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[13]  R Abagyan,et al.  The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop. , 1993, Structure.

[14]  P. Terpstra,et al.  Cloning and overexpression of the triosephosphate isomerase genes from psychrophilic and thermophilic bacteria. Structural comparison of the predicted protein sequences. , 1993, Journal of molecular biology.

[15]  J. Martial,et al.  Synthesis, purification and initial structural characterization of octarellin, a de novo polypeptide modelled on the alpha/beta-barrel proteins. , 1990, Protein engineering.

[16]  H. Balaram,et al.  Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design. , 1997, Structure.

[17]  B. Matthews,et al.  Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. , 1993, Biochemistry.

[18]  L Serrano,et al.  Alpha-helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of alanine by glycine or serine at solvent-exposed surfaces. , 1992, Journal of molecular biology.

[19]  F. Opperdoes,et al.  Simultaneous purification of hexokinase, class-I fructose-bisphosphate aldolase, triosephosphate isomerase and phosphoglycerate kinase from Trypanosoma brucei. , 1984, European journal of biochemistry.

[20]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[21]  E. Neria,et al.  Molecular dynamics of an enzyme reaction: proton transfer in TIM , 1997 .

[22]  M. M. Bradford.  A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[23]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[24]  M Karplus,et al.  Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. , 1990, Science.

[25]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[26]  Axel T. Brunger,et al.  X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .

[27]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[28]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[29]  F. C. Hartman,et al.  Structure of yeast triosephosphate isomerase at 1.9-A resolution. , 1990, Biochemistry.

[30]  K. Kirschner,et al.  The importance of surface loops for stabilizing an eightfold βα barrel protein , 1992 .

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

[32]  J. Hiltunen,et al.  Crystallization experiments with 2-enoyl-CoA hydratase, using an automated 'fast-screening' crystallization protocol. , 1994, Acta crystallographica. Section D, Biological crystallography.

[33]  M. Noble,et al.  Structure of triosephosphate isomerase from Escherichia coli determined at 2.6 A resolution. , 1993, Acta crystallographica. Section D, Biological crystallography.

[34]  J. Martial,et al.  Crystal structure of recombinant human triosephosphate isomerase at 2.8 Å resolution. Triosephosphate isomerase‐related human genetic disorders and comparison with the trypanosomal enzyme , 1994, Protein science : a publication of the Protein Society.

[35]  G. Farber,et al.  The structure and evolution of a/β barrel proteins , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

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

[37]  Characteristics of a de novo designed protein , 1994, Protein science : a publication of the Protein Society.