Triosephosphate isomerase structure

Noble M E M, R K Wierenga, A-M Lambeir, F R Opperdoes, W H Thunnissen, K H Kalk, H Groendijk and W G J Hoi 1991. The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes. Proteins Structure, Function and Genetics 10 50-69. 

Figure 2.10 Examples of schematic diagrams of the type pioneered by Jane Richardson. Diagram (a) illustrates the structure of myoglobin in the same orientation as the computer-drawn diagrams of Figures 2.9b-d. Diagram (b), which is adapted from J. Richardson, illustrates the structure of the enzyme triosephosphate isomerase, determined to 2.5 A resolution in the laboratory of David Phillips, Oxford University. Such diagrams can easily be obtained from databases of protein structures, such as PDB, SCOP or CATH, available on the World Wide Web.

This motif is called a beta-alpha-beta motif (Figure 2.17) and is found as part of almost every protein structure that has a parallel p sheet. For example, the molecule shown in Figure 2.10b, triosephosphate isomerase, is entirely built up by repeated combinations of this motif, where two successive motifs share one p strand. Alternatively, it can be regarded as being built up from four consecutive p-a-p-a motifs. 

Table 4.1 The amino acid residues of the eight parallel p strands in the barrel structure of the enzyme triosephosphate isomerase from chicken muscle...

Transition state theory, 46,208 Transmission factor, 42,44-46,45 Triosephosphate isomerase, 210 Trypsin, 170. See also Trypsin enzyme family active site of, 181 activity of, steric effects on, 210 potential surfaces for, 180 Ser 195-His 57 proton transfer in, 146, 147 specificity of, 171 transition state of, 226 Trypsin enzyme family, catalysis of amide hydrolysis, 170-171. See also Chymotrypsin Elastase Thrombin Trypsin Plasmin Tryptophan, structure of, 110... 

M10. Maquat, L. E Chilcote, R., and Ryan, P. M., Human triosephosphate isomerase cDNA and protein structure Studies of triosephosphate isomerase in man. J. Biol. Chem. 260, 3748-3753 (1985). 

Fig. 15. Thermal denaturation of triosephosphate isomerase with FTIR (upper left), second-derivative FTIR (upper right), and VCD (bottom) showing irreversible aggregation effects. The IR shift from a simple maximum at 1650-1640 cm-1 to a lower frequency distorted to low wavenumber is seen to be irreversible when the original spectrum is not recovered. The second-derivative result makes the changes more dramatic and shows the original native state spectrum to be more complex (negative second derivatives correspond to peak positions). Loss of structure is even more evident in the VCD, which loses most of its intensity at 60°C.

Parallel /3 structure usually forms large, moderately twisted sheets such as in Fig. 23, although occasionally it rolls up into a cylinder with helices around the outside (e.g., triosephosphate isomerase). Large antiparallel sheets, on the other hand, usually roll up either partially (as in the first domain of thermolysin or in ribonuclease) or completely around to join edges into a cylinder or barrel. Occurrence, topology, and classification of /3 barrels will be discussed in Section III,D, but here we will consider the interaction between the /3 sheets on opposite sides of the barrel, especially in terms of the angle at which opposite strands cross. 

Fig. 71. Examples of protein domains with different numbers of layers of backbone structure (a) two-layer cytochrome c (b) three-layer phosphoglycerate kinase domain 2 (c) four-layer triosephosphate isomerase. The arrows above each drawing point to the backbone layers.

The ultimate objective of an X-ray cryoenzymological study is the mapping of the structures of all kinetically significant species along the reaction pathway. In the case of ribonuclease A this has been largely achieved, as described above. Other enzymatic reactions now await application of the same techniques. Unfortunately, not all crystalline enzymes lend themselves to study by this method. In some cases it may be impossible to find a suitable cryoprotective mother liquor in others, the reaction may occur too rapidly at ordinary temperature. A reaction with Acat of 10 seconds and an activation enthalpy of —6 kcal mol will not be quenched even at — 75°C. The approach we have described in this article can be applied to only a small number of enzymes. Two likely candidates for successors to ribonuclease are the enzymes yeast triosephosphate isomerase and porcine pancreatic elastase. 

Noble MEM, Verlinde CLMJ, Groendijk H, Kalk KH, Wierenga RK, Hoi WGJ. Crystallographic and molecular modeling studies on trypanosomal triosephosphate isomerase a critical assessment of the predicted and observed structures of the complex with 2-phospho-glycerate. J Med Chem 1991 34 2709-2718. 

The enzyme triosephosphate isomerase, abbreviated to TIM, was found to have an important type of structure, now called an a//3 or TIM barrel, consisting of at least 200 residues. In its idealized form, the barrel consists of eight parallel /3 strands connected by eight helixes (Figure 1.19). The strands form the staves of the barrel while the helixes are on the outside and are also parallel (Figure 1.20). (3 strands 1 and 8 are adjacent and form hydrogen bonds with each other. The center of the barrel is a hydrophobic core composed of the side chains of alternate residues of the strands, primarily those of the branched... 

The first attempts to determine the structure of a productively bound enzyme-substrate complex were based on extrapolation from the structures of stable enzyme-inhibitor complexes. (The classic example of this, lysozyme, is discussed in section F3.) Such extrapolation may be done in several ways. For example, a portion of the substrate may be bound to the enzyme and the structure of the remainder determined by model building. An alternative method is to use a substrate analogue that is unreactive because its reactive bond is modified. Typical examples are the binding of phosphoglycolohydroxamate, a substrate analogue, to triosephosphate isomerase,44 or a piece of DNA, which lacks the reactive 2 -OH groups, to a ribonuclease.45... 

Lack of congruence of structure and mechanism Common structure does not imply a common mechanism The /1-barrel structures triosephosphate isomerase and xylose isomerase function by hydride transfer through enol, whereas aldose reductase performs hydride transfer through a metal ion. 

Structural studies of the oxy-Cope catalytic antibody system reinforce the idea that conformational dynamics of both protein and substrate are intimately intertwined with enzyme catalysis, and consideration of these dynamics is essential for complete understanding of biologically catalyzed reactions. Indeed, recent single molecule kinetic studies of enzyme-catalyzed reactions also suggest that different conformations of proteins are associated with different catalytic rates (Xie and Lu, 1999). In addition, a number of enzymes are known to undergo conformational changes on binding of substrate (Koshland, 1987) that lead to enhanced catalysis two examples are hexokinase (Anderson and Steitz, 1975 Dela-Fuente and Sols, 1970) and triosephosphate isomerase (Knowles, 1991). 

Fig. 4-8 Stylized representations of protein structures in which a helices are represented as coiled ribbons and p strands are represented by arrows pointing in the N — C direction, p proteins contain predominantly /3-sheet structure (e.g., retinol binding protein and the antigen binding fragment of antibodies) while a proteins contain predominantly a helices (e.g., myoglobin), alp proteins contain a mixture of a helix and p sheet (e.g., triosephosphate isomerase).

Fig. 4-10 Topology diagram for (a) retinol binding protein (RBP) and (b) triosephosphate isomerase (TPI). The arrows represent p strands (numbered from N to C) and the dark boxes represent a helices. Note from Fig. 4-8 that both of these proteins form a barrel structure comprised of eight p strands with the first strand hydrogen bonded to last strand in order to "close the barrel. However, whereas the p strands are antiparallel in RBP, they are arranged in parallel in TPI and are surrounded by an outer layer of a helices which connect each p strand to the next in the barrel.

There are five classes of flavin-binding structural folds presented in Table 1 that are identified by the prototype protein in which they were first discovered. These are flavodoxin (FDX), ferredoxin reductase (FNR), triosephosphate isomerase (TIM), glutathione reductase (GR) and p-cresol methylhydroxylase (PCMH). The topologies of four of these five domains are shown in Figure 2. There are also four classes of primary acceptor/donor domain folds that are identified by the prototype protein where they were first discovered. They are cytochrome P450BMP (BMP), cytochrome b5 (CYTB5), cytochrome c (CYTC) and the 2Fe-2S plant-type ferredoxin (FDN). 

R.C. Davenport, P.A. Bash, B.A. Seaton, M. Karplus, G.A. Petsko, and D. Ringe. 1991. Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex An analogue of the intermediate on the reaction pathway Biochemistry 30 5821-5826. (PubMed)... 

D. Maes, J.P. Zeelen, N. Thanki, N. Beaucamp, M. Alvarez, M.H. Thi, J. Backmann, J.A. Martial, L. Wyns, R. Jaenicke, and R.K. Wierenga. 1999. The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima A comparative thermostability structural analysis of ten different TIM structures Proteins 37 441-453. (PubMed)... 

Compound V or glycidol phosphate was used by Rose and O Connell (1969) to study muscle triosephosphate isomerase because it closely resembles the presumed ene-diol intermediate in this enzyme s reaction mechanism. Coincidentally, it also proved to be an effective inhibitor of enolase even though it is not closely analogous to substrates of this enzyme. The structure of glycidol phosphate is similar to phosphononomycin (DC), an antibiotic isolated from fermentation broths of Streptomyces fradiae (Christensen et al. 1969). 

Mande SC, Mainfiroid V, Kalk KH, Goraj K, Martial JA, Hoi WG. Crystal structure of recombinant human triosephosphate isomerase at 2.8 A resolution. Triosephosphate isomerase-related human genetic disorders and comparison with the trypanosoma enzyme. Protein Sci 1994 3 810-21. 

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