TIM barrel enzyme

Wise EL, Rayment I. 2004. Understanding the importance of protein structure to nature s routes for divergent evolution in TIM barrel enzymes. Acc Chem Res 37 149-158. 

It is well established that the same three-dimensional scaffolding in proteins often carries constellations of amino acids with diverse enzymatic functions. A classic example is the large family of a/jS, or TIM, barrel enzymes (Farber and Petsko, 1990 Lesk et ai, 1989). It appears that lipases are no exception to date five other hydrolases with similar overall tertiary folds have been identified. They are AChE from Torpedo calif arnica (Sussman et al., 1991) dienelactone hydrolase, a thiol hydrolase, from Pseudomonas sp. B13 (Pathak and Ollis, 1990 Pathak et al, 1991) haloalkane dehalogenase, with a hitherto unknown catalytic mechanism, from Xanthobacter autotrophicus (Franken et al, 1991) wheat serine carboxypeptidase II (Liao et al, 1992) and a cutinase from Fusa-rium solani (Martinez et al, 1992). Table I gives some selected physical and crystallographic data for these proteins. They all share a similar overall topology, described by Ollis et al (1992) as the a/jS hydrolase... 

Protein Structure to Nature s Routes for Divergent Evolution in Tim Barrel Enzymes. 

The crystal structure of a pentamer of GlcNAc residues, representing the chitin polymer (poly-/l-(l-4)-GlcNAc), boimd to the chitinase enzyme ChiB from Serratia marcescens, revealed a narrow, timnel-like active site in the center of the TIM barrel fold [167]. Several conserved residues near the center of the site, which are important in catalysis, interact with the substrate via hydrogen bonds, while interactions farther from the center depend on van der Waals interactions. The sugar in the - 1 subsite adopts a boat conformation, presumably due to interactions with these critical active-site residues. 

Figure 13-6 Stereoscopic view into the active site of triose phosphate isomerase showing side chains of some charged residues PGH, a molecule of bound phosphoglycolohydroxamate, an analog of the substrate enolate.138 The peptide backbone, as an alpha-carbon plot, is shown in light lines.147 The (a/ (S)8-barrel structure is often called a TIM barrel because of its discovery in this enzyme. Courtesy of M. Karplus.

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... 

As already discussed in Chapter 11, there are more than 10 000 protein structures known but only about 30 3D structure types. This might be traced to a limited number of possible stable polypeptide structures but most probably reflects the evolutionary history of the diversity of proteins. There are structural motifs which repeat themselves in a multitude of enzymes which are otherwise neither structurally nor functionally related, such as TIM barrel proteins, four-helix bundle proteins, Rossmann folds, or a/j3-folds of hydrolases (Figure 16.1). 

The study of //J-barrel proteins, also called TIM barrels after the first enzyme investigated in this class, triose phosphate isomerase, or (/3a)8-barrel enzymes after the... 

Like transketolase, transaldolase (TA, E.C. 2.2.1.2) is an enzyme in the oxidative pentose phosphate pathway. TA is a class one lyase that operates through a Schiff-base intermediate and catalyzes the transfer of the C(l)-C(3) aldol unit from D-sedoheptulose 7-phosphate to glyceraldehyde-3-phosphate (G3P) to produce D-Fru 6-P and D-erythrose 4-phosphate (Scheme 5.59). TA from human as well as microbial sources have been cloned.110 111 The crystal structure of the E. coliu and human112 transaldolases have been reported and its similarity to the aldolases is apparent, since it consists of an eight-stranded (o /(3)s or TIM barrel domain as is common to the aldolases. As well, the active site lysine residue that forms a Schiff base with the substrate was identified.14112 Thus, both structurally and mechanistically it is related to the type I class of aldolases. 

The existence of -barrels was established for chymotrypsin at a very early stage in the now common protein crystal structure analyses. This enzyme contains two distorted six-stranded -barrels with identical topologies (Birktoft and Blow, 1972). A selection of -barrels in water-soluble proteins is given in Table I. The very abundant TIM-barrel consisting of eight parallel /1-strands was also detected rather early (Banner et al., 1975). Additional eight-stranded /1-barrels of this group are those of streptavidin (Hendrickson et al., 1989) and of the lipocalins (Newcomer et al., 1984). 

Crystal structures exist of two bacterial PI-PLC enzymes, the protein from B. cereus (Heinz et al., 1995), which can cleave GPI-anchors, and the PI-PLC from Listeria monocytogenes (Moser et al., 1997), which is not able to effectively release GPI-anchored proteins. While the sequence homology of these two proteins is limited, the structures are very similar. The bacterial PI-PLC proteins are folded into a distorted TIM-barrel, where the parallel (3-strands form an inner circular and closed barrel with a-helices located on the outside between neighboring (3-strands, that is structurally very similar to the catalytic domain of PLC8j, the only mammalian PI-PLC for which there is a structure (Essen et al., 1996 Heinz et al., 1998). The availability of structures and results of mutagenesis provide details on the catalytic mechanism for this type of enzyme (for review and more extensive references see Mihai et al. (2003)). 

Both methylmalonyl-CoA mutase and glutamate mutase share strikingly similar global folds (Figure 8), even though sequence similarity is limited to the small a/ 3 domain and their quaternary structures are quite different. The icatalytici domains of both enzymes take the form of a ( a/p)s TIM-barrel the Ca atoms of the two structures can be superimposed with an r.m.s. deviation of only 2 (Reitzer et al., 1999). However, the active site residues of these enzymes (other than those involved in binding the lower face of the coenzyme) do not seem to be conserved and the substrates are bound very differently. 

A systematic assessment of the relationship between protein function and structure has been performed by Hegyi and Gerstein [259] via relating yeast enzymes classified by the Enzyme Commission (EC numbers) to structural SCOP domains. In this study it has been found that different structural folds have different propensities for various functions. Most versatile functions (hydrolases and O-glycosyl glucosidases) have been identified to be mounted onto seven different folds, whereas the most versatile folds (e.g. TIM-barrel and Rossmann folds) realize up to 16 different functions. 

Table 1 summarizes the general characteristics of representative urease, hydrogenase and CODHs. As it will be further discussed below, the X-ray structures of only two Ni-containing proteins, urease and hydrogenase, are known [16, 17]. The former has the well known triose phosphate isomerase (TIM) barrel topology (Fig. 1) whereas the latter displays a so far unique folding (Fig. 2). The next challenge will be the elucidation of the crystal structures of the CODH/ACS enzyme of Clostridium thermoaceticum and of the simpler CODH from Rhodospirillum rubrum. 

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