TIM barrel fold

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. 

In principle, nature has decoupled protein function and protein fold. The most commonly known example for a fold conveying a broad variety of functions is the TIM barrel. First found in triosephosphate isomerase, the TIM barrel also occurs in proteins as diverse as aldose reductase, enolase, and adenosine deaminase (see, e.g., the review by Nagano et al. [104]). To date, the TIM barrel fold, as a generic scaffold, is associated with 15 different types of enzymatic functions. 

R. K. Wlerenga, FEBS Lett., 492, 193 (2001). The Tim-Barrel Fold A Versatile Framework... 

Fig. 6. Distribution of the most common folds in selected bacterial, archaeal, and eukaryotic proteomes. The vertical axis shows the fraction of all predicted folds in the respective proteome. Fold name abbreviations FAD/NAD, FAD/NAD(P)-binding Rossman-like domains TIM, TIM-barrel domains SAM-MTR, S-adenosylmethionine-dependent methyltransferases PK, serine-threonine protein kinases PP-Loop, ATP pyrophosphatases. mge, Mycoplasma genitalium rpr, Rickettsiaprowazekii hh x, Borrelia burgdorferi ctr, Chlamydia trachomatis hpy, Helicobacter pylori tma, Thermotoga maritima ssp, Synechocystis sp. mtu, Mycobacterium tuberculosis eco, Escherichia coli mja, Methanococcus jannaschii pho, Pyrococcus horikoshii see, Saccharomyces cerevisiae, cel, Caenorhabditis elegans.

In each of the three divisions of life, the most common fold is the P-loop NTPase. Four common folds, namely P-loop NTPases, Triose Phosphate Isomerase (TIM) barrels, ferredoxin-like domains, and Rossmann-fold domains, are see in the top-10 lists for all three divisions (Table IV). 

Branden CL The TIM barrel—the most frequently occurring folding motif in proteins. Curr Opin Struct Biol 1991 1 978-983. 

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). 

J. M. Thornton, One fold with many functions The evolutionary relationships between TIM barrel families based on their sequences, structures and functions,... 

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. 

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... 

Figure 13.1. Structural classes of protein folds, showing how the folds can be classified into different structural classes. Top row the three basic fold classes a, containing only a helices a and p, containing a helices and p sheets and p, containing only p sheets. Middle row three different architectural subclasses of the a and p class triosephosphate isomerase (TIM) barrel, three-layer sandwich, and roll. Bottom row two different arrangements of the "three-layer sandwich . The spiral conformations are the a helices, and the broad arrows are the p sheets. (From Orengo, C. A., Michie, A. D., Jones, S. et al. [1997]. CATH - a hierarchic classification of protein domain structures [Figure 2]. Structure, 5, 1093-108. Copyright 1997, Elsevier Science. Reprinted with permission.)...

In some cases, families are further grouped into clans. The largest such clan is the glycosyl hydrolase Clan A (clan GH-A), all of which have a protein fold of eight alternating a-helices and p-sheets, giving the (p/a)g sructure, sometimes called a TIM barrel because it was first encountered with triose phosphate isomerase. 

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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