Closed barrel structures

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

Each repeat forms a right-handed P-loop-a structure similar to those found in the two other classes of a/p structures described earlier. Sequential p-loop-a repeats are joined together in a similar way to those in the a/P-bar-rel stmctures. The P strands form a parallel p sheet, and all the a helices are on one side of the P sheet. However, the P strands do not form a closed barrel instead they form a curved open stmcture that resembles a horseshoe with a helices on the outside and a p sheet forming the inside wall of the horseshoe (Figure 4.11). One side of the P sheet faces the a helices and participates in a hydrophobic core between the a helices and the P sheet the other side of the P sheet is exposed to solvent, a characteristic other a/p structures do not have. 

In the next class of a/p structures there are a helices on both sides of the p sheet. This has at least three important consequences. First, a closed barrel cannot be formed unless the p strands completely enclose the a helices on one side of the p sheet. Such structures have never been found and are very unlikely to occur, since a large number of p strands would be required to enclose even a single a helix. Instead, the p strands are arranged into an open twisted p sheet such as that shown in Figure 4.1b. 

The simplest topology is obtained if each successive p strand is added adjacent to the previous strand until the last strand is joined by hydrogen bonds to the first strand and the barrel is closed (Figure 5.2). These are called up-and-down P sheets or barrels. The arrangement of p strands is similar to that in the a/P-barrel structures we have just described in Chapter 4, except that here the strands are antiparallel and all the connections are hairpins. The structural and functional versatility of even this simple arrangement will be illustrated by two examples. 

Individual mice express a combinatorial pattern of MUPs (typically at least 7-12 isoforms) reflecting multiple allelic variants and multiple expressed loci (Robertson et al. 1997). Among wild mice, individuals each express a different pattern even when captured from the same population (Payne, Malone, Humphries, Bradbrook, Veggerby, Beynon and Hurst 2001 Beynon et al. 2002), with the exception of very closely related animals that have inherited the same haplotypes from their parents (a 25% chance among outbred sibs, similar to MHC type sharing). The extreme heterogeneity in the sequence of MUPs is mostly confined to strands B, C and D and the intervening turns of the 8-barrel structure (Beynon et al. 2002). 

The commonest subgroup of antiparallel /3 barrel structures has a Greek key topology, with -3,+1,+1,-3 connections or a close variant. The first Greek key barrel structures were compared in Richardson et al. (1976), and they and the up-and-down barrels were described as categories in Richardson (1977). Figure 96 illustrates Cu,Zn superoxide dismutase as an example of a Greek key j8 barrel. 

The southern bean mosaic virus has an eight-stranded antiparallel (3-barrel structure closely similar to that of the major domain of the bushy stunt viruses but lacking the second hinged domain. The problem of quasi-equivalence is resolved by the presence of an N-terminal extension that binds onto a subunit across the quasi-six-fold axis to give a set of three subunits (labeled C in Fig. 7-19) that associate with true three-fold symmetry and another set (B) with a slightly different conformation fitting between them.68 92 The subunits A, which have a third conformation, fit together around the five-fold axis in true cyclic symmetry. 

In green plants, which contain little or no cholesterol, cydoartenol is the key intermediate in sterol biosynthesis.161-1623 As indicated in Fig. 22-6, step c, cydoartenol can be formed if the proton at C-9 is shifted (as a hydride ion) to displace the methyl group from C-8. A proton is lost from the adjacent methyl group to close the cyclopropane ring. There are still other ways in which squalene is cyclized,162/163/1633 including some that incorporate nitrogen atoms and form alkaloids.1631 One pathway leads to the hop-anoids. These triterpene derivatives function in bacterial membranes, probably much as cholesterol does in our membranes. The three-dimensional structure of a bacterial hopene synthase is known.164 1643 Like glucoamylase (Fig. 2-29) and farnesyl transferase, the enzyme has an (a,a)6-barrel structure in one domain and a somewhat similar barrel in a second domain. 

The comparison of protein folds has proved to be difficult the three-dimensional structures are frequently complicated, and quite significant differences can exist between structures that are, on the basis of sequence similarity, clearly related in evolutionary terms. On the other hand structures may sometimes resemble each other very closely, but fail to display any sequence similarity the classic example of this is the parallel beta barrel structure which has now been found in more than twenty proteins with no amino-acid sequence homology [35], In these cases the interpretation of the meaning of a similarity can be less than straightforward it may indicate that the proteins are evolutionary related ( divergent evolution ), that they are unrelated but have evolved similar structures because they carry out similar functions ( convergent evolution ) or the common structure may simply be a particularly stable one that is adopted by a large number of proteins. In addition to three similarities between complete protein folds, there may also be partial similarities. 

Closed ft a [l Barrel Structures. Chicken triose phosphate isomerase (Figure 12.lj) is typical of a large number of structures that contain eight (S-tx. units in which the strands form a sheet wrapped around into a closed structure, cylindrical in topology. The helices are on the outside of the sheet. 

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.

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)). 

One end of the -barrel is closed by the amino-terminal peptide segment that runs across its bottom between fhe two short loops connecting strands B/C and F/ G, respectively, before it enters into /i-slrarid A. Dense packing of side chains in this region and wifhin the adjacent interior of fhe barrel structure leads to fhe formation of a hydrophobic core. The other end of fhe / -barrel is open to the solvent and forms a characteristic pocket. In the case of RBP, retinol is encapsulated as a ligand and protrudes into the barrel by almost half of its depth. The entrance to the pocket is formed by a set of four loops, which connect fhe eight antiparallel strands in a pairwise fashion. Because of the chalice-like shape of fhe protein (Fig. 8.2) and since many members of fhis family complex lipophilic compounds, the term lipocalins was proposed [25]. 

The solution structure of recombinant mouse 25 kDa ThTPase has been determined (Song et al. 2008) and the residues responsible for binding Mg and ThTP were determined from nuclear magnetic resonance (NMR) titration experiments. While the free enzyme has an open cleft form, the enzyme-ThTP complex tends to adopt a closed tunnel-fold, resembling the p-barrel structure of yeast RNA triphosphatase. 

Strand which then returns via two hairpin connections to the strand adjacent to the first. This feature contains a handedness that is only observed in one sense as shown in Fig. 13a. Connection of two of these features gives rise to an eight stranded y3-barrel however, Greek Key motifs are utilized in many ways to form closed structures. An alternative way of forming a closed barrel is found in proteins that exhibit a jelly roll topology (Fig. 13b). This is an abundant motif that is commonly found in virus capsid proteins. 

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