Eight-stranded 0-barrel

The VP1, VP2, and VP3 all contain a core eight-stranded antiparallel (3 barrel (Figure 2). These polypeptides have surfaces on both the exterior and interior of the virion particle, facing both solvent and viral RNA. The fourth polypeptide, VP4, is considerably smaller than the others and does not contain the eight-stranded barrel motif. The VP4 resides entirely on the interior surface of the virion, in close association with the viral RNA. The N-terminus of VP4 is known to be myristoylated in both rhino-andpolioviruses [18,19]. 

Fig. 15.30. Ribbon diagram [54] of the parallel eight-stranded barrel in triose phosphate isomerase (1 TIM [46])...

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.)...

The eight-stranded a/p-barrel stmcture is one of the largest and most regular of all domain stmctures. A minimum of about 200 residues are required to form this structure. It has been found in many different proteins, most of which are enzymes, with completely different amino acid sequences and... 

There is one exception to the rule that requires bulky hydrophobic residues to fill the interior of eight-stranded a/p barrels in order to form a tightly packed hydrophobic core. The coenzyme Biz-dependent enzyme methylmalonyl-coenzyme A mutase, the x-ray structure of which was determined by Phil Evans and colleagues at the MRC Laboratory of Molecular... 

All known eight-stranded a/p-barrel domains have enzymatic functions that include isomerization of small sugar molecules, oxidation by flavin coenzymes, phosphate transfer, and degradation of sugar polymers. In some of these enzymes the barrel domain comprises the whole subunit of the protein in others the polypeptide chain is longer and forms several additional domains. An enzymatic function in these multidomain subunits, however, is always associated with the barrel domain. 

There is a second family of small lipid-binding proteins, the P2 family, which include among others cellular retinol- and fatty acid-binding proteins as well as a protein, P2, from myelin in the peripheral nervous system. However, members of this second family have ten antiparallel p strands in their barrels compared with the eight strands found in the barrels of the RBP superfamily. Members of the P2 family show no amino acid sequence homology to members of the RBP superfamily. Nevertheless, their three-dimensional structures have similar architecture and topology, being up-and-down P barrels. 

We saw in Chapter 2 that the Greek key motif provides a simple way to connect antiparallel p strands that are on opposite sides of a barrel structure. We will now look at how this motif is incorporated into some of the simple antiparallel P-barrel structures and show that an antiparallel P sheet of eight strands can be built up only by hairpin and/or Greek key motifs, if the connections do not cross between the two ends of the p sheet. 

Figure 5.10 Idealized diagrams of the Greek key motif. This motif is formed when one of the connections of four antiparallel fi strands is not a hairpin connection. The motif occurs when strand number n is connected to strand + 3 (a) or - 3 (b) instead of -r 1 or - 1 in an eight-stranded antiparallel P sheet or barrel. The two different possible connections give two different hands of the Greek key motif. In all protein structures known so far only the hand shown in (a) has been observed.

Another important parallel /3-array is the eight-stranded parallel j8-barrel, exemplified in the structures of triose phosphate isomerase and pyruvate kinase (Figure 6.30). Each /3-strand in the barrel is flanked by an antiparallel a-helix. The a-helices thus form a larger cylinder of parallel helices concentric with the /3-barrel. Both cylinders thus formed have a right-handed twist. Another parallel /3-structure consists of an internal twisted wall of parallel or mixed /3-sheet protected on both sides by helices or other substructures. This structure is called the doubly wound parallel j8-sbeet because the structure can be... 

FIGURE 6.30 Parallel /3-array proteins—the eight-stranded /3-barrels of triose phosphate iso-merase (a, side view, and b, top view) and (c) pyruvate kinase. (Jane Richardson)... 

HRVs are non-enveloped viruses of icosahedral overall shape [44]. Located on the exterior of the viral capsid are three structural proteins (VPl, VP2 and VP3), each consisting of an eight-stranded antiparallel -barrel. VP4 is found at the interface with the RNA inside the virus. A pocket factor is usually bound to a hydrophobic canyon binding site within the VPl -barrel. This lipid-like molecule is important for the stability of the capsid and has been... 

We have completed several structures each of NPl, NP2, and NP4 (31, 46 9, 110). These structures reveal the Rhodnius nitrophorins to have a fold dominated by an eight-stranded antiparallel beta-barrel, as shown in Fig. 15, and to rely on a remarkable ligand-induced conformational change for NO transport, described later. The structures confirm that the nitrophorins are completely unrelated to the globins, the only other heme-based gas transport proteins whose structures are known. Rather, their fold places them in the lipocalin family, for which several other examples are known (111-113). Our initial nitrophorin structure was of NPl and was determined using standard MIR and... 

A ribbon diagram of the trimer is shown in Figure 4B. Each monomer contains an eight-stranded (3 sheet and a five-stranded (3 sheet that join to form a distorted (3 barrel. Seven a helices surround this (3 sheet structure. 

The eight-stranded P cylinder of plastocyanin (Fig. 2-16A) is somewhat flattened and can also be regarded as a P sandwich.116118 However, the P barrel of triose phosphate isomerase (see Fig. 2-28) is surrounded by eight a helices which provide additional stability and a high symmetry. Bacterial outer membranes contain pores created by very large P cylinders within proteins called porins.119120 Tire one shown in Fig. 8-20 has 16 strands. 

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. 

The folding pattern of cytochrome b5 is also found in the complex heme protein flavocytochrome b2 from yeast (Chapter 15)133 and probably also in liver sulfite oxidase134,135 Both are 58-kDa peptides which can be cleaved by trypsin to 11-kDa fragments that have spectroscopic similarities and sequence homology with cytochrome b5. Sulfite oxidase also has a molybdenum center (Section H). The 100-residue N-terminal portion of flavocytochrome b2 has the cytochrome b5 folding pattern but the next 386 residues form an eight-stranded (a / P)8 barrel that binds a molecule of FMN.133,136 All of these proteins pass electrons to cytochrome c. In contrast, the folding of cytochrome... 

Enzyme preparations from Clostridium perfringens and Escherichia coli are commercially available, and the latter enzyme [69] has been cloned, overexpressed [70-72], and crystallized [73]. Its spatial structure has been determined recently by X-ray crystallography at 2.2 A resolution which has revealed that the enzyme is a tetramer and belongs to the a//l-barrel class of proteins [74] (Fig. 4). The active site pocket is located at the carboxy-terminal end of the eight-stranded /1-barrel, and the reactive lysine residue, forming a Schiff base with pyruvate, has been identified to be Lysl65 (Fig. 5). However, the current X-ray model excludes the catalytic participation of a histidine residue [74],... 

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