P-Barrel structure

The packing interactions between a helices and p strands are dominated by the residues Val (V), He (I), and Leu (L), which have branched hydrophobic side chains. This is reflected in the amino acid composition these three amino acids comprise approximately 40% of the residues of the P strands in parallel P sheets. The important role that these residues play in packing a helices against P sheets is particularly obvious in a/P-barrel structures, as shown in Table 4.1. 

Figure 4.3 In most a/p-barrel structures the eight p strands of the barrel enclose a tightly packed hydrophobic core formed entirely by side chains from the p strands. The core is arranged in three layers, with each layer containing four side chains from alternate p strands. The schematic diagram shows this packing arrangement in the a/p barrel of the enzyme glycolate oxidase, the structure of which was determined by Carl Branden and colleagues in Uppsala, Sweden.

Figure 4.7 Two of the enzymatic activities involved in the biosynthesis of tryptophan in E. coli, phosphoribosyl anthranilate (PRA) isomerase and indoleglycerol phosphate (IGP) synthase, are performed by two separate domains in the polypeptide chain of a bifunctional enzyme. Both these domains are a/p-barrel structures, oriented such that their active sites are on opposite sides of the molecule. The two catalytic reactions are therefore independent of each other. The diagram shows the IGP-synthase domain (residues 48-254) with dark colors and the PRA-isomerase domain with light colors. The a helices are sequentially labeled a-h in both barrel domains. Residue 255 (arrow) is the first residue of the second domain. (Adapted from J.P. Priestle et al., Proc.

We have described a general relationship between structure and function for the a/p-barrel structures. They all have the active site at the same position with respect to their common structure in spite of having different functions as well as different amino acid sequences. We can now ask if similar relationships also occur for the open a/p-sheet structures in spite of their much greater variation in structure. Can the position of the active sites be predicted from the structures of many open-sheet a/p proteins ... 

In almost every one of the more than 100 different known a/p structures 1 of this class the active site is at the carboxy edge of the p sheet. Functional residues are provided by the loop regions that connect the carboxy end of the strands with the amino end of the a helices. In this one respect a fun-I damental similarity therefore exists between the a/p-barrel structures and the I open a/p-sheet structures. 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

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. 

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. 

Pectate lyase C from the plant pathogen Erwinia, which causes soft-rot in many different plants, has a parallel P barrel structure (Fig. 13-3)77 which is similar to that of the tailspike protein shown in Fig. 2-17 and represents what may be a very large structural family of proteins.78 The location of the active site is not... 

A number of starch-converting enzymes belong to a single family termed the a-amylase family or family 13 hydrolases. This group of enzymes shares common characteristics such as an eight-stranded a/p barrel structure, the ability to hydrolyze 1,4-a-D-glucosidic linkages of attached polysaccharides in a-conformation, and conserved amino acid residues in the active sites of the enzymes (van der Maarel et al. 2002). 

VDAC plays a role in the regulated flux of metabolites—usually anionic species such as phosphate, chloride, organic anions, and the adenine nucleotides—across the outer membrane. VDAC appears to form an open p -barrel structure similar to that of the bacterial porins (Section 12.5.2). although mitochondrial porins and bacterial porins may have evolved independently. Some cytoplasmic kinases bind to VDAC, thereby obtaining preferential access to the exported ATP. In contrast, the inner membrane is intrinsically impermeable to nearly all ions and polar molecules. A large family of transporters shuttles metabolites such as ATP, pyruvate, and citrate across the inner mitochondrial membrane. The two faces of this membrane will be referred to as the matrix side and the cytosolic side (the latter because it is freely accessible to most small molecules in the cytosol). They are also called the N and P sides, respectively, because the membrane potential is negative on the matrix side and positive on the cytosolic side. 

Figure 6.2(a) Illustration of the so-called a/p barrel structure for triose phosphate isomerase after [1]. The parallel P-sheet chains are drawn in red and they form a catenoid. Outside the catenoid there are eight a-helices (green). (Adapted from [1].)... 

Figure 2-28 The eight-fold a/p barrel structure of triose phosphate isomerase. From Richardson. (A) Stereoscopic view. (B) Ribbon drawing. Courtesy of Jane Richardson." ...

The southern bean mosaic virus has an eight-stranded antiparallel P-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. 2 The subunits A, which have a third conformation, fit together around the five-fold axis in true cyclic symmetry. 

Interestingly, the secretion of FGF family members that mediate tissue repair resembles IL-1 secretion, that is, not involving the Golgi. The FGF family proteins also bind to their receptors by P-barrel structures that interact with a glycan (in this case known to be heparin) during activation. Hyaluronan and heparin are glycosaminoglycans (Sect. 6.3.1). 

Fig. 31. The Ramachandran plot of a P-barrel structure (D-xylose isomerase) (Courtesy of H. L. Carrel]).

Closed P-a-P barrel structures. Chicken triose phosphate isomerase (Figure 5.1 OH) is typical of a large number of structures that contain eight p-a-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. 

Another type of domain that recognizes phosphotyrosine residues is the PTB (phosphotyrosine binding) domain (alternatively, phosphotyrosine interaction domain, PID). The specificity of interaction is determined by the sequence of amino acids immediately on the N-terminal side of the phosphorylated tyrosine, NPXYp. The tertiary structure shows a p-barrel structure and a long a-heUx that packs against one end. The target phosphotyrosine binds to one side of the P-barrel. 

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