Barrel axis

Figure S.l The enzyme superoxide dismutase (SOD). SOD is a P structure comprising eight antiparallel P strands (a). In addition, SOD has two metal atoms, Cu and Zn (yellow circles), that participate in the catalytic action conversion of a superoxide radical to hydrogen peroxide and oxygen. The eight p strands are arranged around the surface of a barrel, which is viewed along the barrel axis in (b) and perpendicular to this axis in (c). [(a) Adapted from J.S. Richardson. The stmcture of SOD was determined in the laboratory of J.S. and D.R. Richardson, Duke University.)...

Fig. 29. An assortment of/3 barrels, viewed down the barrel axis (a) staphylococcal nuclease, 5-stranded (b) soybean trypsin inhibitor, 6-stranded (c) chymotrypsin, 6-stranded (d) immunoglobulin (McPC603 CH1) constant domain, 7-stranded (e) Cu,Zn superoxide dismutase, 8-stranded (f) triosephosphate isomerase, 8-stranded (g) im-... 

Figure 10.4 Diagram for the operation of barrel supports. The barrel slides on the supports during thermal expansion, allowing the barrel axis to maintain its elevation. If the barrel support does not allow the barrel to slide, then the discharge end of the barrel is forced down and possibly out of alignment...

Fig. 4. Stereo ribbon plot [76] of a NeuA subunit viewed down the /J-barrel axis from its carboxy-terminal end...

Fig. 9. Stereo ribbon plots [76] of FruA subunits viewed down the /1-barrel axis from their carboxy-terroinal end to illustrate the flexibility of the C-terminal chain as proposed for the catalytic function. A) Crystal structure of the FruA from rabbit muscle B) crystal structure of the FruA from Drosophila melanogaster...

If the strand order were 1 2 3 4 5 6, all five connections would be on the same side of the sheet, and no crevice would be formed. However, when eight strands are aligned in this way, a closed barrel of twisted strands can be formed in which strand number 8 is adjacent to strand number 1 (Fig. 34) [72], The helical connections lie outside the barrel, and diverge from the barrel axis, giving geometrical conditions favourable for the formation of crevices at the carboxyl end of the barrel [72], This arrangement occurs in triose-phosphate isomerase [161], pyruvate kinase [162] and glycollate oxidase [163]. 

FIGURE 16.19. Details of / -sheet folding in the lining of a (/ a)8 barrel. Amino-acid residues are shown as open circles, joined by solid lines these indicate the backbone. Hydrogen bonds are indicated by thick broken lines. These bind the various strands (1 to 8) into a / sheet. The direction of the strands in the sheet is inclined at an angle (as shown) to the l3a)s barrel axis. 

Fig. zi. 1 hree-dimensional structure of the sialate-pyruvate lyase from Escherichia coli. (top) Viewed down the (3-barrel axis from the carboxy-terminal end of this aldolase. The putative catalytic residue Lys-165 is shown in ball-and-stick representation, (bottom) Putative active site of Neu5Ac lyase showing the side chains of nine of the residues forming the surface of the pocket. Carbon atoms are white, oxygens black and nitrogens grey. From ref. [899] by permission of Current Biology Ltd., London. 

Triosephosphate isomerase was the first enzyme shown to contain an (a//3)g barrel and thus established this motif as the TIM barrel. This fold consists of eight parallel /3-strands connected by right-handed helical crossovers and is one of the most common folds found in enzymes. The TIM barrel typically contains approximately 200 amino acid residues. Contrary to the appearance of the ribbon drawing (Fig. 14a), the interior of the barrel is closely packed by the side chains protruding from the /3-strands. The strands are inclined at an angle of approximately 30° to barrel axis, which is necessary to allow efficient packing of the interior. The necessity to form a closely packed interior explains why these barrels are almost always formed from eight strands. There are several variations on the TIM barrel that include the addition and subtraction of j8-strands as well as the introduction of antiparallel /3-strands as observed in enolase. These variations attest to the versatility of this fold. 

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