Triose phosphate isomerase barrel structure

The a/8-barrel structure seen in triose phosphate isomerase. This structure consists of eight /i-pleated sheets (represented by arrows) arranged in a cylindrical manner and surrounded by eight a-helices. (Reproduced with permission from J.S. Richardson.)... 

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 4.9 (a) Triose phosphate isomerase (TIM), has a (3-a-(3 structure made up of eight P-a motifs terminating in a final a-helix, which form a barrel-like structure, (b) An open twisted P-sheet with helices on both sides, such as the coenzyme-binding domain of many dehydrogenases. (From Branden and Tooze, 1991. Reproduced by permission of Garland Publishing, Inc.)... 

Figure 3. Model of (p a)s TIM barrel from triose phosphate isomerase. Numbered arrow and twisted ribbon structures are beta sheets and alpha helicies, respectively. (Adapted and reproduced from Ref. 66 with permission. Cop3night 1984 American Association for the Advancement of Science.)...

Figure 2-28 The eight-fold oc/(3 barrel structure of triose phosphate isomerase. From Richardson. (A) Stereoscopic view. (B) Ribbon drawing. Courtesy of Jane Richardson.117...

Figure 13-6 Stereoscopic view into the active site of triose phosphate isomerase showing side chains of some charged residues PGH, a molecule of bound phosphoglycolohydroxamate, an analog of the substrate enolate.138 The peptide backbone, as an alpha-carbon plot, is shown in light lines.147 The (a/ (S)8-barrel structure is often called a TIM barrel because of its discovery in this enzyme. Courtesy of M. Karplus.

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. 

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 12.36. Various types of protein tertiary structure, (a) An antiparallel a structure (cytochrome 6502) an up-and-down helix bundle (Ref. 113), (b) an antiparallel / structure (Cu,Zn superoxide dismutase) a Greek key (3 barrel (Ref. 114), and (c) and a parallel aj structure (triose phosphate isomerase) a singly wound parallel 0 barrel (Ref. 115). (Courtesy Jane S. Richardson)... 

P barrel The folding of a polypeptide chain to form a barrel-shaped structure with eight p strands as the lining. Eight a helices lie outside this p sheet. Both the a helices and the P strands follow a right-handed spiral around the axis of the barrel. The amino acid sequence in such a protein is such that p sheet and a helix alternate to give Pa)s- This motif was first seen in triose phosphate isomerase, and has since been observed in many other protein structures. 

Figure 1. Schematic representations of protein structures (a) myohemerythrin, an a-helical protein with antiparallel helices ( >) V2 domain of an immunoglobulin, a (3-sheet protein (c) triose phosphate isomerase, a parallel a-ff protein with a central (3 barrel (d) carboxypepti-dase, a parallel a- 3 protein with a central ( -sheet structure (e)para-hydroxybenzoate hydrolase, a complex protein structure with more than one domain. (From Ref. S3 courtesy of J. Richardson.)...

Figure 4. The structure of triose phosphate isomerase. A) Stereo view of one monomer down the axis of the eight-stranded alpha-beta barrell. B) Stereo view orthogonal to the first view. C) A view of one dimer looking down the two-fold axis relating each subunit. In both B) and C) the loop that moves when substrate binds is indicated by an arrow. 

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. 

FIGURE 16.5 Structure of triose phosphate isomerase. This enzyme consists of a central core of eight parallel j8 strands (orange) surrounded by eight a helices (blue). This structural motif, called an afi barrel, is also found in the glycolytic enzymes aldolase, enolase, and pyruvate kinase. Histidine 95 and glutamate 165, essential components of the active site of triose phosphate isomerase, are located in the barrel. A loop (red) closes off the active site on substrate binding. 

Figure 7 Topology (a) and cartoon representation (b) of the TIM barrel. The protein chain alternates between P and a secondary structure type, giving rise to a barrel P-sheet in the center surrounded by a large ring of a-helix on the outside. This structure, first seen in the triose phosphate isomerase of chicken, has been observed in many unrelated proteins since then. The topology is drawn using TOPS (http //www.tops.leed.ac.uk/), and the cartoon is generated using MOLSCRIPT. ...

Eight-stranded p-barrel this is a pattern of considerable structural importance, the query being derived from the motifs occurrence in subunit A of triose phosphate isomerase (Protein Data Bank code ITIM). 

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