Triose phosphate isomerase TIM barrel

In each of the three divisions of life, the most common fold is the P-loop NTPase. Four common folds, namely P-loop NTPases, Triose Phosphate Isomerase (TIM) barrels, ferredoxin-like domains, and Rossmann-fold domains, are see in the top-10 lists for all three divisions (Table IV). 

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 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 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.

The study of //J-barrel proteins, also called TIM barrels after the first enzyme investigated in this class, triose phosphate isomerase, or (/3a)8-barrel enzymes after the... 

FIGURE 12. Prototypical (a/fi)i barrel of the TIM fold of triose phosphate isomerase, containing a transition-state analogue phosphoglycohydroxamate inhibitor (PDB ID 3YPI, Plate XXV)... 

In some cases, families are further grouped into clans. The largest such clan is the glycosyl hydrolase Clan A (clan GH-A), all of which have a protein fold of eight alternating a-helices and p-sheets, giving the (p/a)g sructure, sometimes called a TIM barrel because it was first encountered with triose phosphate isomerase. 

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

The methylated reductase (apo form) folds into an unusual a/p-barrel, unlike other AKR members which exhibit (a/p)g barrels, known as triose-phosphate isomerase barrel (TIM barrel).This unique topology presents only six P-strands (a8/P6 barrel fold). The a8/P6 barrel fold of PR... 

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. ...

---