Rossmann fold

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). 

A more detailed breakdown of the fold abundance by individual genomes shows the same trends, as well as a number of unique features (Fig. 6, see color insert). The latter include, for example, the marked overrepresentation of Rossmann-fold domains in Mycobacterium, flavo-doxins in Synechocystis and methyltransferases in Helicobacter. Furthermore, the differences in fold distribution between the multicellular eukaryote Caenorhabditis elegans and the unicellular yeast become readily apparent. In the nematode, the protein kinases are the most common fold, with the P-loops relegated to the second position in contrast, the yeast distribution is more similar to that seen in prokaryotes (Fig. 6). 

The class III deacetylases, named sirtuins, are structurally and functionally different from other HDACs. In contrast to the zinc-dependent deacetylation of classic HDACs, sirtuins depend on NAD" to carry out catalytic reactions. A variety of sirtuin crystal structures have been published over the past few years. The structures of human Sirt2 and SirtS as well as several bacterial Sir2 proteins could be derived, whereas no 3D structure is available for Sirtl and the other subtypes [69]. All solved sirtuin structures contain a conserved 270-amino-acid catalytic domain with variable N- and C-termini. The structure of the catalytic domain consists of a large classic Rossmann fold and a small zinc binding domain. The interface between the large and the small subdomain is commonly subdivided into A, B and C pockets. This division is based on the interaction of adenine (A), ribose (B) and nicotinamide (C) which are parts of the NAD" cofactor. (Figure 3.5) Whereas the interaction of adenine and... 

Figure 2. Pharmacofamilies of the NADH cofactor (structure shown in panel A) binding to oxi-doreductases. Panel B shows an overlay of a subset of NAD(P)(H) geometries obtained from 288 crystal structures of oxidoreductases. The two largest pharmacofamilies are shown, corresponding to the two-domain Rossmann fold enzymes in pharmacofamilies 1 (anti) and 2 (syn). Panel C shows the corresponding pharmacophores with all protein heteroatoms indicated that are within hydrogen bonding distance of atoms in the cofactor. (Figure adapted with permission from original work of Sem ef o/. ).

The AdoMet binding motif is similar to the Rossmann fold, which is well known from the nucleotide binding proteins [22]. It has been shown that the known crystal structures of methyltransferases are strikingly similar in the AdoMet-binding regions [23], which indicates that all AdoMet-utilizing enzymes may share a common divergent evolution. 

NAD(P)-binding Rossmann-fold domains NAD(P)-binding Rossmann-fold domains Alcohol/glucose dehydrogenases, carboxyl-terminal domain Alcohol dehydrogenase Human Homo sapiens)... 

Most dehydrogenases that use NAD or NADP bind the cofactor in a conserved protein domain called the Rossmann fold (named for Mchael Rossmann, who deduced the structure of lactate dehydrogenase and first described this structural motif). The Rossmann fold typically consists of a six-stranded parallel /3 sheet and four associated a helices (Fig. 13-16). 

RGURE 13-16 The nucleotide binding domain of the enzyme lactate dehydrogenase, (a) The Rossmann fold is a structural motif found in the NAD-binding site of many dehydrogenases It consists of a six-stranded parallel /3 sheet and four a helices inspection reveals the arrangement to be a pair of structurally similar motifs... 

The acceptor of hydrogen in the glyceraldehyde 3-phosphate dehydrogenase reaction is NAD+ (see Fig. 13-15), bound to a Rossmann fold as shown in Figure 13-16. The reduction of NAD+ proceeds by the enzymatic transfer of a hydride ion ( H ) from the aldehyde group of glyceraldehyde 3-phosphate to the nicoti-... 

Figure 2-27 Topologies of the folds of three families of nucleotide binding oc/p proteins. Cylinders represent a helices and arrows p strands. (A) The ATPase fold for the clathrin-uncoating ATPase (B) The G-protein fold that hinds GTP and is found in ras proteins (C) The Rossmann fold that hinds NAD in several dehydrogenases. From Branden.262...

Rocky Mountain spotted fever 7 Rods (visual receptor cells) 390 Root hairs, dimensions of 30 Roseoflavin 788, 789s Rossmann fold. See Nucleotide-binding domain Rotamases 488 Rotary diffusion constant 463 Rotation of molecules 462,463 Rotational barrier 44 Rotifers 24, 25... 

As already discussed in Chapter 11, there are more than 10 000 protein structures known but only about 30 3D structure types. This might be traced to a limited number of possible stable polypeptide structures but most probably reflects the evolutionary history of the diversity of proteins. There are structural motifs which repeat themselves in a multitude of enzymes which are otherwise neither structurally nor functionally related, such as TIM barrel proteins, four-helix bundle proteins, Rossmann folds, or a/j3-folds of hydrolases (Figure 16.1). 

Both NADP-IDH and the homologous isopropylmalate dehydrogenase (IMDH, EC 1.1.1.85) belong to the non-Rossmann-fold p-decarboxylating dehy-... 

Despite sharing only 25% sequence identity, structural analysis indicates that both proteins of E. coli NADP-IDH and T. thermophilus NAD-IMDH are homodimers which share a common protein fold that lacks the p p p motif characteristic of the nucleotide binding Rossmann fold [23], The strict and distinct specificities of these enzymes provide an attractive model system for engineering specificity, while the extensive knowledge of substrate and coenzyme binding and catalysis provide the sound foundation critical for rational design. 

E. coli NADP-IDH and the homologous T. thermophilus NAD-IMDH have similar nucleotide-binding pockets that are quite distinct from the Rossmann fold found in many other dehydrogenases [16,17,22,23]. The pocket is constructed from three loops and an a-helix in IDH, the latter being substituted by a p-tum in IMDH (Fig. 1). Calculated as the ratio of kaJKm the E. coli NADP-IDH is 7000-fold more active with NADP than with NAD [1], whereas IMDH exhibits a 100-fold preference for NAD. 

Fig. 10. Schematic representation of a glulathionc reductase subunit, from the work of Schulz and colleagues [53], Rectangles are a-helix, arrows are strands of /3-sheet. Rossmann folds are hatched.

The overall fold of MIPS is similar to that of diaminopimelic acid dehydrogenase from Corynebacterium glutamicum and dihydrodipicolinate reductase from E. coli. Though the reactions catalyzed by these enzymes are quite different, they all use either NAD+ or NADP+ bound to a structurally similar Rossmann fold domain, and all three contain a (3 sheet domain located underneath the Rossmann fold and directly beneath the nicotinamide moiety that defines part of the active site (Norman et al., 2002 Stein and Geiger, 2002). 

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