NAD-binding fold

A fold also can be formed by one domain. In the example of secondary structures provided by lactate dehydrogenase (see Fig. 7.8), domain 1 alone forms the nucleotide binding fold. This fold is a binding site for NAD or, in other proteins, molecules with a generally similar structure (e.g., riboflavin). However, many proteins that bind NAD or NADP contain a very different fold from a separate fold family. These two different NAD binding folds arise from different ancestral lines and have different structures, but have similar properties and function. They are believed to be the product of convergent evolution. 

Figure 1. Diagrammatic representation of the NAD binding fold motif. The five parallel beta-strands are labelled a to e and the two alpha-hebces B and X.

Once the similarities for the output from the initial search have been calculated, the structures can be displayed via FRODO for visual inspection and evaluation of the rankings. The effectiveness of the algorithm was tested using the three motifs described above i.e., the eight-stranded P-barrel, the NAD-binding fold and the calcium-binding fold. 

The initial search was run with angular and mid-point distance tolerances of 35° and 10 A. The latter value is small compared with the previous run even so, no less than 181 separate hits were obtained from 34 different proteins. The ranking obtained was inspected to discover the whereabouts of the matched patterns corresponding to strands a to e and helices B and X in the hits for the dehydrogenases mentioned in the previous section on the NAD-binding fold. In... 

The efficiencies of the parallel and serial versions of the similarity algorithm have been investigated using the three query motifs (calcium binding fold, -barrel and NAD binding fold) discussed in the paper by Artymiuk et The serial... 

Parameters Calcium binding fold / -barrel NAD binding fold ... 

Fig. 2.24. Diagrammatic representation of the NAD" binding fold in dehydrogenase indicating the connectivities of the strands from the N- to the C-termini (according to Rossmann et al, 1974 courtesy of M. G. Rossmann).

The functions of a large proportion of the proteins encoded by the human genome are presently unknown. Recent advances in bioinformatics permit researchers to compare amino acid sequences to discover clues to potential properties, physiologic roles, and mechanisms of action of proteins. Algorithms exploit the tendency of nature to employ variations of a structural theme to perform similar functions in several proteins (eg, the Rossmarm nucleotide binding fold to bind NAD(P)H,... 

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... 

A domain is an independently folded region of a protein e.g., the NAD+-binding domain of glyceraldehyde-3-phosphate dehydrogenase. 

MIPS crystal structure is characterized by a homotetrameric association, with a 222 symmetry where two monomers are related by a non crystallographic twofold axis in an asymmetric unit and two such molecules are related by a crystallographic two-fold axis at one end. The holoenzyme seems to have three well defined domains, where the N and C terminal ends are a part of the central domain which is involved in subunit interactions, an NAD binding domain containing a modified Rossman fold and a catalytic domain which contains the active site amino acids and residues that occur at the tetrameriza-tion interface (Jin et al., 2004 Majumder et al., 2003 Stein and Geiger, 2002). 

Figure 16.13. NAD+ -binding region in dehydrogenases. The nicotinamide-binding half (yellow) is structurally similar to the adenine-binding half (red). The two halves together form a structural motif called a Rossmann fold. The...

Fig. 7.8. Ribbon drawing showing the arrangement of secondary structures into a three-dimensional pattern in domain 1 of lactate dehydrogenase. The individual polyjjeptide strands in the six-stranded P-sheet are shown with arrows. Different strands are connected by helices and by nonrepetitive structures (mrns, coils and loops), shown in blue. This domain is the nucleotide binding fold. NAD is bound to a site created by the helices (upper left of figure.) (Modified from Richardson JS. Adv Protein Chem. The anatomy and taxonomy of protein structure 1981 34 167).

Folds are relatively large patterns of three-dimensional strnctnre that have been recognized in many proteins, including proteins from different branches of the phylogenetic tree. A characteristic activity is associated with each fold, such as ATP binding and hydrolysis (the actin fold) or NAD binding (the nucleotide-binding fold). These three examples of fold patterns are discussed below. 

E. coli B G85A/G89A/ EMPD203-206VRKH/P210R wild 4.32 X 10 vs 5.82 x 10 for A 6.32 x 10 vs 1.58 x 10 forB. replacement of eunino acids in the (iaP-fold of the NAD -binding domain which is unfavorable to NAD but favorable to NADP. thus converts the NADF inactive wild-type to mutants with high NADP activity. 

P-strand) and therefore protein folds. For example, lactate dehydrogenase (LDH) and NADH peroxidase (NHPOx) shares the common FAD/NAD binding motif (GxGxxG). The conversion of a connector helix C in LDH with 3 stranded P-meander (2 ERYEGDGRVQKVVTDKNAY in NHPOx) in NHPOx results in different PPa architecture (versus apa) and thus different folds for these homologs. 

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