Rational proteomics II: electrostatic nature of cofactor preference in the short-chain oxidoreductase (SCOR) enzyme family

Abstract

The dominant role of long-range electrostatic interatomic interactions in nicotinamide adenine dinucleotide/nicotinamide adenine dinucleotide phosphate (NAD/NADP) cofactor recognition has been shown for enzymes of the short-chain oxidoreductase (SCOR) family. An estimation of cofactor preference based only on the contribution of the electrostatic energy term to the total energy of enzyme-cofactor interaction has been tested for approximately 40 known three-dimensional (3D) crystal complexes and approximately 330 SCOR enzymes, with cofactor preference predicted by the presence of Asp or Arg recognition residues at specific 3D positions in the beta2alpha3 loop (Duax et al., Proteins 2003;53:931-943). The results obtained were found to be consistent with approximately 90% reliable cofactor assignments for those subsets. The procedure was then applied to approximately 170 SCOR enzymes with completely uncertain NAD/NADP dependence, due to the lack of Asp and Arg marker residues. The proposed 3D electrostatic approach for cofactor assignment ("3D_DeltaE(el)") has been implemented in an automatic screening procedure, and together with the use of marker residues proposed earlier (Duax et al., Proteins 2003;53:931-943), increases the level of reliable predictions for the putative SCORs from approximately 70% to approximately 90%. It is expected to be applicable for any NAD/NADP-dependent enzyme subset having at least 25-30% sequence identity, with at least one enzyme of known 3D crystal structure.

Fig. 1

LIGPLOT schematics illustrating the hydrogen bond ( ≤3.35Å) net work around (a) the NAD cofactor in 7α-hydroxysteroid dehydrogenase (1FMC) and (b) the NADP cofactor in mouse carbonyl reductase (1CYD). The names (one letter code) of the residues making identical, similar and distinctly different contacts are shown in black, green and red respectively. The major differences (indicated by red) are mostly located around the adenine part of the cofactor. The conserved water molecules are marked by W symbols.

Fig. 2

The histogram of the cofactor preference assignment for the enzymes from (a) “D38” and (b) “R39” subsets with indicated numbers of predictions for each ΔE_el energy shell.