On the Advantage of Being a Dimer, a Case Study Using the DimericSerratia Nuclease and the Monomeric Nuclease fromAnabaena sp. Strain PCC 7120

Abstract

The extracellular endonucleases from Serratia marcescens and Anabaena sp. are members of a family of nonspecific endonucleases. In contrast to the monomeric Anabaena nuclease, the Serratia nuclease is a dimer of two identical subunits. To find out whether the two active sites of the Serratia nuclease function independently of each other and what the advantage of being a dimer for this enzyme might be, we produced (i) dimers in which the two subunits were cross-linked, (ii) heterodimers consisting of a wild type and an inactive mutant subunit which were also cross-linked, and (iii) monomeric variants which are unable to dimerize. The monomeric H184R variant and the cross-linked S140C variant exhibit the same activity as the wild type enzyme, while the cross-linked heterodimer with one inactive subunit shows only half of the activity of the wild type enzyme, demonstrating functional independence of the two subunits of the Serratia nuclease. On the other hand at low enzyme and substrate concentrations dimeric forms of the Serratia nuclease are relatively more active than monomeric forms or the monomeric Anabaena nuclease in cleaving polynucleotides, not, however, oligonucleotides, which is correlated with the ability of dimeric forms of the Serratia nuclease to form large enzyme-substrate networks with high molecular weight DNA and to cleave polynucleotides in a processive manner. We conclude that in the natural habitat of Serratia marcescens where the supply of nutrients may become growth limiting the dimeric nuclease can fulfil its nutritive function more efficiently than a monomeric enzyme.

Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions

“…Although the functional significance, if any, of the Type II MTase dimer is unclear, one possibility is that the dimeric form of HhaI MTase allows formation of a large enzyme-substrate network with high molecular weight DNA, as demonstrated for Serratia nuclease (Franke et al, 1999). Although the two subunits of Serratia nuclease function independently of each other, they bind simultaneously to one macromolecular DNA, forming a large network between the enzyme and the substrate.…”

Sugar non-specific endonucleases

“…Moreover, the dimeric forms of non-speci¢c endonucleases from S. racemosum [34] and S. marcescens [87] are held together purely by non-covalent interactions and not by disul¢de [86]. Although the monomeric variants were functionally independent, in the presence of low enzyme concentration and high molecular mass DNA the native dimeric form of S. marcescens nuclease was relatively more active than the monomeric form or the heterodimer with one inactive subunit [89]. In S. cerevisiae and N. crassa multiple nucleases having similar catalytic properties, but with subtle di¡erences in their physical properties, have been reported.…”

Structural Basis for Stable DNA Complex Formation by the Caspase-activated DNase

“…Whereas the latter mostly act as dimers or pseudo-dimers and exhibit complex protein⅐DNA interfaces, the nonspecific nucleases typically act as monomers or dimers with independent active sites. They usually form only a minimum of contacts sufficient to bring about DNA cleavage, at the same time avoiding specific DNA complex formation (14,19,38). On the other hand, different from restriction enzymes or homing endonucleases, the stable DNA complexes formed by CAD are nonspecific and thus enable the enzyme to degrade DNA, still without selectivity, a prerequisite for the physiological function of the enzyme, which is to cut any accessible linker DNA it engages.…”