PHOSPHOESTERASE DOMAINS ASSOCIATED WITH DNA-POLYMERASES OF DIVERSE ORIGINS

Computer analysis of DMA polymerase protein sequences revealed previou sly unidentified conserved domains that belong to two distinct superfa milies of phosphoesterases. The alpha subunits of bacterial DNA polyme rase III and two distinct family X DNA polymerases are shown to contai n an N-terminal domain that defines a novel enzymatic superfamily, des ignated PHP, after polymerase and histidinol phosphatase. The predicte d catalytic site of the PHP superfamily consists of four motifs contai ning conserved histidine residues that are likely to be Involved in me tal-dependent catalysis of phosphoester bond hydrolysis. The PHP domai n is highly conserved in all bacterial polymerase ill alpha subunits, but in proteobacteria and mycoplasmas, the conserved motifs are distor ted, suggesting a loss of the enzymatic activity. Another conserved do main, found in the small subunits of archaeal DNA polymerase II and eu karyotic DNA polymerases alpha and delta, is shown to belong to-the su perfamily of calcineurin-like phosphoesterases, which unites a variety of phosphatases and nucleases, The conserved motifs required for phos phoesterase activity are intact in the archaeal DNA polymerase subunit s, but are disrupted in their eukaryotic orthologs. A hypothesis is pr oposed that bacterial and archaeal replicative DNA polymerases possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate rele ased during nucleotide polymerization. As proposed previously, pyropho sphate hydrolysis may be necessary to drive the polymerization reactio n forward, The phosphoesterase domains with disrupted catalytic motifs may assume an allosteric, regulatory function and/or bind other subun its of DNA polymerase holoenzymes. In these cases, the pyrophosphate m ay be hydrolyzed by a stand-alone phosphatase, and candidates for such a role were identified among bacterial PHP superfamily members.