PolyA polymerase (PAP) adds a polyA tail onto the 3'-end of RNAs without a nucleic acid template, using ATP as a substrate. The mechanism for the selection of substrates by eubacterial PAP remains obscure. Structural and structure-based biochemical studies of Escherichia coli PAP (EcPAP) revealed that both the shape and size of the nucleobase-interacting pocket of EcPAP are maintained by a rigid intra-molecular hydrogen-bonding-network. It makes the pocket suitable for the accommodation of only ATP using a single amino acid residue in the pocket. The rigidity of the pocket structure of EcPAP is sustained by interactions between the catalytic core domain and the RNA-binding domain. EcPAP has a flexible, unstructured, basic C-terminal region that functions as an RNA translocator for processive RNA polymerization. A comparison of the EcPAP structure with those of other template-independent RNA polymerases suggests that structural changes of domain(s) outside the conserved catalytic core domain altered the substrate specificities and processivities of the template-independent RNA polymerases.