The 3D polymerase domain of the poliovirus 3CD polypeptide plays a role in modulating its RNA binding and protein processing activities, even though the proteinase catalytic site and RNA binding determinants appear to reside within the 3C(pro) portion of the molecule. In this study, we have generated recombinant 3CD polypeptides that contain chimeric 3D polymerase domains representing suballelic sequence exchanges between poliovirus type 1 (PV1) and coxsackievirus B3 (CVB3) to determine which portions of the 3D domain are responsible for influencing these activities. By utilizing these recombinant protein chimeras in protein processing and RNA binding studies in vitro, we have generated data suggesting the presence of separate subdomains within the polymerase domain of 3CD that may independently modulate its RNA binding and protein processing activities. In predicting where our sequence exchanges map by utilizing the previously published three-dimensional structure of the PV1 3D polymerase, we present evidence that sequences contained within the RNA recognition motif of the polymerase are critical for 3CD function in recognizing the 5' RNA cloverleaf. Furthermore, our protein processing data indicate that at least some of the substrate recognition and processing determinants within the 3D domain of 3CD are separate and distinct from the RNA binding determinants in this domain.