The phosphoramidate of CCdAp and puromycin (CCdApPuro) is a potent inh
ibitor of ribosomal peptidyl transferase, as assayed by the fragment r
eaction. Inhibition is competitive at the ribosomal A-site. CCdApPuro
protects P-site-associated bases in the peptidyl transferase loop regi
on of 23S rRNA from carbodiimide modification. The K-i's of structural
homologues of CCdApPuro suggest that both the CCdA and puromycin moie
ties participate in binding. Thus, CCdApPuro appears to bridge the A-
and P-sites of the ribosome, implying that substrates are juxtaposed w
ith a geometry suitable for direct reaction during peptidyl transfer.