The pokeweed antiviral protein (PAP) belongs to
a family of ribosome-inactivating proteins (RIP), which
depurinate ribosomal RNA through their site-specific N-glycosidase
activity. We report low temperature, three-dimensional
structures of PAP co-crystallized with adenyl-guanosine
(ApG) and adenyl-cytosine-cytosine (ApCpC). Crystal structures
of 2.0–2.1 Å resolution revealed that both
ApG or ApCpC nucleotides are cleaved by PAP, leaving only
the adenine base clearly visible in the active site pocket
of PAP. ApCpC does not resemble any known natural substrate
for any ribosome-inactivating proteins and its cleavage
by PAP provides unprecedented evidence for a broad spectrum
N-glycosidase activity of PAP toward adenine-containing
single stranded RNA. We also report the analysis of a 2.1
Å crystal structure of PAP complexed with the RIP
inhibitor pteoric acid. The pterin ring is strongly bound
in the active site, forming four hydrogen bonds with active
site residues and one hydrogen bond with the coordinated
water molecule. The second 180° rotation conformation
of pterin ring can form only three hydrogen bonds in the
active site and is less energetically favorable. The benzoate
moiety is parallel to the protein surface of PAP and forms
only one hydrogen bond with the guanido group of Arg135.