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The binding of IMP to Ribonuclease A
Author(s) -
Hatzopoulos George N.,
Leonidas Demetres D.,
Kardakaris Rozina,
Kobe Joze,
Oikonomakos Nikos G
Publication year - 2005
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2005.04822.x
Subject(s) - ribonuclease , ribonuclease iii , chemistry , biochemistry , rna , gene , rna interference
The binding of inosine 5′ phosphate (IMP) to ribonuclease A has been studied by kinetic and X‐ray crystallographic experiments at high (1.5 Å) resolution. IMP is a competitive inhibitor of the enzyme with respect to C>p and binds to the catalytic cleft by anchoring three IMP molecules in a novel binding mode. The three IMP molecules are connected to each other by hydrogen bond and van der Waals interactions and collectively occupy the B 1 R 1 P 1 B 2 P 0 P ‐1 region of the ribonucleolytic active site. One of the IMP molecules binds with its nucleobase in the outskirts of the B 2 subsite and interacts with Glu111 while its phosphoryl group binds in P 1 . Another IMP molecule binds by following the retro‐binding mode previously observed only for guanosines with its nucleobase at B 1 and the phosphoryl group in P ‐1 . The third IMP molecule binds in a novel mode towards the C‐terminus. The RNase A–IMP complex provides structural evidence for the functional components of subsite P ‐1 while it further supports the role inferred by other studies to Asn71 as the primary structural determinant for the adenine specificity of the B 2 subsite. Comparative structural analysis of the IMP and AMP complexes highlights key aspects of the specificity of the base binding subsites of RNase A and provides a structural explanation for their potencies. The binding of IMP suggests ways to develop more potent inhibitors of the pancreatic RNase superfamily using this nucleotide as the starting point.