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High‐resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure‐based design of ribonucleolytic inhibitors
Author(s) -
Leonidas Demetres D.,
Chavali Gayatri B.,
Oikonomakos Nikos G.,
Chrysina Evangelia D.,
Kosmopoulou Magda N.,
Vlassi Metaxia,
Frankling Claire,
Acharya K. Ravi
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.03196603
Subject(s) - angiogenin , rnase p , chemistry , ribonuclease , stereochemistry , active site , nucleotide , binding site , biochemistry , rnase h , enzyme , rna , biology , cancer research , angiogenesis , gene
The crystal structures of bovine pancreatic ribonuclease A (RNase A) in complex with 3′,5′‐ADP, 2′,5′‐ADP, 5′‐ADP, U‐2′‐p and U‐3′‐p have been determined at high resolution. The structures reveal that each inhibitor binds differently in the RNase A active site by anchoring a phosphate group in subsite P 1 . The most potent inhibitor of all five, 5′‐ADP ( K i = 1.2 μM), adopts a syn conformation (in contrast to 3′,5′‐ADP and 2′,5′‐ADP, which adopt an anti ), and it is the β‐ rather than the α‐phosphate group that binds to P 1 . 3′,5′‐ADP binds with the 5′‐phosphate group in P 1 and the adenosine in the B 2 pocket. Two different binding modes are observed in the two RNase A molecules of the asymmetric unit for 2′,5′‐ADP. This inhibitor binds with either the 3′ or the 5′ phosphate groups in subsite P 1 , and in each case, the adenosine binds in two different positions within the B 2 subsite. The two uridilyl inhibitors bind similarly with the uridine moiety in the B 1 subsite but the placement of a different phosphate group in P 1 (2′ versus 3′) has significant implications on their potency against RNase A. Comparative structural analysis of the RNase A, eosinophil‐derived neurotoxin (EDN), eosinophil cationic protein (ECP), and human angiogenin (Ang) complexes with these and other phosphonucleotide inhibitors provides a wealth of information for structure‐based design of inhibitors specific for each RNase. These inhibitors could be developed to therapeutic agents that could control the biological activities of EDN, ECP, and ANG, which play key roles in human pathologies.