2OJ3

Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)

Summary for 2OJ3

• Entry DOI: 10.2210/pdb2oj3/pdb
• Descriptor: HDV RIBOZYME, U1 small nuclear ribonucleoprotein A, COBALT HEXAMMINE(III), ... (5 entities in total)
• Functional Keywords: tl+ and cobalt hexammine compete for binding sites., structural protein-rna complex, structural protein/rna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 2
• Total formula weight: 37821.51

Authors

Ke, A.,Ding, F.,Batchelor, J.D.,Doudna, J.A. (deposition date: 2007-01-12, release date: 2007-03-27, Last modification date: 2023-12-27)

Primary citation

Ke, A.,Ding, F.,Batchelor, J.D.,Doudna, J.A.
Structural roles of monovalent cations in the HDV ribozyme.
Structure, 15:281-287, 2007

PubMed Abstract: The hepatitis delta virus (HDV) ribozyme catalyzes viral RNA self-cleavage through general acid-base chemistry in which an active-site cytidine and at least one metal ion are involved. Monovalent metal ions support slow catalysis and were proposed to substitute for structural, but not catalytic, divalent metal ions in the RNA. To investigate the role of monovalent cations in ribozyme structure and function, we determined the crystal structure of the precursor HDV ribozyme in the presence of thallium ions (Tl(+)). Two Tl(+) ions can occupy a previously observed divalent metal ion hexahydrate-binding site located near the scissile phosphate, but are easily competed away by cobalt hexammine, a magnesium hexahydrate mimic and potent reaction inhibitor. Intriguingly, a third Tl(+) ion forms direct inner-sphere contacts with the ribose 2'-OH nucleophile and the pro-S(p) scissile phosphate oxygen. We discuss possible structural and catalytic implications of monovalent cation binding for the HDV ribozyme mechanism.

PubMed: 17355864
DOI: 10.1016/j.str.2007.01.017

Experimental method

X-RAY DIFFRACTION (2.9 Å)