2NUG

Crystal structure of RNase III from Aquifex aeolicus complexed with ds-RNA at 1.7-Angstrom Resolution

Summary for 2NUG

• Entry DOI: 10.2210/pdb2nug/pdb
• Related: 1RC7 1YYO 1YYW 1YZ9 2EZ6 2NUE 2NUF
• Descriptor: 5'-R(P*AP*AP*GP*GP*UP*CP*AP*UP*UP*CP*G)-3', 5'-R(P*AP*GP*UP*GP*GP*CP*CP*UP*UP*GP*C)-3', Ribonuclease III, ... (5 entities in total)
• Functional Keywords: ribonuclease iii, dsrna, rna interference, endonucleolytic cleavage, hydrolase-rna complex, hydrolase/rna
• Biological source: Aquifex aeolicus
• Cellular location: Cytoplasm : O67082
• Total number of polymer chains: 6
• Total formula weight: 66769.06

Authors

Gan, J.H.,Shaw, G.,Tropea, J.E.,Waugh, D.S.,Court, D.L.,Ji, X. (deposition date: 2006-11-09, release date: 2007-11-20, Last modification date: 2023-08-30)

Primary citation

Gan, J.,Shaw, G.,Tropea, J.E.,Waugh, D.S.,Court, D.L.,Ji, X.
A stepwise model for double-stranded RNA processing by ribonuclease III.
Mol.Microbiol., 67:143-154, 2007

PubMed Abstract: RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a valuable model system for the family. Previously, we have shown that RNase III uses two catalytic sites to create the 2-nucleotide (nt) 3' overhangs in its products. Here, we present three crystal structures of RNase III in complex with double-stranded RNA, demonstrating how Mg(2+) is essential for the formation of a catalytically competent protein-RNA complex, how the use of two Mg(2+) ions can drive the hydrolysis of each phosphodiester bond, and how conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover, we have modelled a protein-substrate complex and a protein-reaction intermediate (transition state) complex on the basis of the crystal structures. Together, the crystal structures and the models suggest a stepwise mechanism for RNase III to execute the phosphoryl transfer reaction.

PubMed: 18047582
DOI: 10.1111/j.1365-2958.2007.06032.x

Experimental method

X-RAY DIFFRACTION (1.7 Å)