Sandbox Reserved 194

This Sandbox is Reserved from Feb 02, 2011, through Jul 31, 2011 for use by the Biochemistry II class at the Butler University at Indianapolis, IN USA taught by R. Jeremy Johnson. This reservation includes Sandbox Reserved 191 through Sandbox Reserved 200.

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Ribonuclease A Substrate Binding

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File:1RTA zoom.png

Thymidylic acid tetramer complexed with ribonuclease A

To determine the structural characteristics of RNA substrate binding to RNase A, X-ray crystallography was used to image inhibitory DNA tetramers bound to the enzyme. DNA lacks the 2′OH essential to RNA cleavage, making the complex more conducive to crystallography. In previous studies, the RNase A - thymidylic acid tetramer (d(pT)4) complex has provided information into the specificity of the binding pocket subunits, B0, B1, B2 and B3.

Further binding pocket characterization was accomplished using the oglionucleotide d(ApTpApApG). While binding of other nucleobases to the B2 and B3 sites is possible, the imaging of this complex elucidated the preference for adenosine bases. RNase A establishes pi stacking between His119 and A3 in addition to hydrogen bonding between Asn71-A3, Gln69-A3 and Gln69-A4.

File:1RCN zoom.png

ApTpApApG complexed with ribonuclease A