Book of Abstracts: Albany 2003

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Conversation 13
Abstract Book
June 17-21 2003

Substrate Specificity in RNase H Family of Enzymes: Modeling the Interaction of (DNA:RNA) Hybrid With RNase H

RNase H enzyme degrades RNA in a DNA:RNA hybrid duplex. The two major families of RNase H classified as type I and II share a common structural fold despite the absence of sequence homology and specificity for interaction with the substrate. Although E.coli type I RNase H is the most thoroughly studied RNase H enzyme, substrate recognition mechanism is still not completely understood. Knowledge of such information is crucial for better understanding of the structural basis of enzyme action as these would facilitate the design of oligonucleotides that will elicit RNase H action, critical in the antisense approach for gene regulation. A recent study from this laboratory has provided some new information towards substrate recognition interactions in type I E.coli RNase H. With a view to enlarge the scope of this study so as to cover the entire RNase H family, we have examined over 50 sequences from various organisms. Multiple sequence alignment along with secondary structural assignment based on E.coli RNase H reveals a generalized scheme for substrate recognition interaction. It is found that despite large variations (20-75%) in the chain lengths, most of the substrate interacting residues are conserved, with the likelihood of them taking up the same tertiary architecture. This is confirmed by homology modeling of RNase H containing the least (117 AA) and the highest (293 AA) sequence lengths. It is found that the residues Cys13, Asn16, Asn 44,Trp 81 and Lys122 seem to be the most critical in substrate recognition in type I RNase H in agreement with mutational studies. Similar investigations have been performed in relation to RNase H II and RT RNase H and the results are compared.

G. Goldsmith
S. Raja
N. Yathindra*

Department of Crystallography and Biophysics
University of Madras
Guindy Campus
Chennai-600 025, India
Fax: 91 44 2 230 0122

References and Footnotes
  1. Premraj, B. J., Raja, S. and Yathindra, N., Biophysical Chemistry 95 , 253-272 (2002).