Structural insights into RNA unwinding and degradation by RNase R

RNase R is a conserved exoribonuclease in the RNase II family that primarily participates in RNA decay in all kingdoms of life. RNase R degrades duplex RNA with a 3' overhang, suggesting that it has RNA unwinding activity in addition to its 3'-to-5' exoribonuclease activity. However,...

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Bibliographic Details
Published in:Nucleic acids research 2017-11, Vol.45 (20), p.12015-12024
Main Authors: Chu, Lee-Ya, Hsieh, Tung-Ju, Golzarroshan, Bagher, Chen, Yi-Ping, Agrawal, Sashank, Yuan, Hanna S
Format: Article
Language:English
Subjects:
Biocatalysis
Catalytic Domain
Crystallography, X-Ray
Escherichia coli Proteins - chemistry
Escherichia coli Proteins - genetics
Escherichia coli Proteins - metabolism
Exoribonucleases - chemistry
Exoribonucleases - genetics
Exoribonucleases - metabolism
Kinetics
Models, Molecular
Mutation
Nucleic Acid Conformation
Protein Binding
Protein Domains
RNA Cleavage
RNA Stability
RNA, Bacterial - chemistry
RNA, Bacterial - genetics
RNA, Bacterial - metabolism
Structural Biology
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Summary:RNase R is a conserved exoribonuclease in the RNase II family that primarily participates in RNA decay in all kingdoms of life. RNase R degrades duplex RNA with a 3' overhang, suggesting that it has RNA unwinding activity in addition to its 3'-to-5' exoribonuclease activity. However, how RNase R coordinates RNA binding with unwinding to degrade RNA remains elusive. Here, we report the crystal structure of a truncated form of Escherichia coli RNase R (residues 87-725) at a resolution of 1.85 Å. Structural comparisons with other RNase II family proteins reveal two open RNA-binding channels in RNase R and suggest a tri-helix 'wedge' region in the RNB domain that may induce RNA unwinding. We constructed two tri-helix wedge mutants and they indeed lost their RNA unwinding but not RNA binding or degrading activities. Our results suggest that the duplex RNA with an overhang is bound in the two RNA-binding channels in RNase R. The 3' overhang is threaded into the active site and the duplex RNA is unwound upon reaching the wedge region during RNA degradation. Thus, RNase R is a proficient enzyme, capable of concurrently binding, unwinding and degrading structured RNA in a highly processive manner during RNA decay.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx880