Nuclear magnetic resonance structure of the prohead RNA E-loop hairpin

Steven Harris; Susan J Schroeder

doi:10.1021/bi100393r

Nuclear magnetic resonance structure of the prohead RNA E-loop hairpin

Biochemistry. 2010 Jul 27;49(29):5989-97. doi: 10.1021/bi100393r.

Authors

Steven Harris¹, Susan J Schroeder

Affiliation

¹ Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019, USA.

PMID: 20550192
DOI: 10.1021/bi100393r

Abstract

The Bacillus subtilis phage phi29 packaging motor requires prohead RNA for genome encapsidation. The nuclear magnetic resonance structure of the prohead RNA E-loop hairpin, r(5'AUUGAGUU), is presented and compared to predictions from MC-SYM. The prohead RNA E-loop hairpins contain sequences similar to rRNA hairpins. Comparison of predicted and experimentally determined prohead and ribosomal hairpin structures reveals that sequence similarity is a stronger determinant of hairpin structural similarity than grouping similar types of RNA. All the hairpins contain a U-turn motif but differ in the first noncanonical pair and backbone orientation. These structures provide benchmarks for further improvements in RNA structure predictions from sequence.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bacillus Phages / chemistry
Bacillus Phages / genetics*
Bacillus subtilis / virology*
Base Sequence
Nuclear Magnetic Resonance, Biomolecular
Nucleic Acid Conformation
RNA, Viral / chemistry*

Substances

RNA, Viral

Associated data

PDB/2KVN