Comparative photocross-linking analysis of the tertiary structures of escherichia coli and bacillus subtilis RNase P RNAs

Jiunn Liang Chen, James M. Nolan, Michael E. Harris, Norman R. Pace

Research output: Contribution to journalArticlepeer-review

112 Scopus citations


Bacterial ribonuclease P contains a catalytic RNA subunit that cleaves precursor sequences from the 5' ends of pre-tRNAs. The RNase P RNAs from Bacillus subtilis and Escherichia coli each contain several unique secondary structural elements not present in the other. To understand better how these phylogenetically variable elements affect the global architecture of the ribozyme, photoaffinity cross-linking studies were carried out. Photolysis of photoagents attached at homologous sites in the two RNAs results in nearly identical cross-linking patterns, consistent with the homology of the RNAs and indicating that these RNAs contain a common, core tertiary structure. Distance constraints were used to derive tertiary structure models using a molecular mechanics-based modeling protocol. The resulting superimposition of large sets of equivalent models provides a low resolution (5-10 Å) structure for each RNA. Comparison of these structure models shows that the conserved core helices occupy similar positions in space. Variably present helical elements that may play a role in global structural stability are found at the periphery of the core structure. The P5.1 and P15.1 helical elements, unique to the B. subtilis RNase P RNA, and the P6/16/17 helices, unique to the E. coli RNA, occupy similar positions in the structure models and, therefore, may have analogous structural function.

Original languageEnglish (US)
Pages (from-to)1515-1525
Number of pages11
JournalEMBO Journal
Issue number5
StatePublished - Mar 2 1998
Externally publishedYes


  • Bacillus subtilis
  • Photoaffinity cross-linking
  • RNA structure
  • RNase P
  • Ribozyme

ASJC Scopus subject areas

  • General Neuroscience
  • Molecular Biology
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology


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