5IPP

Structure of Bacillus NanoRNase A active site mutant bound to a mononucleotide

Summary for 5IPP

• Entry DOI: 10.2210/pdb5ipp/pdb
• Related: 5IUF
• Descriptor: Bifunctional oligoribonuclease and PAP phosphatase NrnA, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: nanorna, rna degradation, exonuclease, rnase, abortive transcripts, pap phosphatase, hydrolase
• Biological source: Bacillus subtilis (strain 168)
• Total number of polymer chains: 4
• Total formula weight: 150361.61

Authors

Schmier, B.J.,Nelersa, C.M.,Malhotra, A. (deposition date: 2016-03-09, release date: 2017-08-02, Last modification date: 2024-03-06)

Primary citation

Schmier, B.J.,Nelersa, C.M.,Malhotra, A.
Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.
Sci Rep, 7:11085-11085, 2017

PubMed Abstract: NanoRNAs are RNA fragments 2 to 5 nucleotides in length that are generated as byproducts of RNA degradation and abortive transcription initiation. Cells have specialized enzymes to degrade nanoRNAs, such as the DHH phosphoesterase family member NanoRNase A (NrnA). This enzyme was originally identified as a 3' → 5' exonuclease, but we show here that NrnA is bidirectional, degrading 2-5 nucleotide long RNA oligomers from the 3' end, and longer RNA substrates from the 5' end. The crystal structure of Bacillus subtilis NrnA reveals a dynamic bi-lobal architecture, with the catalytic N-terminal DHH domain linked to the substrate binding C-terminal DHHA1 domain via an extended linker. Whereas this arrangement is similar to the structure of RecJ, a 5' → 3' DHH family DNase and other DHH family nanoRNases, Bacillus NrnA has gained an extended substrate-binding patch that we posit is responsible for its 3' → 5' activity.

PubMed: 28894100
DOI: 10.1038/s41598-017-09403-x

Experimental method

X-RAY DIFFRACTION (1.95 Å)