5iuf

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Bacillus NanoRNase A active site mutant bound to pAp

Structural highlights

5iuf is a 4 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:A3P
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NRNA_BACSU Bifunctional enzyme which has both oligoribonuclease and pAp-phosphatase activities. Degrades RNA and DNA oligonucleotides with a length of 5 nucleotides and shorter, with a preference for 3-mers. Directionality is controversial; shown to degrade 5-mers and less in a 3' to 5' direction (PubMed:17586819), and 11-mers in a 5' to 3' direction (PubMed:21087930). Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP.[1] [2] [3]

Publication Abstract from PubMed

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.

Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.,Schmier BJ, Nelersa CM, Malhotra A Sci Rep. 2017 Sep 11;7(1):11085. doi: 10.1038/s41598-017-09403-x. PMID:28894100[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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See Also

References

  1. ↑ Mechold U, Fang G, Ngo S, Ogryzko V, Danchin A. YtqI from Bacillus subtilis has both oligoribonuclease and pAp-phosphatase activity. Nucleic Acids Res. 2007;35(13):4552-61. Epub 2007 Jun 22. PMID:17586819 doi:http://dx.doi.org/10.1093/nar/gkm462
  2. ↑ Wakamatsu T, Kim K, Uemura Y, Nakagawa N, Kuramitsu S, Masui R. Role of RecJ-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation. J Biol Chem. 2011 Jan 28;286(4):2807-16. doi: 10.1074/jbc.M110.161596. Epub 2010 , Nov 18. PMID:21087930 doi:http://dx.doi.org/10.1074/jbc.M110.161596
  3. ↑ Postic G, Danchin A, Mechold U. Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae. RNA. 2012 Jan;18(1):155-65. doi: 10.1261/rna.029132.111. Epub 2011 Nov 23. PMID:22114320 doi:http://dx.doi.org/10.1261/rna.029132.111
  4. ↑ Schmier BJ, Nelersa CM, Malhotra A. Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA. Sci Rep. 2017 Sep 11;7(1):11085. doi: 10.1038/s41598-017-09403-x. PMID:28894100 doi:http://dx.doi.org/10.1038/s41598-017-09403-x

Contents


PDB ID 5iuf

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OCA

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