5ipp

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

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Categories: Bacillus subtilis subsp. subtilis str. 168 | Large Structures | Malhotra A | Nelersa CM | Schmier BJ

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 ==Structure of Bacillus NanoRNase A active site mutant bound to a mononucleotide==
-<StructureSection load='5ipp' size='340' side='right' caption='[[5ipp]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='5ipp' size='340' side='right'caption='[[5ipp]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ipp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IPP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ipp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IPP FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5iuf|5iuf]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nrnA, ytqI, BSU29250 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3'(2'),5'-bisphosphate_nucleotidase 3'(2'),5'-bisphosphate nucleotidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.7 3.1.3.7] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ipp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipp OCA], [https://pdbe.org/5ipp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ipp RCSB], [https://www.ebi.ac.uk/pdbsum/5ipp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipp ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ipp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ipp OCA], [http://pdbe.org/5ipp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ipp RCSB], [http://www.ebi.ac.uk/pdbsum/5ipp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ipp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NRNA_BACSU 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.<ref>PMID:17586819</ref> <ref>PMID:21087930</ref> <ref>PMID:22114320</ref>
+[https://www.uniprot.org/uniprot/NRNA_BACSU 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.<ref>PMID:17586819</ref> <ref>PMID:21087930</ref> <ref>PMID:22114320</ref>
-<div style="background-color:#fffaf0;">
-== 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' --&gt; 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' --&gt; 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' --&gt; 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<ref>PMID:28894100</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5ipp" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ribonuclease|Ribonuclease]]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-[[Category: Malhotra, A]]
+[[Category: Large Structures]]
-[[Category: Nelersa, C M]]
+[[Category: Malhotra A]]
-[[Category: Schmier, B J]]
+[[Category: Nelersa CM]]
-[[Category: Abortive transcript]]
+[[Category: Schmier BJ]]
-[[Category: B. subitli]]
-[[Category: Exonuclease]]
-[[Category: Hydrolase]]
-[[Category: Nanorna]]
-[[Category: Pap phosphatase]]
-[[Category: Rna degradation]]
-[[Category: Rnase]]
-[[Category: X-ray]]

5ipp

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

Structural highlights

Function

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References

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