5j21

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==Structure of Bacillus NanoRNase A (WT)==
==Structure of Bacillus NanoRNase A (WT)==
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<StructureSection load='5j21' size='340' side='right' caption='[[5j21]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='5j21' size='340' side='right'caption='[[5j21]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5j21]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J21 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J21 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5j21]] 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=5J21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J21 FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ipp|5ipp]], [[5iuf|5iuf]], [[5izo|5izo]], [[3dev|3dev]]</td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5j21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j21 OCA], [https://pdbe.org/5j21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j21 RCSB], [https://www.ebi.ac.uk/pdbsum/5j21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j21 ProSAT]</span></td></tr>
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<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=5j21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j21 OCA], [http://pdbe.org/5j21 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j21 RCSB], [http://www.ebi.ac.uk/pdbsum/5j21 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j21 ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[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>
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[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;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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The final step in RNA degradation is the hydrolysis of RNA fragments five nucleotides or less in length (nanoRNA) to mononucleotides. In Escherichia coli this step is carried out by oligoribonuclease (Orn), a DEDD-family exoribonuclease that is conserved throughout eukaryotes. However, many bacteria lack Orn homologs, and an unrelated DHH-family phosphoesterase, NrnA, has recently been identified as one of the enzymes responsible for nanoRNA degradation in Bacillus subtilis. To understand its mechanism of action, B. subtilis NrnA was purified and crystallized at room temperature using the hanging-drop vapor-diffusion method with PEG 4000, PEG 3350 or PEG MME 2000 as precipitant. The crystals belonged to the primitive monoclinic space group P2(1), with unit-cell parameters a = 50.62, b = 121.3, c = 123.4 A, alpha = 90, beta = 91.31, gamma = 90 degrees .
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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.
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Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation.,Nelersa CM, Schmier BJ, Malhotra A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1235-8., doi: 10.1107/S1744309111026509. Epub 2011 Sep 29. PMID:22102036<ref>PMID:22102036</ref>
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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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
==See Also==
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*[[Ribonuclease|Ribonuclease]]
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Malhotra, A]]
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[[Category: Bacillus subtilis subsp. subtilis str. 168]]
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[[Category: Nelersa, C M]]
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[[Category: Large Structures]]
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[[Category: Schmier, B J]]
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[[Category: Malhotra A]]
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[[Category: Abortive transcript]]
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[[Category: Nelersa CM]]
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[[Category: B. subtili]]
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[[Category: Schmier BJ]]
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[[Category: Exonuclease]]
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[[Category: Hydrolase]]
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[[Category: Nanorna]]
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[[Category: Pap phosphatase]]
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[[Category: Rna degradation]]
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[[Category: Rnase]]
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Current revision

Structure of Bacillus NanoRNase A (WT)

PDB ID 5j21

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