5izo: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:


==Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site==
==Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site==
<StructureSection load='5izo' size='340' side='right' caption='[[5izo]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='5izo' size='340' side='right'caption='[[5izo]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5izo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IZO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IZO FirstGlance]. <br>
<table><tr><td colspan='2'>[[5izo]] 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=5IZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IZO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ipp|5ipp]], [[5iuf|5iuf]], [[5j2z|5j2z]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [http://pdbe.org/5izo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [http://www.ebi.ac.uk/pdbsum/5izo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</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=5izo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5izo OCA], [https://pdbe.org/5izo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5izo RCSB], [https://www.ebi.ac.uk/pdbsum/5izo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5izo ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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 .
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.


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>
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>
Line 21: Line 21:


==See Also==
==See Also==
*[[Ribonuclease|Ribonuclease]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Malhotra, A]]
[[Category: Bacillus subtilis subsp. subtilis str. 168]]
[[Category: Nelersa, C M]]
[[Category: Large Structures]]
[[Category: Schmier, B J]]
[[Category: Malhotra A]]
[[Category: Abortive transcript]]
[[Category: Nelersa CM]]
[[Category: B. subtili]]
[[Category: Schmier BJ]]
[[Category: Exonuclease]]
[[Category: Hydrolase]]
[[Category: Nanorna]]
[[Category: Pap phosphatase]]
[[Category: Rna degradation]]
[[Category: Rnase]]

Latest revision as of 13:40, 6 September 2023

Bacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active siteBacillus NanoRNase A (H103A) + 2 divalent cations + PO4 at the active site

Structural highlights

5izo 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:,
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.

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

5izo, resolution 1.95Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=5izo&oldid=3870736"