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| | <StructureSection load='6n6h' size='340' side='right'caption='[[6n6h]], [[Resolution|resolution]] 1.76Å' scene=''> | | <StructureSection load='6n6h' size='340' side='right'caption='[[6n6h]], [[Resolution|resolution]] 1.76Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6n6h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6n6h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N6H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.757Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">orn ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=6n6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6h OCA], [http://pdbe.org/6n6h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6h RCSB], [http://www.ebi.ac.uk/pdbsum/6n6h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6h 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=6n6h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6h OCA], [https://pdbe.org/6n6h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n6h RCSB], [https://www.ebi.ac.uk/pdbsum/6n6h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6h ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0H6V4D7_VIBCL A0A0H6V4D7_VIBCL]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045][SAAS:SAAS00859727] | + | [https://www.uniprot.org/uniprot/ORN_VIBCH ORN_VIBCH] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6n6h" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6n6h" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Exonuclease 3D structures|Exonuclease 3D structures]] |
| | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillo virgola del koch trevisan 1884]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lormand, J D]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Sondermann, H]] | + | [[Category: Vibrio cholerae]] |
| - | [[Category: 3'-5' exoribonuclease]] | + | [[Category: Lormand JD]] |
| - | [[Category: Rna binding protein]] | + | [[Category: Sondermann H]] |
| - | [[Category: Rna binding protein-rna complex]]
| + | |
| Structural highlights
Function
ORN_VIBCH 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045]
Publication Abstract from PubMed
Degradation of RNA polymers, an ubiquitous process in all cells, is catalyzed by specific subsets of endo- and exoribonucleases that together recycle RNA fragments into nucleotide monophosphate. In gamma-proteobacteria, 3-'5' exoribonucleases comprise up to eight distinct enzymes. Among them, Oligoribonuclease (Orn) is unique as its activity is required for clearing short RNA fragments, which is important for cellular fitness. However, the molecular basis of Orn's unique cellular function remained unclear. Here, we show that Orn exhibits exquisite substrate preference for diribonucleotides. Crystal structures of substrate-bound Orn reveal an active site optimized for diribonucleotides. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, Orn is the one and only diribonucleotidase that completes the terminal step of RNA degradation. Together, our studies indicate RNA degradation as a step-wise process with a dedicated enzyme for the clearance of a specific intermediate pool, diribonucleotides, that affects cellular physiology and viability.
A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.,Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT Elife. 2019 Jun 21;8. pii: 46313. doi: 10.7554/eLife.46313. PMID:31225796[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT. A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation. Elife. 2019 Jun 21;8. pii: 46313. doi: 10.7554/eLife.46313. PMID:31225796 doi:http://dx.doi.org/10.7554/eLife.46313
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