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| | <StructureSection load='6wug' size='340' side='right'caption='[[6wug]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='6wug' size='340' side='right'caption='[[6wug]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6wug]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WUG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WUG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6wug]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WUG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UBG:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl+(2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl+dihydrogen+diphosphate+(non-preferred+name)'>UBG</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]] 1.9Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UBG:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl+(2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl+dihydrogen+diphosphate+(non-preferred+name)'>UBG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">din1, SPAC19D5.06c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=6wug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wug OCA], [https://pdbe.org/6wug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wug RCSB], [https://www.ebi.ac.uk/pdbsum/6wug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wug ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6wug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wug OCA], [http://pdbe.org/6wug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wug RCSB], [http://www.ebi.ac.uk/pdbsum/6wug PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wug ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DXO_SCHPO DXO_SCHPO]] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping and pyrophosphohydrolase activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA (By similarity). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates. Stimulates exoribonuclease activity of rat1, allowing it to degrade RNAs with stable secondary structure more effectively.<ref>PMID:19194460</ref> | + | [https://www.uniprot.org/uniprot/DXO_SCHPO DXO_SCHPO] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping and pyrophosphohydrolase activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA (By similarity). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates. Stimulates exoribonuclease activity of rat1, allowing it to degrade RNAs with stable secondary structure more effectively.<ref>PMID:19194460</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cbs 356]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Doamekpor, S K]] | + | [[Category: Schizosaccharomyces pombe]] |
| - | [[Category: Tong, L]] | + | [[Category: Doamekpor SK]] |
| - | [[Category: 3'-fadp]] | + | [[Category: Tong L]] |
| - | [[Category: Cap]]
| + | |
| - | [[Category: Decapping]]
| + | |
| - | [[Category: Fad]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Rai1]]
| + | |
| - | [[Category: Rna]]
| + | |
| Structural highlights
Function
DXO_SCHPO Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping and pyrophosphohydrolase activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA (By similarity). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates. Stimulates exoribonuclease activity of rat1, allowing it to degrade RNAs with stable secondary structure more effectively.[1]
Publication Abstract from PubMed
In eukaryotes, the DXO/Rai1 enzymes can eliminate most of the incomplete and non-canonical NAD caps through their decapping, deNADding and pyrophosphohydrolase activities. Here, we report that these enzymes can also remove FAD and dephospho-CoA (dpCoA) non-canonical caps from RNA, and we have named these activities deFADding and deCoAping. The crystal structures of mammalian DXO with 3'-FADP or CoA and fission yeast Rai1 with 3'-FADP provide elegant insight to these activities. FAD and CoA are accommodated in the DXO/Rai1 active site by adopting folded conformations. The flavin of FAD and the pantetheine group of CoA contact the same region at the bottom of the active site tunnel, which undergoes conformational changes to accommodate the different cap moieties. We have developed FAD-capQ to detect and quantify FAD-capped RNAs and determined that FAD caps are present on short RNAs (with less than approximately 200 nucleotides) in human cells and that these RNAs are stabilized in the absence of DXO.
DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs.,Doamekpor SK, Grudzien-Nogalska E, Mlynarska-Cieslak A, Kowalska J, Kiledjian M, Tong L Nucleic Acids Res. 2020 May 6. pii: 5831185. doi: 10.1093/nar/gkaa297. PMID:32374864[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Xiang S, Cooper-Morgan A, Jiao X, Kiledjian M, Manley JL, Tong L. Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1. Nature. 2009 Apr 9;458(7239):784-8. Epub 2009 Feb 4. PMID:19194460 doi:http://dx.doi.org/10.1038/nature07731
- ↑ Doamekpor SK, Grudzien-Nogalska E, Mlynarska-Cieslak A, Kowalska J, Kiledjian M, Tong L. DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs. Nucleic Acids Res. 2020 May 6. pii: 5831185. doi: 10.1093/nar/gkaa297. PMID:32374864 doi:http://dx.doi.org/10.1093/nar/gkaa297
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