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| | <StructureSection load='7e44' size='340' side='right'caption='[[7e44]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='7e44' size='340' side='right'caption='[[7e44]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7e44]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecobd Ecobd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E44 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E44 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7e44]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7E44 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7E44 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COD:DEPHOSPHO+COENZYME+A'>COD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nudC, ECBD_4036, HO396_19860 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=469008 ECOBD])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COD:DEPHOSPHO+COENZYME+A'>COD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/NAD(+)_diphosphatase NAD(+) diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.22 3.6.1.22] </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=7e44 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e44 OCA], [https://pdbe.org/7e44 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e44 RCSB], [https://www.ebi.ac.uk/pdbsum/7e44 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e44 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=7e44 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7e44 OCA], [https://pdbe.org/7e44 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7e44 RCSB], [https://www.ebi.ac.uk/pdbsum/7e44 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7e44 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/A0A140SS78_ECOBD A0A140SS78_ECOBD]] mRNA decapping enzyme that specifically removes the nicotinamide adenine dinucleotide (NAD) cap from a subset of mRNAs by hydrolyzing the diphosphate linkage to produce nicotinamide mononucleotide (NMN) and 5' monophosphate mRNA. The NAD-cap is present at the 5'-end of some mRNAs and stabilizes RNA against 5'-processing. Has preference for mRNAs with a 5'-end purine. Catalyzes the hydrolysis of a broad range of dinucleotide pyrophosphates.[HAMAP-Rule:MF_00297]
| + | [https://www.uniprot.org/uniprot/NUDC_ECOLI NUDC_ECOLI] |
| | <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: Ecobd]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Guan, Z Y]] | + | [[Category: Guan ZY]] |
| - | [[Category: Yin, P]] | + | [[Category: Yin P]] |
| - | [[Category: Zhang, D L]] | + | [[Category: Zhang DL]] |
| - | [[Category: Zhou, W]] | + | [[Category: Zhou W]] |
| - | [[Category: Dpcoa]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nudc]]
| + | |
| Structural highlights
Function
NUDC_ECOLI
Publication Abstract from PubMed
Various kinds of cap structures, such as m(7)G, triphosphate groups, NAD and dpCoA, protect the 5' terminus of RNA. The cap structures bond covalently to RNA and affect its stability, translation, and transport. The removal of the caps is mainly executed by Nudix hydrolase family proteins, including Dcp2, RppH and NudC. Numerous efforts have been made to elucidate the mechanism underlying the removal of m(7)G, triphosphate group, and NAD caps. In contrast, few studies related to the cleavage of the RNA dpCoA cap have been conducted. Here, we report the hydrolytic activity of Escherichia coli NudC towards dpCoA and dpCoA-capped RNA in vitro. We also determined the crystal structure of dimeric NudC in complex with dpCoA at 2.0 A resolution. Structural analysis revealed that dpCoA is recognized and hydrolysed in a manner similar to NAD. In addition, NudC may also remove other dinucleotide derivative caps of RNA, which comprise the AMP moieties. NudC homologs in Saccharomyces cerevisiae and Arabidopsis thaliana exhibited similar dpCoA decapping (deCoAping) activity. These results together indicate a conserved mechanism underpinning the hydrolysis of dpCoA-capped RNA in both prokaryotes and eukaryotes.
Structural insights into dpCoA-RNA decapping by NudC.,Zhou W, Guan Z, Zhao F, Ye Y, Yang F, Yin P, Zhang D RNA Biol. 2021 Jun 18:1-10. doi: 10.1080/15476286.2021.1936837. PMID:34074215[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Zhou W, Guan Z, Zhao F, Ye Y, Yang F, Yin P, Zhang D. Structural insights into dpCoA-RNA decapping by NudC. RNA Biol. 2021 Jun 18:1-10. doi: 10.1080/15476286.2021.1936837. PMID:34074215 doi:http://dx.doi.org/10.1080/15476286.2021.1936837
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