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| | <StructureSection load='5iw4' size='340' side='right'caption='[[5iw4]], [[Resolution|resolution]] 2.60Å' scene=''> | | <StructureSection load='5iw4' size='340' side='right'caption='[[5iw4]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5iw4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_b354 Escherichia coli b354]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IW4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IW4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5iw4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B354 Escherichia coli B354]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IW4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5iw5|5iw5]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nudC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550677 Escherichia coli B354])</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=5iw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iw4 OCA], [https://pdbe.org/5iw4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iw4 RCSB], [https://www.ebi.ac.uk/pdbsum/5iw4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iw4 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_diphosphatase NAD(+) diphosphatase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5iw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iw4 OCA], [http://pdbe.org/5iw4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iw4 RCSB], [http://www.ebi.ac.uk/pdbsum/5iw4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iw4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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: Escherichia coli b354]] | + | [[Category: Escherichia coli B354]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Du, J]] | + | [[Category: Du J]] |
| - | [[Category: Li, S]] | + | [[Category: Li S]] |
| - | [[Category: Patel, D J]] | + | [[Category: Patel DJ]] |
| - | [[Category: Capping]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Nad]]
| + | |
| - | [[Category: Nudix]]
| + | |
| - | [[Category: Rna]]
| + | |
| Structural highlights
Function
NUDC_ECOLI
Publication Abstract from PubMed
RNA capping and decapping are thought to be distinctive features of eukaryotes. The redox cofactor NAD was recently discovered to be attached to small regulatory RNAs in bacteria in a cap-like manner, and Nudix hydrolase NudC was found to act as a NAD-decapping enzyme in vitro and in vivo. Here, crystal structures of Escherichia coli NudC in complex with substrate NAD and with cleavage product NMN reveal the catalytic residues lining the binding pocket and principles underlying molecular recognition of substrate and product. Biochemical mutation analysis identifies the conserved Nudix motif as the catalytic center of the enzyme, which needs to be homodimeric, as the catalytic pocket is composed of amino acids from both monomers. NudC is single-strand specific and has a purine preference for the 5'-terminal nucleotide. The enzyme strongly prefers NAD-linked RNA (NAD-RNA) over NAD and binds to a diverse set of cellular RNAs in an unspecific manner.
Structure and function of the bacterial decapping enzyme NudC.,Hofer K, Li S, Abele F, Frindert J, Schlotthauer J, Grawenhoff J, Du J, Patel DJ, Jaschke A Nat Chem Biol. 2016 Sep;12(9):730-4. doi: 10.1038/nchembio.2132. Epub 2016 Jul, 18. PMID:27428510[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hofer K, Li S, Abele F, Frindert J, Schlotthauer J, Grawenhoff J, Du J, Patel DJ, Jaschke A. Structure and function of the bacterial decapping enzyme NudC. Nat Chem Biol. 2016 Sep;12(9):730-4. doi: 10.1038/nchembio.2132. Epub 2016 Jul, 18. PMID:27428510 doi:http://dx.doi.org/10.1038/nchembio.2132
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