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| | ==High resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes== | | ==High resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes== |
| - | <StructureSection load='3o90' size='340' side='right' caption='[[3o90]], [[Resolution|resolution]] 1.94Å' scene=''> | + | <StructureSection load='3o90' size='340' side='right'caption='[[3o90]], [[Resolution|resolution]] 1.94Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3o90]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O90 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O90 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3o90]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O90 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O90 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.94Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3o91|3o91]], [[3o92|3o92]], [[3o93|3o93]], [[3o94|3o94]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SP_1583 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</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=3o90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o90 OCA], [https://pdbe.org/3o90 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o90 RCSB], [https://www.ebi.ac.uk/pdbsum/3o90 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o90 ProSAT]</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=3o90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o90 OCA], [http://pdbe.org/3o90 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o90 RCSB], [http://www.ebi.ac.uk/pdbsum/3o90 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3o90 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A0A0H2UR34_STRPN A0A0H2UR34_STRPN] |
| - | Nicotinamidases are salvage enzymes that convert nicotinamide to nicotinic acid. These enzymes are essential for the recycling of nicotinamide into NAD(+) in most prokaryotes and most single-cell and multicellular eukaryotes, but not in mammals. The significance of these enzymes for nicotinamide salvage and for NAD(+) homeostasis has stimulated interest in nicotinamidases as possible antibiotic targets. Nicotinamidases are also regulators of intracellular nicotinamide concentrations, thereby regulating signaling of downstream NAD(+)-consuming enzymes, such as the NAD(+)-dependent deacetylases (sirtuins). Here, we report several high-resolution crystal structures of the nicotinamidase from Streptococcus pneumoniae (SpNic) in unliganded and ligand-bound forms. The structure of the C136S mutant in complex with nicotinamide provides details about substrate binding, while a trapped nicotinoyl thioester in a complex with SpNic reveals the structure of the proposed thioester reaction intermediate. Examination of the active site of SpNic reveals several important features, including a metal ion that coordinates the substrate and the catalytically relevant water molecule and an oxyanion hole that both orients the substrate and offsets the negative charge that builds up during catalysis. Structures of this enzyme with bound nicotinaldehyde inhibitors elucidate the mechanism of inhibition and provide further details about the catalytic mechanism. In addition, we provide a biochemical analysis of the identity and role of the metal ion that orients the ligand in the active site and activates the water molecule responsible for hydrolysis of the substrate. These data provide structural evidence of several proposed reaction intermediates and allow for a more complete understanding of the catalytic mechanism of this enzyme.
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| - | High-resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into the catalytic mechanism and inhibition by aldehydes .,French JB, Cen Y, Sauve AA, Ealick SE Biochemistry. 2010 Oct 12;49(40):8803-12. Epub 2010 Sep 20. PMID:20853856<ref>PMID:20853856</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3o90" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Strpn]] | + | [[Category: Large Structures]] |
| - | [[Category: Cen, Y]] | + | [[Category: Streptococcus pneumoniae TIGR4]] |
| - | [[Category: Ealick, S E]] | + | [[Category: Cen Y]] |
| - | [[Category: French, J B]] | + | [[Category: Ealick SE]] |
| - | [[Category: Sauve, A A]] | + | [[Category: French JB]] |
| - | [[Category: Hydrolase]] | + | [[Category: Sauve AA]] |
| - | [[Category: Nicotinamidase]]
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