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| | ==The crystal structure of pyrazinamidase/nicotinamidase from streptococcus mutans UA159== | | ==The crystal structure of pyrazinamidase/nicotinamidase from streptococcus mutans UA159== |
| - | <StructureSection load='3s2s' size='340' side='right' caption='[[3s2s]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='3s2s' size='340' side='right'caption='[[3s2s]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3s2s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S2S FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3s2s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S2S FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAD:CACODYLIC+ACID'>CAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pncA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1309 Streptococcus mutans])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAD:CACODYLIC+ACID'>CAD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nicotinamidase Nicotinamidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.19 3.5.1.19] </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=3s2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2s OCA], [https://pdbe.org/3s2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s2s RCSB], [https://www.ebi.ac.uk/pdbsum/3s2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s2s ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s2s RCSB], [http://www.ebi.ac.uk/pdbsum/3s2s PDBsum]</span></td></tr> | + | </table> |
| - | <table> | + | == Function == |
| - | <div style="background-color:#fffaf0;">
| + | [https://www.uniprot.org/uniprot/Q8DSG2_STRMU Q8DSG2_STRMU] |
| - | == Publication Abstract from PubMed == | + | |
| - | The crystal structures of two proteins, a putative pyrazinamidase/nicotinamidase from the dental pathogen Streptococcus mutans (SmPncA) and the human caspase-6 (Casp6), were solved by de novo arsenic single-wavelength anomalous diffraction (As-SAD) phasing method. Arsenic (As), an uncommonly used element in SAD phasing, was covalently introduced into proteins by cacodylic acid, the buffering agent in the crystallization reservoirs. In SmPncA, the only cysteine was bound to dimethylarsinoyl, which is a pentavalent arsenic group (As (V)). This arsenic atom and a protein-bound zinc atom both generated anomalous signals. The predominant contribution, however, was from the As anomalous signals, which were sufficient to phase the SmPncA structure alone. In Casp6, four cysteines were found to bind cacodyl, a trivalent arsenic group (As (III)), in the presence of the reducing agent, dithiothreitol (DTT), and arsenic atoms were the only anomalous scatterers for SAD phasing. Analyses and discussion of these two As-SAD phasing examples and comparison of As with other traditional heavy atoms that generate anomalous signals, together with a few arsenic-based de novo phasing cases reported previously strongly suggest that As is an ideal anomalous scatterer for SAD phasing in protein crystallography.
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| - | Get phases from arsenic anomalous scattering: de novo SAD phasing of two protein structures crystallized in cacodylate buffer.,Liu X, Zhang H, Wang XJ, Li LF, Su XD PLoS One. 2011;6(9):e24227. Epub 2011 Sep 2. PMID:21912678<ref>PMID:21912678</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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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Nicotinamidase]] | + | [[Category: Large Structures]] |
| | [[Category: Streptococcus mutans]] | | [[Category: Streptococcus mutans]] |
| - | [[Category: Liu, X.]] | + | [[Category: Liu X]] |
| - | [[Category: Su, X D.]] | + | [[Category: Su X-D]] |
| - | [[Category: Zhang, H.]] | + | [[Category: Zhang H]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Pyrazinamidase/nicotinamidase]]
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