3ag5: Difference between revisions

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 ==Crystal Structure of Pantothenate Synthetase from Staphylococcus aureus==
-<StructureSection load='3ag5' size='340' side='right' caption='[[3ag5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='3ag5' size='340' side='right'caption='[[3ag5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ag5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Staa8 Staa8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AG5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AG5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ag5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AG5 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ag6|3ag6]]</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]] 2.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">panC, SAOUHSC_02918 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</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=3ag5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ag5 OCA], [https://pdbe.org/3ag5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ag5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ag5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ag5 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/Pantoate--beta-alanine_ligase Pantoate--beta-alanine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.1 6.3.2.1] </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=3ag5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ag5 OCA], [http://pdbe.org/3ag5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ag5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ag5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ag5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PANC_STAA8 PANC_STAA8]] Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity).
+[https://www.uniprot.org/uniprot/PANC_STAA8 PANC_STAA8] Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ag/3ag5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ag/3ag5_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 19: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ag5 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Pantothenate synthetase (PS, EC 6.3.2.1) is the last enzyme in the pantothenate biosynthesis pathway, a metabolic pathway identified as a potential target for new antimicrobials. PS catalyzes the ATP-dependent condensation of pantoate and beta-alanine to form pantothenate. Here we report the overexpression, purification, enzyme assay, and tertiary structure of PS from Staphylococcus aureus. PS activity was experimentally confirmed, indicating a k(cat) value comparable to those of enzymes from other organisms. The structures of the apoenzyme and the reaction intermediate (pantoyl adenylate; PA) complex were determined by X-ray crystallography to resolutions of 2.5 and 1.85 A, respectively. Structural analysis indicated that the apoenzyme adopts an open and relatively mobile structure, while the complex structure is closed and entirely rigid. Structural comparison of the apoenzyme and the complex revealed how S. aureus PS undergoes open/close conformational change, and also determined the key interactions with the adenine ring of PA for a hinge bending domain closure. In the complex structure, PA and acetate are bound in the active site. We suggest that the acetate mimics the substrate beta-alanine. Therefore, the complex structure seems to represent a catalytic state poised for in-line nucleophilic attack on PA. These data also offer an alternative strategy for designing novel compounds that selectively inhibit PS activity.
-Substrate-Induced Closing of the Active Site Revealed by the Crystal Structure of Pantothenate Synthetase from Staphylococcus aureus.,Satoh A, Konishi S, Tamura H, Stickland HG, Whitney HM, Smith AG, Matsumura H, Inoue T Biochemistry. 2010 Jul 8. PMID:20568730<ref>PMID:20568730</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3ag5" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Pantothenate synthetase|Pantothenate synthetase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Pantoate--beta-alanine ligase]]
+[[Category: Large Structures]]
-[[Category: Staa8]]
+[[Category: Staphylococcus aureus subsp. aureus NCTC 8325]]
-[[Category: Inoue, T]]
+[[Category: Inoue T]]
-[[Category: Konishi, S]]
+[[Category: Konishi S]]
-[[Category: Matsumura, H]]
+[[Category: Matsumura H]]
-[[Category: Satoh, A]]
+[[Category: Satoh A]]
-[[Category: Smith, A G]]
+[[Category: Smith AG]]
-[[Category: Stickland, H G]]
+[[Category: Stickland HG]]
-[[Category: Tamura, H]]
+[[Category: Tamura H]]
-[[Category: Whitney, H M]]
+[[Category: Whitney HM]]
-[[Category: Atp-binding]]
-[[Category: Atp-dependent enzyme]]
-[[Category: Ligase]]
-[[Category: Nucleotide-binding]]
-[[Category: Open/close mechanism]]
-[[Category: Pantothenate biosynthesis]]
-[[Category: Pantothenate synthetase]]