4z1d: Difference between revisions

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 <StructureSection load='4z1d' size='340' side='right'caption='[[4z1d]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4z1d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z1D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4z1d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z1D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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]] 1.65&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4z1a|4z1a]], [[4z1b|4z1b]], [[4z1c|4z1c]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEP:PHOSPHOENOLPYRUVATE'>PEP</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">kdsA, HP_0003 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</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=4z1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z1d OCA], [https://pdbe.org/4z1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z1d RCSB], [https://www.ebi.ac.uk/pdbsum/4z1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z1d 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/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=4z1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z1d OCA], [http://pdbe.org/4z1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z1d RCSB], [http://www.ebi.ac.uk/pdbsum/4z1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z1d ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/KDSA_HELPY KDSA_HELPY]
-The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDO8PS) from Helicobacter pylori (HpKDO8PS) was determined alone and within various complexes, revealing an extra helix (HE) that is absent in the structures of KDO8PS from other organisms. In contrast to the metal coordination of the KDO8PS enzyme from Aquifex aeolicus, HpKDO8PS is specifically coordinated with Cd(2+) or Zn(2+) ions, and isothermal titration calorimetry (ITC) and differential scanning fluorimetry (DSF) revealed that Cd(2+) thermally stabilizes the protein structure more efficiently than Zn(2+). In the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. Using the structures of HpKDO8PS and API [arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) bisubstrate inhibitor], we generated 21 compounds showing potential HpKDO8PS-binding properties via in silico virtual screening. The capacity of three, avicularin, hyperin, and MC181, to bind to HpKDO8PS was confirmed through saturation transfer difference (STD) experiments, and we identified their specific ligand binding modes by combining competition experiments and docking simulation analysis. Hyperin was confirmed to bind to the A5P binding site, primarily via hydrophilic interaction, whereas MC181 bound to both the PEP and A5P binding sites through hydrophilic and hydrophobic interactions. These results were consistent with the epitope mapping by STD. Our results are expected to provide clues for the development of HpKDO8PS inhibitors.
-Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-d-manno-octulosonate 8-phosphate synthase (HpKDO8PS).,Cho S, Im H, Lee KY, Chen J, Kang HJ, Yoon HJ, Min KH, Lee KR, Park HJ, Lee BJ Eur J Med Chem. 2016 Jan 27;108:188-202. doi: 10.1016/j.ejmech.2015.11.036. Epub , 2015 Dec 1. PMID:26649906<ref>PMID:26649906</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4z1d" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: 3-deoxy-8-phosphooctulonate synthase]]
+[[Category: Helicobacter pylori 26695]]
-[[Category: Campylobacter pylori]]
 [[Category: Large Structures]]
-[[Category: Cho, S]]
+[[Category: Cho S]]
-[[Category: Im, H]]
+[[Category: Im H]]
-[[Category: Lee, B J]]
+[[Category: Lee BJ]]
-[[Category: Yoon, H J]]
+[[Category: Yoon HJ]]
-[[Category: Helicobacter pylori]]
-[[Category: Ligand bound]]
-[[Category: Lipopolysaccharide biosynthesis]]
-[[Category: Transferase]]