5b49: Difference between revisions

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 ==Crystal structure of LpxH with manganese from Pseudomonas aeruginosa==
-<StructureSection load='5b49' size='340' side='right' caption='[[5b49]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+<StructureSection load='5b49' size='340' side='right'caption='[[5b49]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5b49]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B49 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B49 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5b49]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B49 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LP5:(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL)+3-HYDROXYTETRADECANOATE'>LP5</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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">[[5b4a|5b4a]], [[5b4b|5b4b]], [[5b4c|5b4c]], [[5b4d|5b4d]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LP5:(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL)+3-HYDROXYTETRADECANOATE'>LP5</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-2,3-diacylglucosamine_diphosphatase UDP-2,3-diacylglucosamine diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.54 3.6.1.54] </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=5b49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b49 OCA], [https://pdbe.org/5b49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b49 RCSB], [https://www.ebi.ac.uk/pdbsum/5b49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b49 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=5b49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b49 OCA], [http://pdbe.org/5b49 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b49 RCSB], [http://www.ebi.ac.uk/pdbsum/5b49 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b49 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LPXH_PSEAE LPXH_PSEAE]] Catalyzes the hydrolysis of the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP.
+[https://www.uniprot.org/uniprot/LPXH_PSEAE LPXH_PSEAE] Catalyzes the hydrolysis of the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Lipid A (also known as endotoxin) is the hydrophobic portion of lipopolysaccharides. It is an essential membrane component required for the viability of gram-negative bacteria. The enzymes involved in its biosynthesis are attractive targets for the development of novel antibiotics. LpxH catalyzes the fourth step of the lipid A biosynthesis pathway and cleaves the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP. Here we present the structures of LpxH from Pseudomonas aeruginosa (PaLpxH). PaLpxH consists of two domains: a catalytic domain that is homologous to the metallophosphoesterases and a helical insertion domain. Lipid X was captured in the crevice between these two domains, with its phosphate group facing the dinuclear metal (Mn(2+)) center and two acyl chains buried in the hydrophobic cavity. The structures reveal that a large conformational change occurs at the lipid X binding site surface upon the binding/release of the product molecule. Based on these observations, we propose a novel model for lipid X embedding, which involves the scissor-like movement of helix alpha6, resulting in the release of lipid X into the lipid bilayer.
-Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa.,Okada C, Wakabayashi H, Kobayashi M, Shinoda A, Tanaka I, Yao M Sci Rep. 2016 Sep 9;6:32822. doi: 10.1038/srep32822. PMID:27609419<ref>PMID:27609419</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5b49" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: UDP-2,3-diacylglucosamine diphosphatase]]
+[[Category: Large Structures]]
-[[Category: Okada, C]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Tanaka, I]]
+[[Category: Okada C]]
-[[Category: Wakabayashi, H]]
+[[Category: Tanaka I]]
-[[Category: Yao, M]]
+[[Category: Wakabayashi H]]
-[[Category: 3-diacylglucosamine]]
+[[Category: Yao M]]
-[[Category: Hydrolase]]
-[[Category: Lipid some]]
-[[Category: Lipid x]]
-[[Category: Lpxh]]
-[[Category: Udp-2]]