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| | <StructureSection load='5b4b' size='340' side='right'caption='[[5b4b]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='5b4b' size='340' side='right'caption='[[5b4b]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5b4b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B4B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5b4b]] 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=5B4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4B 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></td></tr> | + | </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></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5b49|5b49]], [[5b4a|5b4a]], [[5b4c|5b4c]], [[5b4d|5b4d]]</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=5b4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4b OCA], [https://pdbe.org/5b4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4b RCSB], [https://www.ebi.ac.uk/pdbsum/5b4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4b ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lpxH, PA1792 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4b OCA], [http://pdbe.org/5b4b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b4b RCSB], [http://www.ebi.ac.uk/pdbsum/5b4b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4b ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pseae]] | + | [[Category: Pseudomonas aeruginosa PAO1]] |
| - | [[Category: UDP-2,3-diacylglucosamine diphosphatase]]
| + | [[Category: Okada C]] |
| - | [[Category: Okada, C]] | + | [[Category: Tanaka I]] |
| - | [[Category: Tanaka, I]] | + | [[Category: Wakabayashi H]] |
| - | [[Category: Wakabayashi, H]] | + | [[Category: Yao M]] |
| - | [[Category: Yao, M]] | + | |
| - | [[Category: 3-diacylglucosamine]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lipid some]]
| + | |
| - | [[Category: Lipid x]]
| + | |
| - | [[Category: Lpxh]]
| + | |
| - | [[Category: Udp-2]]
| + | |
| Structural highlights
Function
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Okada C, Wakabayashi H, Kobayashi M, Shinoda A, Tanaka I, Yao M. Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa. Sci Rep. 2016 Sep 9;6:32822. doi: 10.1038/srep32822. PMID:27609419 doi:http://dx.doi.org/10.1038/srep32822
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