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| | <StructureSection load='5wly' size='340' side='right'caption='[[5wly]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='5wly' size='340' side='right'caption='[[5wly]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5wly]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WLY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5wly]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WLY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lpxH, AUQ13_20415, BK337_17315, BUE81_23120, EC3234A_5c00260, PGD_02789 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=5wly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wly OCA], [https://pdbe.org/5wly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wly RCSB], [https://www.ebi.ac.uk/pdbsum/5wly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wly 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=5wly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wly OCA], [http://pdbe.org/5wly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wly RCSB], [http://www.ebi.ac.uk/pdbsum/5wly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wly ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q0P6L0_ECOLX Q0P6L0_ECOLX]] Hydrolyzes the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[HAMAP-Rule:MF_00575] | + | [https://www.uniprot.org/uniprot/LPXH_ECOLI LPXH_ECOLI] Hydrolyzes the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom (PubMed:12000770). Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell (PubMed:12000770, PubMed:12000771). Is essential for E.coli growth (PubMed:12000771). Does not cleave the unacylated UDP-GlcNAc, the mono-acylated UDP-3-O-(R)-3-hydroxymyristoyl-GlcNAc, and CDP-diacylglycerol (PubMed:12000770).<ref>PMID:12000770</ref> <ref>PMID:12000771</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: UDP-2,3-diacylglucosamine diphosphatase]]
| + | [[Category: Aihara H]] |
| - | [[Category: Aihara, H]] | + | [[Category: Bohl TE]] |
| - | [[Category: Bohl, T E]] | + | [[Category: Lee JK]] |
| - | [[Category: Lee, J K]] | + | [[Category: Shi K]] |
| - | [[Category: Shi, K]] | + | |
| - | [[Category: Apha/beta-hydrolase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lipid a synthesis]]
| + | |
| - | [[Category: Open conformation]]
| + | |
| - | [[Category: Udp-diacyl-glucosamine pyrophosphohydrolase]]
| + | |
| Structural highlights
Function
LPXH_ECOLI Hydrolyzes the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom (PubMed:12000770). Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell (PubMed:12000770, PubMed:12000771). Is essential for E.coli growth (PubMed:12000771). Does not cleave the unacylated UDP-GlcNAc, the mono-acylated UDP-3-O-(R)-3-hydroxymyristoyl-GlcNAc, and CDP-diacylglycerol (PubMed:12000770).[1] [2]
Publication Abstract from PubMed
Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen-deuterium exchange mass spectrometry provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors.
The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release.,Bohl TE, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir O, Kurahashi K, Amaro RE, Wang Z, Aihara H J Biol Chem. 2018 Apr 6. pii: RA118.002503. doi: 10.1074/jbc.RA118.002503. PMID:29626094[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Babinski KJ, Ribeiro AA, Raetz CR. The Escherichia coli gene encoding the UDP-2,3-diacylglucosamine pyrophosphatase of lipid A biosynthesis. J Biol Chem. 2002 Jul 19;277(29):25937-46. PMID:12000770 doi:10.1074/jbc.M204067200
- ↑ Babinski KJ, Kanjilal SJ, Raetz CR. Accumulation of the lipid A precursor UDP-2,3-diacylglucosamine in an Escherichia coli mutant lacking the lpxH gene. J Biol Chem. 2002 Jul 19;277(29):25947-56. PMID:12000771 doi:10.1074/jbc.M204068200
- ↑ Bohl TE, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir O, Kurahashi K, Amaro RE, Wang Z, Aihara H. The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. J Biol Chem. 2018 Apr 6. pii: RA118.002503. doi: 10.1074/jbc.RA118.002503. PMID:29626094 doi:http://dx.doi.org/10.1074/jbc.RA118.002503
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