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| | <StructureSection load='6p8a' size='340' side='right'caption='[[6p8a]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='6p8a' size='340' side='right'caption='[[6p8a]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6p8a]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P8A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P8A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6p8a]] is a 3 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=6P8A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P8A FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=O3V:3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one'>O3V</scene>, <scene name='pdbligand=O4D:2-[4,6-dimethyl-3-(1H-pyrrol-1-yl)-1H-pyrazolo[3,4-b]pyridin-1-yl]-N-[3-(morpholin-4-yl)propyl]acetamide'>O4D</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]] 1.8Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-3-O-(3-hydroxymyristoyl)glucosamine_N-acyltransferase UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.191 2.3.1.191] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=O3V:3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one'>O3V</scene>, <scene name='pdbligand=O4D:2-[4,6-dimethyl-3-(1H-pyrrol-1-yl)-1H-pyrazolo[3,4-b]pyridin-1-yl]-N-[3-(morpholin-4-yl)propyl]acetamide'>O4D</scene></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=6p8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p8a OCA], [http://pdbe.org/6p8a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p8a RCSB], [http://www.ebi.ac.uk/pdbsum/6p8a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p8a ProSAT]</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=6p8a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p8a OCA], [https://pdbe.org/6p8a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p8a RCSB], [https://www.ebi.ac.uk/pdbsum/6p8a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p8a ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q0P6M7_ECOLX Q0P6M7_ECOLX]] Catalyzes the N-acylation of UDP-3-O-(hydroxytetradecanoyl)glucosamine using 3-hydroxytetradecanoyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell.[HAMAP-Rule:MF_00523] | + | [https://www.uniprot.org/uniprot/LPXD_ECOLI LPXD_ECOLI] Catalyzes the N-acylation of UDP-3-O-(hydroxymyristoyl)glucosamine using 3-hydroxymyristoyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. Prefers R-3-hydroxymyristoyl-ACP over R-3-hydroxypalmitoyl-ACP as the acyl donor in vitro, which is consistent with the structure of E.coli lipid A that contains over 95% (R)-3-hydroxymyristate at the 2 and 2' positions.<ref>PMID:8444173</ref> <ref>PMID:19655786</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6p8a" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6p8a" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase|UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ma, X]] | + | [[Category: Ma X]] |
| - | [[Category: Shia, S]] | + | [[Category: Shia S]] |
| - | [[Category: Lps synthesis]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transferase-inhibitor complex]]
| + | |
| Structural highlights
Function
LPXD_ECOLI Catalyzes the N-acylation of UDP-3-O-(hydroxymyristoyl)glucosamine using 3-hydroxymyristoyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. Prefers R-3-hydroxymyristoyl-ACP over R-3-hydroxypalmitoyl-ACP as the acyl donor in vitro, which is consistent with the structure of E.coli lipid A that contains over 95% (R)-3-hydroxymyristate at the 2 and 2' positions.[1] [2]
Publication Abstract from PubMed
LpxD, acyl-ACP-dependent N-acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound 1), that inhibit the enzymatic activity of Escherichia coli (E. coli) LpxD. Here, we use these inhibitors to chemically validate LpxD as an attractive antibacterial target. We first found that compound 1 was oxidized in solution to the more stable aromatized tetrahydro-pyrazolo-quinolinone compound 1o. From the Escherichia coli strain deficient in efflux, we isolated a mutant that was less susceptible to compound 1o and had an lpxD missense mutation (Gly268Cys), supporting the cellular on-target activity. Using surface plasma resonance, we showed direct binding to E. coli LpxD for compound 1o and other reported LpxD inhibitors in vitro. Furthermore, we determined eight cocrystal structures of E. coli LpxD/inhibitor complexes. These costructures pinpointed the 4'-phosphopantetheine binding site as the common ligand binding hotspot, where hydrogen bonds to Gly269 and/or Gly287 were important for inhibitor binding. In addition, the LpxD/compound 1o costructure rationalized the reduced activity of compound 1o in the LpxDGly268Cys mutant. Moreover, we obtained the LpxD structure in complex with a previously reported LpxA/LpxD dual targeting peptide inhibitor, RJPXD33, providing structural rationale for the unique dual targeting properties of this peptide. Given that the active site residues of LpxD are conserved in multidrug resistant Enterobacteriaceae, this work paves the way for future LpxD drug discovery efforts combating these Gram-negative pathogens.
Structural and Biological Basis of Small Molecule Inhibition of Escherichia coli LpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis.,Ma X, Prathapam R, Wartchow C, Chie-Leon B, Ho CM, De Vicente J, Han W, Li M, Lu Y, Ramurthy S, Shia S, Steffek M, Uehara T ACS Infect Dis. 2019 Aug 22. doi: 10.1021/acsinfecdis.9b00127. PMID:31402665[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Helander IM, Lindner B, Seydel U, Vaara M. Defective biosynthesis of the lipid A component of temperature-sensitive firA (omsA) mutant of Escherichia coli. Eur J Biochem. 1993 Mar 1;212(2):363-9. PMID:8444173
- ↑ Bartling CM, Raetz CR. Crystal Structure and Acyl Chain Selectivity of Escherichia coli LpxD, the N-Acyltransferase of Lipid A Biosynthesis. Biochemistry. 2009 Aug 5. PMID:19655786 doi:10.1021/bi901025v
- ↑ Ma X, Prathapam R, Wartchow C, Chie-Leon B, Ho CM, De Vicente J, Han W, Li M, Lu Y, Ramurthy S, Shia S, Steffek M, Uehara T. Structural and Biological Basis of Small Molecule Inhibition of Escherichia coli LpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis. ACS Infect Dis. 2019 Aug 22. doi: 10.1021/acsinfecdis.9b00127. PMID:31402665 doi:http://dx.doi.org/10.1021/acsinfecdis.9b00127
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