3plr: Difference between revisions
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==Crystal structure of Klebsiella pneumoniae UDP-glucose 6-dehydrogenase complexed with NADH and UDP-glucose== | ==Crystal structure of Klebsiella pneumoniae UDP-glucose 6-dehydrogenase complexed with NADH and UDP-glucose== | ||
<StructureSection load='3plr' size='340' side='right' caption='[[3plr]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='3plr' size='340' side='right'caption='[[3plr]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3plr]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3plr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_ntuh-k2044 Klebsiella pneumoniae ntuh-k2044]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PLR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PLR FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3pln|3pln]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3pln|3pln]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KP1_3701, ugd ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KP1_3701, ugd ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=484021 Klebsiella pneumoniae NTUH-K2044])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-glucose_6-dehydrogenase UDP-glucose 6-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.22 1.1.1.22] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3plr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3plr OCA], [https://pdbe.org/3plr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3plr RCSB], [https://www.ebi.ac.uk/pdbsum/3plr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3plr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Klebsiella pneumoniae ntuh-k2044]] | [[Category: Klebsiella pneumoniae ntuh-k2044]] | ||
[[Category: Large Structures]] | |||
[[Category: UDP-glucose 6-dehydrogenase]] | [[Category: UDP-glucose 6-dehydrogenase]] | ||
[[Category: Chen, W H]] | [[Category: Chen, W H]] | ||
Revision as of 11:44, 25 May 2022
Crystal structure of Klebsiella pneumoniae UDP-glucose 6-dehydrogenase complexed with NADH and UDP-glucoseCrystal structure of Klebsiella pneumoniae UDP-glucose 6-dehydrogenase complexed with NADH and UDP-glucose
Structural highlights
Publication Abstract from PubMedCationic modification of lipid A with 4-amino-4-deoxy-L-arabinopyranose (L-Ara4N) allows the pathogen Klebsiella pneumoniae to resist the antibiotic polymyxin and other cationic antimicrobial peptides. UDP-glucose dehydrogenase (Ugd) catalyzes the NAD-dependent twofold oxidation of UDP-glucose (UPG) to produce UDP-glucuronic acid (UGA), a requisite precursor in the biosynthesis of L-Ara4N and bacterial exopolysaccharides. Here we report five crystal structures of K. pneumoniae Ugd (KpUgd) in its apo form, in complex with UPG, UPG/NADH, two UGA molecules, and finally with a C-terminal His-tag. The UGA-complex structure differs from the others by a 14 degrees rotation of the N-terminal domain toward the C-terminal domain, and represents a closed enzyme conformation. It also reveals that the second UGA molecule binds to a pre-existing positively charged surface patch away from the active site. The enzyme is thus inactivated by moving the catalytically important residues C253, K256 and D257 from their original positions. Kinetic data also suggest that KpUgd has multiple binding sites for UPG, and that UGA is a competitive inhibitor. The conformational changes triggered by UGA binding to the allosteric site can be exploited in designing potent inhibitors. Conformational change upon product binding to Klebsiella pneumoniae UDP-glucose dehydrogenase: a possible inhibition mechanism for the key enzyme in polymyxin resistance.,Chen YY, Ko TP, Lin CH, Chen WH, Wang AH J Struct Biol. 2011 Sep;175(3):300-10. Epub 2011 Apr 23. PMID:21536136[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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