3sxp: Difference between revisions
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==Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)== | ==Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)== | ||
<StructureSection load='3sxp' size='340' side='right' caption='[[3sxp]], [[Resolution|resolution]] 2.55Å' scene=''> | <StructureSection load='3sxp' size='340' side='right'caption='[[3sxp]], [[Resolution|resolution]] 2.55Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3sxp]] is a 5 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3sxp]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Helpg Helpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SXP FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1eq2|1eq2]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1eq2|1eq2]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hp0859, HPG27_813 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hp0859, HPG27_813 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=563041 HELPG])</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/ADP-glyceromanno-heptose_6-epimerase ADP-glyceromanno-heptose 6-epimerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.20 5.1.3.20] </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=3sxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sxp OCA], [https://pdbe.org/3sxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sxp RCSB], [https://www.ebi.ac.uk/pdbsum/3sxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sxp ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/B5Z7L9_HELPG B5Z7L9_HELPG]] Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose (By similarity).[SAAS:SAAS001509_004_016636] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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[[Category: ADP-glyceromanno-heptose 6-epimerase]] | [[Category: ADP-glyceromanno-heptose 6-epimerase]] | ||
[[Category: Helpg]] | [[Category: Helpg]] | ||
[[Category: Large Structures]] | |||
[[Category: Cendron, L]] | [[Category: Cendron, L]] | ||
[[Category: Shaik, M M]] | [[Category: Shaik, M M]] | ||
Revision as of 11:15, 29 June 2022
Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)Crystal Structure of Helicobacter pylori ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD, HP0859)
Structural highlights
Function[B5Z7L9_HELPG] Catalyzes the interconversion between ADP-D-glycero-beta-D-manno-heptose and ADP-L-glycero-beta-D-manno-heptose via an epimerization at carbon 6 of the heptose (By similarity).[SAAS:SAAS001509_004_016636] Publication Abstract from PubMedHelicobacter pylori, the human pathogen that affects about half of the world population and that is responsible for gastritis, gastric ulcer and adenocarcinoma and MALT lymphoma, owes much of the integrity of its outer membrane on lipopolysaccharides (LPSs). Together with their essential structural role, LPSs contribute to the bacterial adherence properties, as well as they are well characterized for the capability to modulate the immuno-response. In H. pylori the core oligosaccharide, one of the three main domains of LPSs, shows a peculiar structure in the branching organization of the repeating units, which displayed further variability when different strains have been compared. We present here the crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859, rfaD), the last enzyme in the pathway that produces L-glycero-D-manno-heptose starting from sedoheptulose-7-phosphate, a crucial compound in the synthesis of the core oligosaccharide. In a recent study, a HP0859 knockout mutant has been characterized, demonstrating a severe loss of lipopolysaccharide structure and a significant reduction of adhesion levels in an infection model to AGS cells, if compared with the wild type strain, in good agreement with its enzymatic role. The crystal structure reveals that the enzyme is a homo-pentamer, and NAD is bound as a cofactor in a highly conserved pocket. The substrate-binding site of the enzyme is very similar to that of its orthologue in Escherichia coli, suggesting also a similar catalytic mechanism. The crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859) from Helicobacter pylori.,Shaik MM, Zanotti G, Cendron L Biochim Biophys Acta. 2011 Dec;1814(12):1641-7. Epub 2011 Sep 25. PMID:21979583[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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