4udk
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 4udk is ON HOLD Authors: Ladeveze, S., Cioci, G., Potocki-Veronese, G., Tranier, S., Mourey, L. Description: Crystal structure of b-1,4-mannopyrano...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from unknown human gut bacteria (Uhgb_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate== | |
| + | <StructureSection load='4udk' size='340' side='right'caption='[[4udk]], [[Resolution|resolution]] 1.76Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4udk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_organism Uncultured organism]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UDK FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.76Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=4udk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4udk OCA], [https://pdbe.org/4udk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4udk RCSB], [https://www.ebi.ac.uk/pdbsum/4udk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4udk ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/D9ZDQ9_9ZZZZ D9ZDQ9_9ZZZZ] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The first crystal structure of Uhgb_MP, a beta-1,4-mannopyranosyl-chitobiose phosphorylase belonging to the GH130 family which is involved in N-glycan degradation by human gut bacteria, was solved at 1.85 A resolution in the apo form and in complex with mannose and N-acetylglucosamine. SAXS and crystal structure analysis revealed a hexameric structure, a specific feature of GH130 enzymes among other glycoside phosphorylases. Mapping of the -1 and +1 subsites in the presence of phosphate confirmed the conserved Asp104 as the general acid/base catalytic residue, which is in agreement with a single-step reaction mechanism involving Man O3 assistance for proton transfer. Analysis of this structure, the first to be solved for a member of the GH130_2 subfamily, revealed Met67, Phe203 and the Gly121-Pro125 loop as the main determinants of the specificity of Uhgb_MP and its homologues towards the N-glycan core oligosaccharides and mannan, and the molecular bases of the key role played by GH130 enzymes in the catabolism of dietary fibre and host glycans. | ||
| - | + | Structural bases for N-glycan processing by mannoside phosphorylase.,Ladeveze S, Cioci G, Roblin P, Mourey L, Tranier S, Potocki-Veronese G Acta Crystallogr D Biol Crystallogr. 2015 Jun;71(Pt 6):1335-46. doi:, 10.1107/S1399004715006604. Epub 2015 May 14. PMID:26057673<ref>PMID:26057673</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 4udk" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Uncultured organism]] | ||
| + | [[Category: Cioci G]] | ||
| + | [[Category: Ladeveze S]] | ||
| + | [[Category: Mourey L]] | ||
| + | [[Category: Potocki-Veronese G]] | ||
| + | [[Category: Tranier S]] | ||
Current revision
Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from unknown human gut bacteria (Uhgb_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate
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