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==Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides plebeius in complex with paranitrophenyl-alpha-L-galactopyranoside== | ==Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides plebeius in complex with paranitrophenyl-alpha-L-galactopyranoside== | ||
<StructureSection load='7lnp' size='340' side='right'caption='[[7lnp]]' scene=''> | <StructureSection load='7lnp' size='340' side='right'caption='[[7lnp]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNP FirstGlance]. <br> | <table><tr><td colspan='2'>[[7lnp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phocaeicola_plebeius_DSM_17135 Phocaeicola plebeius DSM 17135]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNP FirstGlance]. <br> | ||
</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=7lnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnp OCA], [https://pdbe.org/7lnp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnp RCSB], [https://www.ebi.ac.uk/pdbsum/7lnp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnp ProSAT]</span></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]] 2.7Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=Y9Y:paranitrophenyl-alpha-L-galactopyranoside'>Y9Y</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=7lnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnp OCA], [https://pdbe.org/7lnp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnp RCSB], [https://www.ebi.ac.uk/pdbsum/7lnp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnp ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/B5CYA5_PHOPM B5CYA5_PHOPM] Alpha-L-fucosidase is responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins.[ARBA:ARBA00004071] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Native porphyran is a hybrid of porphryan and agarose. As a common element of edible seaweed, this algal galactan is a frequent component of the human diet. Bacterial members of the human gut microbiota have acquired polysaccharide utilization loci (PULs) that enable the metabolism of porphyran or agarose. However, the molecular mechanisms that underlie the deconstruction and use of native porphyran remains incompletely defined. Here, we have studied two human gut bacteria, porphyranolytic Bacteroides plebeius and agarolytic Bacteroides uniformis, that target native porphyran. This reveals an exo-based cycle of porphyran depolymerization that incorporates a keystone sulfatase. In both PULs this cycle also works together with a PUL-encoded agarose depolymerizing machinery to synergistically reduce native porphyran to monosaccharides. This provides a framework for understanding the deconstruction of a hybrid algal galactan, and insight into the competitive and/or syntrophic relationship of gut microbiota members that target rare nutrients. | |||
Metabolism of a hybrid algal galactan by members of the human gut microbiome.,Robb CS, Hobbs JK, Pluvinage B, Reintjes G, Klassen L, Monteith S, Giljan G, Amundsen C, Vickers C, Hettle AG, Hills R, Nitin, Xing X, Montina T, Zandberg WF, Abbott DW, Boraston AB Nat Chem Biol. 2022 Mar 14. pii: 10.1038/s41589-022-00983-y. doi:, 10.1038/s41589-022-00983-y. PMID:35289327<ref>PMID:35289327</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7lnp" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Galactosidase 3D structures|Galactosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Phocaeicola plebeius DSM 17135]] | |||
[[Category: Boraston AB]] | [[Category: Boraston AB]] | ||
[[Category: Robb CS]] | [[Category: Robb CS]] | ||
Latest revision as of 18:54, 18 October 2023
Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides plebeius in complex with paranitrophenyl-alpha-L-galactopyranosideStructure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides plebeius in complex with paranitrophenyl-alpha-L-galactopyranoside
Structural highlights
FunctionB5CYA5_PHOPM Alpha-L-fucosidase is responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins.[ARBA:ARBA00004071] Publication Abstract from PubMedNative porphyran is a hybrid of porphryan and agarose. As a common element of edible seaweed, this algal galactan is a frequent component of the human diet. Bacterial members of the human gut microbiota have acquired polysaccharide utilization loci (PULs) that enable the metabolism of porphyran or agarose. However, the molecular mechanisms that underlie the deconstruction and use of native porphyran remains incompletely defined. Here, we have studied two human gut bacteria, porphyranolytic Bacteroides plebeius and agarolytic Bacteroides uniformis, that target native porphyran. This reveals an exo-based cycle of porphyran depolymerization that incorporates a keystone sulfatase. In both PULs this cycle also works together with a PUL-encoded agarose depolymerizing machinery to synergistically reduce native porphyran to monosaccharides. This provides a framework for understanding the deconstruction of a hybrid algal galactan, and insight into the competitive and/or syntrophic relationship of gut microbiota members that target rare nutrients. Metabolism of a hybrid algal galactan by members of the human gut microbiome.,Robb CS, Hobbs JK, Pluvinage B, Reintjes G, Klassen L, Monteith S, Giljan G, Amundsen C, Vickers C, Hettle AG, Hills R, Nitin, Xing X, Montina T, Zandberg WF, Abbott DW, Boraston AB Nat Chem Biol. 2022 Mar 14. pii: 10.1038/s41589-022-00983-y. doi:, 10.1038/s41589-022-00983-y. PMID:35289327[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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