This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3zmr

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Bacteroides ovatus GH5 xyloglucanase in complex with a XXXG heptasaccharide

Structural highlights

3zmr is a 2 chain structure with sequence from Bacteroides ovatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.43Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BGH5A_BACO1 Catalyzes endohydrolysis of 1,4-beta-D-glucosidic linkages in xyloglucan with retention of the beta-configuration of the glycosyl residues in xyloglucan degradation. Cleaves the backbone of the 3 major types of natural xyloglucans (seed galactoxyloglucan from tamarind kernel, dicot fucogalactoxyloglucan from lettuce leaves, and solanaceous arabinogalactoxyloglucan from tomato fruit), to produce xyloglucan oligosaccharides.^[1]

Publication Abstract from PubMed

A well-balanced human diet includes a significant intake of non-starch polysaccharides, collectively termed 'dietary fibre', from the cell walls of diverse fruits and vegetables. Owing to the paucity of alimentary enzymes encoded by the human genome, our ability to derive energy from dietary fibre depends on the saccharification and fermentation of complex carbohydrates by the massive microbial community residing in our distal gut. The xyloglucans (XyGs) are a ubiquitous family of highly branched plant cell wall polysaccharides whose mechanism(s) of degradation in the human gut and consequent importance in nutrition have been unclear. Here we demonstrate that a single, complex gene locus in Bacteroides ovatus confers XyG catabolism in this common colonic symbiont. Through targeted gene disruption, biochemical analysis of all predicted glycoside hydrolases and carbohydrate-binding proteins, and three-dimensional structural determination of the vanguard endo-xyloglucanase, we reveal the molecular mechanisms through which XyGs are hydrolysed to component monosaccharides for further metabolism. We also observe that orthologous XyG utilization loci (XyGULs) serve as genetic markers of XyG catabolism in Bacteroidetes, that XyGULs are restricted to a limited number of phylogenetically diverse strains, and that XyGULs are ubiquitous in surveyed human metagenomes. Our findings reveal that the metabolism of even highly abundant components of dietary fibre may be mediated by niche species, which has immediate fundamental and practical implications for gut symbiont population ecology in the context of human diet, nutrition and health.

A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes.,Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, Klinter S, Pudlo NA, Urs K, Koropatkin NM, Creagh AL, Haynes CA, Kelly AG, Cederholm SN, Davies GJ, Martens EC, Brumer H Nature. 2014 Jan 19. doi: 10.1038/nature12907. PMID:24463512^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, Klinter S, Pudlo NA, Urs K, Koropatkin NM, Creagh AL, Haynes CA, Kelly AG, Cederholm SN, Davies GJ, Martens EC, Brumer H. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature. 2014 Jan 19. doi: 10.1038/nature12907. PMID:24463512 doi:http://dx.doi.org/10.1038/nature12907
↑ Larsbrink J, Rogers TE, Hemsworth GR, McKee LS, Tauzin AS, Spadiut O, Klinter S, Pudlo NA, Urs K, Koropatkin NM, Creagh AL, Haynes CA, Kelly AG, Cederholm SN, Davies GJ, Martens EC, Brumer H. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature. 2014 Jan 19. doi: 10.1038/nature12907. PMID:24463512 doi:http://dx.doi.org/10.1038/nature12907

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3zmr"

@@ Line 3: / Line 3: @@
 <StructureSection load='3zmr' size='340' side='right'caption='[[3zmr]], [[Resolution|resolution]] 1.43&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3zmr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacteroides_fragilis_subsp._ovatus"_(eggerth_and_gagnon_1933)_holdeman_and_moore_1970 "bacteroides fragilis subsp. ovatus" (eggerth and gagnon 1933) holdeman and moore 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZMR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3zmr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_ovatus Bacteroides ovatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZMR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZMR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>, <scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</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]] 1.43&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xyloglucan-specific_endo-beta-1,4-glucanase Xyloglucan-specific endo-beta-1,4-glucanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.151 3.2.1.151] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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=3zmr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zmr OCA], [https://pdbe.org/3zmr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zmr RCSB], [https://www.ebi.ac.uk/pdbsum/3zmr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zmr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/BGH5A_BACO1 BGH5A_BACO1] Catalyzes endohydrolysis of 1,4-beta-D-glucosidic linkages in xyloglucan with retention of the beta-configuration of the glycosyl residues in xyloglucan degradation. Cleaves the backbone of the 3 major types of natural xyloglucans (seed galactoxyloglucan from tamarind kernel, dicot fucogalactoxyloglucan from lettuce leaves, and solanaceous arabinogalactoxyloglucan from tomato fruit), to produce xyloglucan oligosaccharides.<ref>PMID:24463512</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 26: @@
 __TOC__
 </StructureSection>
+[[Category: Bacteroides ovatus]]
 [[Category: Large Structures]]
-[[Category: Xyloglucan-specific endo-beta-1,4-glucanase]]
+[[Category: Brumer H]]
-[[Category: Brumer, H]]
+[[Category: Cederholm SN]]
-[[Category: Cederholm, S N]]
+[[Category: Davies GJ]]
-[[Category: Davies, G J]]
+[[Category: Hemsworth GR]]
-[[Category: Hemsworth, G R]]
+[[Category: Kelly AG]]
-[[Category: Kelly, A G]]
+[[Category: Klinter S]]
-[[Category: Klinter, S]]
+[[Category: Larsbrink J]]
-[[Category: Larsbrink, J]]
+[[Category: Martens EC]]
-[[Category: Martens, E C]]
+[[Category: McKee LS]]
-[[Category: McKee, L S]]
+[[Category: Pudlo NA]]
-[[Category: Pudlo, N A]]
+[[Category: Rogers TE]]
-[[Category: Rogers, T E]]
+[[Category: Spadiut O]]
-[[Category: Spadiut, O]]
+[[Category: Urs K]]
-[[Category: Urs, K]]
-[[Category: Hydrolase]]
-[[Category: Xyloglucan]]

3zmr

From Proteopedia

Current revision

Bacteroides ovatus GH5 xyloglucanase in complex with a XXXG heptasaccharide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox