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5jox

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Revision as of 19:01, 20 September 2023

Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ

Structural highlights

5jox 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 1.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GH43A_BACO1 Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.^[1]

Publication Abstract from PubMed

The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an alpha-xylosidase, a beta-glucosidase, and two alpha-l-arabinofuranosidases from the Bacteroides ovatus XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.

Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut.,Hemsworth GR, Thompson AJ, Stepper J, Sobala LF, Coyle T, Larsbrink J, Spadiut O, Goddard-Borger ED, Stubbs KA, Brumer H, Davies GJ Open Biol. 2016 Jul;6(7). pii: 160142. doi: 10.1098/rsob.160142. PMID:27466444^[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
↑ Hemsworth GR, Thompson AJ, Stepper J, Sobala LF, Coyle T, Larsbrink J, Spadiut O, Goddard-Borger ED, Stubbs KA, Brumer H, Davies GJ. Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut. Open Biol. 2016 Jul;6(7). pii: 160142. doi: 10.1098/rsob.160142. PMID:27466444 doi:http://dx.doi.org/10.1098/rsob.160142

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jox"

@@ Line 3: / Line 3: @@
 <StructureSection load='5jox' size='340' side='right'caption='[[5jox]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jox]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JOX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JOX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jox]] 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=5JOX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JOX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDG:1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL'>EDG</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]] 1.8&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDG:1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL'>EDG</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jox OCA], [http://pdbe.org/5jox PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jox RCSB], [http://www.ebi.ac.uk/pdbsum/5jox PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jox ProSAT]</span></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=5jox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jox OCA], [https://pdbe.org/5jox PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jox RCSB], [https://www.ebi.ac.uk/pdbsum/5jox PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jox ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GH43A_BACO1 GH43A_BACO1]] Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.<ref>PMID:24463512</ref>
+[https://www.uniprot.org/uniprot/GH43A_BACO1 GH43A_BACO1] Alpha-L-arabinofuranosidase involved in xyloglucan degradation by mediating the cleavage of terminal non-reducing alpha-L-arabinofuranoside residues in xyloglucan branches, converting the 'S' units to 'X' units.<ref>PMID:24463512</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Bacteroides ovatus]]
 [[Category: Large Structures]]
-[[Category: Non-reducing end alpha-L-arabinofuranosidase]]
+[[Category: Brumer H]]
-[[Category: Brumer, H]]
+[[Category: Coyle T]]
-[[Category: Coyle, T]]
+[[Category: Davies GJ]]
-[[Category: Davies, G J]]
+[[Category: Hemsworth GR]]
-[[Category: Hemsworth, G R]]
+[[Category: Larsbrink J]]
-[[Category: Larsbrink, J]]
+[[Category: Sobala LF]]
-[[Category: Sobala, L F]]
+[[Category: Spadiut O]]
-[[Category: Spadiut, O]]
+[[Category: Stepper J]]
-[[Category: Stepper, J]]
+[[Category: Stubbs KA]]
-[[Category: Stubbs, K A]]
+[[Category: Thompson AJ]]
-[[Category: Thompson, A J]]
-[[Category: Gh43]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]

5jox

From Proteopedia

Revision as of 19:01, 20 September 2023

Bacteroides ovatus Xyloglucan PUL GH43A in complex with AraDNJ

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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