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| | <StructureSection load='5joy' size='340' side='right'caption='[[5joy]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='5joy' size='340' side='right'caption='[[5joy]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5joy]] is a 2 chain structure with sequence from [http://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=5JOY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JOY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5joy]] 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=5JOY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JOY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6LW:(2~{Z},3~{R},4~{R},5~{S})-2-HYDROXYIMINO-5-(HYDROXYMETHYL)OXOLANE-3,4-DIOL'>6LW</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.9Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BACOVA_02654 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28116 "Bacteroides fragilis subsp. ovatus" (Eggerth and Gagnon 1933) Holdeman and Moore 1970])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6LW:(2~{Z},3~{R},4~{R},5~{S})-2-HYDROXYIMINO-5-(HYDROXYMETHYL)OXOLANE-3,4-DIOL'>6LW</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5joy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5joy OCA], [https://pdbe.org/5joy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5joy RCSB], [https://www.ebi.ac.uk/pdbsum/5joy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5joy ProSAT]</span></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=5joy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5joy OCA], [http://pdbe.org/5joy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5joy RCSB], [http://www.ebi.ac.uk/pdbsum/5joy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5joy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Bacteroides ovatus]] |
| | [[Category: Large Structures]] | | [[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]]
| + | |
| Structural highlights
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
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