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| ==Crystal structure of a putative beta-1,4-endoglucanase / cellulase from Prevotella bryantii== | | ==Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella bryantii B14== |
| <StructureSection load='3vdh' size='340' side='right' caption='[[3vdh]], [[Resolution|resolution]] 1.62Å' scene=''> | | <StructureSection load='3vdh' size='340' side='right'caption='[[3vdh]], [[Resolution|resolution]] 1.62Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3vdh]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_(prevotella)_ruminicola_subsp._brevis_biovar_3 Bacteroides (prevotella) ruminicola subsp. brevis biovar 3]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3l55 3l55]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VDH FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3vdh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Prevotella_bryantii Prevotella bryantii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3l55 3l55]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VDH FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.62Å</td></tr> |
| <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5d9m|5d9m]], [[5d9n|5d9n]], [[5d9o|5d9o]], [[5d9p|5d9p]]</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=3vdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdh OCA], [https://pdbe.org/3vdh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vdh RCSB], [https://www.ebi.ac.uk/pdbsum/3vdh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdh ProSAT]</span></td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdh OCA], [http://pdbe.org/3vdh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vdh RCSB], [http://www.ebi.ac.uk/pdbsum/3vdh PDBsum]</span></td></tr> | |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| | == Function == |
| == Publication Abstract from PubMed == | | [https://www.uniprot.org/uniprot/O06842_PREBR O06842_PREBR] |
| The recent classification of Glycoside Hydrolase Family 5 (GH5) members into subfamilies enhances the prediction of substrate specificity by phylogenetic analysis. However, the small number of well-characterized members is a current limitation to understanding the molecular basis of the diverse specificity observed across individual GH5 subfamilies. GH5 Subfamily 4 (GH5_4) is one of the largest, with known activities comprising (carboxymethyl)cellulases, mixed-linkage endo-glucanases, and endo-xyloglucanases. Through detailed structure-function analysis, we have revisited the characterization of a classic GH5_4 carboxymethylcellulase, PbGH5A (also known as Orf4, CMCase, and Cel5A) from the symbiotic rumen Bacteroidetes Prevotella bryantii B14. We demonstrate that CMC and phosphoric acid-swollen cellulose (PASC) are in fact strikingly poor substrates for PbGH5A, which instead exhibits clear primary specificity for the plant storage and cell wall polysaccharide, mixed-linkage beta-glucan. Significant activity toward the plant cell wall polysaccharide xyloglucan was also observed. Determination of PbGH5A crystal structures in the apo form and in complex with (xylo)glucan oligosaccharides and an active-site affinity label, together with detailed kinetic analysis using a variety of well-defined oligosaccharide substrates, revealed the structural determinants of polysaccharide substrate specificity. In particular, this analysis highlighted the PbGH5A active-site motifs which engender predominant mixed-linkage endo-glucanase activity vis-a-vis predominant endo-xyloglucanases in GH5_4. However the detailed phylogenetic analysis of GH5_4 members did not delineate particular clades of enzymes sharing these sequence motifs; the phylogeny was instead dominated by bacterial taxonomy. Nonetheless, our results provide key enzyme functional and structural reference data for future bioinformatics analyses of meta(genomes) to elucidate the biology of complex gut ecosystems.
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| Structure-function analysis of a mixed-linkage Beta-glucanase/xyloglucanase from key ruminal Bacteroidetes Prevotella bryantii B14.,McGregor N, Morar M, Fenger TH, Stogios P, Lenfant N, Yin V, Xu X, Evdokimova E, Cui H, Henrissat B, Savchenko A, Brumer H J Biol Chem. 2015 Oct 27. pii: jbc.M115.691659. PMID:26507654<ref>PMID:26507654</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 3vdh" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Edwards, A M]] | | [[Category: Large Structures]] |
| [[Category: Egorova, O]] | | [[Category: Prevotella bryantii]] |
| [[Category: Evdokimova, E]] | | [[Category: Edwards AM]] |
| [[Category: Joachimiak, A]] | | [[Category: Egorova O]] |
| [[Category: Structural genomic]] | | [[Category: Evdokimova E]] |
| [[Category: Savchenko, A]] | | [[Category: Joachimiak A]] |
| [[Category: Stogios, P J]] | | [[Category: Savchenko A]] |
| [[Category: Yim, V]] | | [[Category: Stogios PJ]] |
| [[Category: 4-endoglucanase]] | | [[Category: Yim V]] |
| [[Category: Cellulase]]
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| [[Category: Glycosyl hydrolase family 5]]
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| [[Category: Mcsg]]
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| [[Category: Mixed alpha-beta]]
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| [[Category: PSI, Protein structure initiative]]
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| [[Category: Psi-biology]]
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| [[Category: Putative beta-1]]
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| [[Category: Tim barrel]]
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| [[Category: Unknown function]]
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