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| | <StructureSection load='6b3p' size='340' side='right'caption='[[6b3p]], [[Resolution|resolution]] 2.01Å' scene=''> | | <StructureSection load='6b3p' size='340' side='right'caption='[[6b3p]], [[Resolution|resolution]] 2.01Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6b3p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Agathobacter_rectalis_m104/1 Agathobacter rectalis m104/1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B3P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B3P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6b3p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Eubacterium_rectale_M104/1 Eubacterium rectale M104/1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B3P FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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]] 2.01Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6az5|6az5]], [[6b15|6b15]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900009:alpha-maltotriose'>PRD_900009</scene>, <scene name='pdbligand=PRD_900010:alpha-maltotetraose'>PRD_900010</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ERE_20420 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=657317 Agathobacter rectalis M104/1])</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=6b3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b3p OCA], [https://pdbe.org/6b3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b3p RCSB], [https://www.ebi.ac.uk/pdbsum/6b3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b3p 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=6b3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b3p OCA], [http://pdbe.org/6b3p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b3p RCSB], [http://www.ebi.ac.uk/pdbsum/6b3p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b3p ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/D4JJZ5_9FIRM D4JJZ5_9FIRM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6b3p" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6b3p" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Cyclin-dependent kinase 3D structures|Cyclin-dependent kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Agathobacter rectalis m104/1]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cockburn, D W]] | + | [[Category: Cockburn DW]] |
| - | [[Category: Koropatkin, N M]] | + | [[Category: Koropatkin NM]] |
| - | [[Category: Medina, K Perez]] | + | [[Category: Perez Medina K]] |
| - | [[Category: Wawrzak, Z]] | + | [[Category: Wawrzak Z]] |
| - | [[Category: Amylase]]
| + | |
| - | [[Category: Carbohydrate binding module]]
| + | |
| - | [[Category: Eubacterium rectale]]
| + | |
| - | [[Category: Gut microbiome]]
| + | |
| - | [[Category: Starch]]
| + | |
| - | [[Category: Sugar binding protein]]
| + | |
| Structural highlights
6b3p is a 2 chain structure with sequence from Eubacterium rectale M104/1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.01Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
D4JJZ5_9FIRM
Publication Abstract from PubMed
Gut bacteria recognize accessible glycan substrates within a complex environment. Carbohydrate binding modules (CBMs) of cell-surface glycoside hydrolases often drive binding to the target substrate. Eubacterium rectale, an important butyrate-producing organism in the gut, consumes a limited range of substrates, including starch. Host consumption of resistant starch increases the abundance of E. rectale in the intestine, likely because it successfully captures the products of resistant starch degradation by other bacteria. Here we demonstrate that the cell wall anchored starch-degrading alpha-amylase, Amy13K of E. rectale harbors five CBMs that all target starch with differing specificities. Intriguingly these CBMs efficiently bind to both regular and high amylose corn starch (a type of resistant starch), but have almost no affinity for potato starch (another type of resistant starch). Removal of these CBMs from Amy13K reduces the activity level of the enzyme towards corn starches by approximately 40-fold, down to the level of activity towards potato starch, suggesting that the CBMs facilitate activity on corn starch and allowing its utilization in vivo. The specificity of the Amy13K CBMs provides a molecular rationale for why E. rectale is able to only use certain starch types without the aid of other organisms.
Novel carbohydrate binding modules in the surface anchored alpha-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut.,Cockburn DW, Suh C, Medina KP, Duvall RM, Wawrzak Z, Henrissat B, Koropatkin NM Mol Microbiol. 2017 Nov 15. doi: 10.1111/mmi.13881. PMID:29139580[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Cockburn DW, Suh C, Medina KP, Duvall RM, Wawrzak Z, Henrissat B, Koropatkin NM. Novel carbohydrate binding modules in the surface anchored alpha-amylase of Eubacterium rectale provide a molecular rationale for the range of starches used by this organism in the human gut. Mol Microbiol. 2017 Nov 15. doi: 10.1111/mmi.13881. PMID:29139580 doi:http://dx.doi.org/10.1111/mmi.13881
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