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| | ==Structure of CBM_E1, a novel carbohydrate-binding module found by sugar cane soil metagenome, complexed with cellopentaose and gadolinium ion== | | ==Structure of CBM_E1, a novel carbohydrate-binding module found by sugar cane soil metagenome, complexed with cellopentaose and gadolinium ion== |
| - | <StructureSection load='5klf' size='340' side='right' caption='[[5klf]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='5klf' size='340' side='right'caption='[[5klf]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5klf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KLF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5klf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KLF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CE5:CELLOPENTAOSE'>CE5</scene>, <scene name='pdbligand=GD:GADOLINIUM+ATOM'>GD</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]] 1.801Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5klc|5klc]], [[5kle|5kle]]</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=GD:GADOLINIUM+ATOM'>GD</scene></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=5klf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klf OCA], [http://pdbe.org/5klf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5klf RCSB], [http://www.ebi.ac.uk/pdbsum/5klf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5klf 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=5klf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klf OCA], [https://pdbe.org/5klf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5klf RCSB], [https://www.ebi.ac.uk/pdbsum/5klf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5klf ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A0R5P8X1_9BACT A0A0R5P8X1_9BACT] |
| | <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: Uncultivated bacterium]] | + | [[Category: Large Structures]] |
| - | [[Category: Campos, B M]] | + | [[Category: Uncultured bacterium]] |
| - | [[Category: Liberato, M V]] | + | [[Category: Campos BM]] |
| - | [[Category: Squina, F M]] | + | [[Category: Liberato MV]] |
| - | [[Category: Zeri, A C.M]] | + | [[Category: Squina FM]] |
| - | [[Category: Biofuel]] | + | [[Category: Zeri ACM]] |
| - | [[Category: Carbohydrate-binding protein]]
| + | |
| - | [[Category: Cellulose]]
| + | |
| - | [[Category: Metagenomic]]
| + | |
| - | [[Category: Sugar binding protein]]
| + | |
| Structural highlights
Function
A0A0R5P8X1_9BACT
Publication Abstract from PubMed
Carbohydrate-binding modules (CBMs) are appended to glycoside hydrolases and can contribute to the degradation of complex recalcitrant substrates such as the plant cell wall. For application in bioethanol production, novel enzymes with high catalytic activity against recalcitrant lignocellulosic material are being explored and developed. In this work, we report the functional and structural study of CBM_E1, discovered through a metagenomics approach, which is the founding member of a novel CBM family, CBMxx. CBM_E1, which is linked to an endoglucanase, displayed affinity for mixed linked beta-1,4-beta-1,3-glucans, xyloglucan, avicel and cellooligosaccharides. The crystal structure of CBM_E1 in complex with cellopentaose displayed a canonical beta-sandwich fold comprising two beta sheets. The planar ligand binding site, observed in a parallel orientation with the beta strands, is a typical feature of Type A CBMs. On the other hand, affinity for bacterial crystalline cellulose was not detected, a ligand recognized by Type A CBMs, while binding to soluble glucans was enthalpically driven, typical of Type B modules. These unique properties of CBM_E1 are at the interface between Type A and Type B CBMs.
A novel carbohydrate-binding module from sugar cane soil metagenome featuring unique structural and carbohydrate affinity properties.,Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri AC, Squina FM J Biol Chem. 2016 Sep 12. pii: jbc.M116.744383. PMID:27621314[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Campos BM, Liberato MV, Alvarez TM, Zanphorlin LM, Ematsu GC, Barud H, Polikarpov I, Ruller R, Gilbert HJ, Zeri AC, Squina FM. A novel carbohydrate-binding module from sugar cane soil metagenome featuring unique structural and carbohydrate affinity properties. J Biol Chem. 2016 Sep 12. pii: jbc.M116.744383. PMID:27621314 doi:http://dx.doi.org/10.1074/jbc.M116.744383
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