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| | ==Crystal Structure of the Cellulosomal CBM4 from Clostridium thermocellum Cellulase CbhA== | | ==Crystal Structure of the Cellulosomal CBM4 from Clostridium thermocellum Cellulase CbhA== |
| - | <StructureSection load='3k4z' size='340' side='right' caption='[[3k4z]], [[Resolution|resolution]] 2.11Å' scene=''> | + | <StructureSection load='3k4z' size='340' side='right'caption='[[3k4z]], [[Resolution|resolution]] 2.11Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3k4z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_thermocellum_dsm_4150 Clostridium thermocellum dsm 4150]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K4Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3k4z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_JW20 Acetivibrio thermocellus JW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K4Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBI:CELLOBIOSE'>CBI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=XGP:1-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>XGP</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]] 2.11Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CtherDRAFT_1062 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=492476 Clostridium thermocellum DSM 4150])</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene>, <scene name='pdbligand=PRD_900005:beta-cellobiose'>PRD_900005</scene>, <scene name='pdbligand=XGP:1-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE'>XGP</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=3k4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k4z OCA], [http://pdbe.org/3k4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k4z RCSB], [http://www.ebi.ac.uk/pdbsum/3k4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k4z 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=3k4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k4z OCA], [https://pdbe.org/3k4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k4z RCSB], [https://www.ebi.ac.uk/pdbsum/3k4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k4z ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k4/3k4z_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k4/3k4z_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Clostridium thermocellum dsm 4150]] | + | [[Category: Acetivibrio thermocellus JW20]] |
| - | [[Category: Alahuhta, P M]] | + | [[Category: Large Structures]] |
| - | [[Category: Himmel, M E]] | + | [[Category: Alahuhta PM]] |
| - | [[Category: Lunin, V V]] | + | [[Category: Himmel ME]] |
| - | [[Category: Xu, Q]] | + | [[Category: Lunin VV]] |
| - | [[Category: Cbha]] | + | [[Category: Xu Q]] |
| - | [[Category: Cbm]]
| + | |
| - | [[Category: Cbm4]]
| + | |
| - | [[Category: Cellulase]]
| + | |
| - | [[Category: Cellulosome]]
| + | |
| - | [[Category: Clostridium thermocellum]]
| + | |
| - | [[Category: Ig-like]]
| + | |
| - | [[Category: Sugar binding protein]]
| + | |
| Structural highlights
3k4z is a 1 chain structure with sequence from Acetivibrio thermocellus JW20. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.11Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of the carbohydrate-binding module (CBM) 4 Ig fused domain from the cellulosomal cellulase cellobiohydrolase A (CbhA) of Clostridium thermocellum was solved in complex with cellobiose at 2.11 A resolution. This is the first cellulosomal CBM4 crystal structure reported to date. It is similar to the previously solved noncellulosomal soluble oligosaccharide-binding CBM4 structures. However, this new structure possesses a significant feature-a binding site peptide loop with a tryptophan (Trp118) residing midway in the loop. Based on sequence alignment, this structural feature might be common to all cellulosomal clostridial CBM4 modules. Our results indicate that C. thermocellum CbhA CBM4 also has an extended binding pocket that can optimally bind to cellodextrins containing five or more sugar units. Molecular dynamics simulations and experimental binding studies with the Trp118Ala mutant suggest that Trp118 contributes to the binding and, possibly, the orientation of the module to soluble cellodextrins. Furthermore, the binding cleft aromatic residues Trp68 and Tyr110 play a crucial role in binding to bacterial microcrystalline cellulose (BMCC), amorphous cellulose, and soluble oligodextrins. Binding to BMCC is in disagreement with the structural features of the binding pocket, which does not support binding to the flat surface of crystalline cellulose, suggesting that CBM4 binds the amorphous part or the cellulose "whiskers" of BMCC. We propose that clostridial CBM4s have possibly evolved to bind the free-chain ends of crystalline cellulose in addition to their ability to bind soluble cellodextrins.
The unique binding mode of cellulosomal CBM4 from Clostridium thermocellum cellobiohydrolase A.,Alahuhta M, Xu Q, Bomble YJ, Brunecky R, Adney WS, Ding SY, Himmel ME, Lunin VV J Mol Biol. 2010 Sep 17;402(2):374-87. Epub 2010 Jul 21. PMID:20654622[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Alahuhta M, Xu Q, Bomble YJ, Brunecky R, Adney WS, Ding SY, Himmel ME, Lunin VV. The unique binding mode of cellulosomal CBM4 from Clostridium thermocellum cellobiohydrolase A. J Mol Biol. 2010 Sep 17;402(2):374-87. Epub 2010 Jul 21. PMID:20654622 doi:10.1016/j.jmb.2010.07.028
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