4avo: Difference between revisions

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<StructureSection load='4avo' size='340' side='right'caption='[[4avo]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='4avo' size='340' side='right'caption='[[4avo]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4avo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AVO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AVO FirstGlance]. <br>
<table><tr><td colspan='2'>[[4avo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobifida_fusca_YX Thermobifida fusca YX]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AVO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AVO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.8&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PRD_900020:beta-cellohexaose'>PRD_900020</scene></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=4avo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4avo OCA], [https://pdbe.org/4avo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4avo RCSB], [https://www.ebi.ac.uk/pdbsum/4avo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4avo 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=4avo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4avo OCA], [https://pdbe.org/4avo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4avo RCSB], [https://www.ebi.ac.uk/pdbsum/4avo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4avo ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q47SA9_THEFY Q47SA9_THEFY]
Cellobiohydrolases (CBHs) are typically major components of natural enzyme cocktails for biomass degradation. Their active sites are enclosed in a tunnel, enabling processive hydrolysis of cellulose chains. Glycoside hydrolase Family 6 (GH6) CBHs act from non-reducing ends by an inverting mechanism, and are present in many cellulolytic fungi and bacteria. The bacterial Thermobifida fusca Cel6B (TfuCel6B) exhibits a longer and more enclosed active site tunnel than its fungal counterparts. Here, we determine the structures of two TfuCel6B mutants co-crystallized with cellobiose, D274A (catalytic acid), and the double mutant D226A/S232A, which targets the putative catalytic base and a conserved serine that binds the nucleophilic water. The ligand binding and the structure of the active site are retained compared to the wild-type structure, supporting the hypothesis that these residues are directly involved in catalysis. One structure exhibits crystallographic waters that enable construction of a model of the alpha-anomer product after hydrolysis. Interestingly, the product sites of TfuCel6B are completely enclosed by an 'exit loop' not present in fungal GH6 CBHs, and an extended 'bottom loop'. From the structures, we hypothesize that either of the loops enclosing the product subsites in the TfuCel6B active site tunnel must open substantially for product release. With simulation, we demonstrate that both loops can readily open to allow product release with equal probability in solution or when the enzyme is engaged on cellulose. Overall, this study reveals new structural details of GH6 CBHs likely important for functional differences amongst enzymes from this important family.
 
Loop motions important to product expulsion in the Thermobifida fusca glycoside hydrolase Family 6 cellobiohydrolase from structural and computational studies.,Wu M, Bu L, Vuong TV, Wilson DB, Crowley MF, Sandgren M, Stahlberg J, Beckham GT, Hansson H J Biol Chem. 2013 Sep 30. PMID:24085303<ref>PMID:24085303</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4avo" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hansson, H]]
[[Category: Thermobifida fusca YX]]
[[Category: Sandgren, M]]
[[Category: Hansson H]]
[[Category: Stahlberg, J]]
[[Category: Sandgren M]]
[[Category: Vuong, T V]]
[[Category: Stahlberg J]]
[[Category: Wilson, D B]]
[[Category: Vuong TV]]
[[Category: Wu, M]]
[[Category: Wilson DB]]
[[Category: Cellulase]]
[[Category: Wu M]]
[[Category: Cellulose degradation]]
[[Category: Glycoside hydrolase family 6]]
[[Category: Hydrolase]]

Revision as of 07:16, 1 May 2024

Thermobifida fusca cellobiohydrolase Cel6B catalytic mutant D274A cocrystallized with cellobiose

4avo, resolution 1.80Å

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