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6ms3

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Current revision (14:44, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6ms3' size='340' side='right'caption='[[6ms3]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
<StructureSection load='6ms3' size='340' side='right'caption='[[6ms3]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ms3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacld Bacld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MS3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MS3 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ms3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis_DSM_13_=_ATCC_14580 Bacillus licheniformis DSM 13 = ATCC 14580]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MS3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MS3 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xynB, BL03023 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=279010 BACLD])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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=6ms3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ms3 OCA], [http://pdbe.org/6ms3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ms3 RCSB], [http://www.ebi.ac.uk/pdbsum/6ms3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ms3 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ms3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ms3 OCA], [https://pdbe.org/6ms3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ms3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ms3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ms3 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q65MB6_BACLD Q65MB6_BACLD]
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Rational design is an important tool for sculpting functional and stability properties of proteins and its potential can be much magnified when combined with in vitro and natural evolutionary diversity. Herein, we report the structure-guided design of a xylose-releasing exo-beta-1,4-xylanase from an inactive member of glycoside hydrolase family 43 (GH43). Structural analysis revealed a nonconserved substitution (Lys(247) ) that results in the disruption of the hydrogen bond network that supports catalysis. The mutation of this residue to a conserved serine restored the catalytic activity and crystal structure elucidation of the mutant confirmed the recovery of the proper orientation of the catalytically relevant histidine. Interestingly, the tailored enzyme can cleave both xylooligosaccharides and xylan, releasing xylose as the main product, being the first xylose-releasing exo-beta-1,4-xylanase reported in the GH43 family. This enzyme presents a unique active-site topology when compared with closely related beta-xylosidases, which is the absence of a hydrophobic barrier at the positive-subsite region, allowing the accommodation of long substrates. Therefore, the combination of rational design for catalytic activation along with naturally occurring differences in the substrate binding interface led to the discovery of a novel activity within the GH43 family. In addition, these results demonstrate the importance of solvation of the beta-propeller hollow for GH43 catalytic function and expand our mechanistic understanding about the diverse modes of action of GH43 members, a key and polyspecific carbohydrate-active enzyme family abundant in most plant cell-wall-degrading microorganisms.
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Structure-guided design combined with evolutionary diversity led to the discovery of the xylose-releasing exo-xylanase activity in the glycoside hydrolase family 43.,Zanphorlin LM, de Morais MAB, Diogo JA, Domingues MN, de Souza FHM, Ruller R, Murakami MT Biotechnol Bioeng. 2019 Apr;116(4):734-744. doi: 10.1002/bit.26899. Epub 2019 Feb, 5. PMID:30556897<ref>PMID:30556897</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6ms3" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacld]]
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[[Category: Bacillus licheniformis DSM 13 = ATCC 14580]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Diogo, J A]]
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[[Category: Diogo JA]]
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[[Category: Morais, M A.B]]
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[[Category: Morais MAB]]
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[[Category: Murakami, M T]]
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[[Category: Murakami MT]]
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[[Category: Zanphorlin, L M]]
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[[Category: Zanphorlin LM]]
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[[Category: Bacillus lincheniformi]]
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[[Category: Gh43]]
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[[Category: Glycoside hydrolase]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of the GH43 protein BlXynB mutant (K247S) from Bacillus licheniformis

PDB ID 6ms3

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