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| | ==Computationally designed endo-1,4-beta-xylanase== | | ==Computationally designed endo-1,4-beta-xylanase== |
| - | <StructureSection load='3mf9' size='340' side='right' caption='[[3mf9]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='3mf9' size='340' side='right'caption='[[3mf9]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3mf9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"acetomadura_flexuosa"_krasil'nikov_and_agre_1964 "acetomadura flexuosa" krasil'nikov and agre 1964]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MF9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MF9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3mf9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermopolyspora_flexuosa Thermopolyspora flexuosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MF9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mf6|3mf6]], [[1m4w|1m4w]], [[3mfa|3mfa]], [[3mfc|3mfc]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xyn11A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=103836 "Acetomadura flexuosa" Krasil'nikov and Agre 1964])</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=3mf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mf9 OCA], [https://pdbe.org/3mf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mf9 RCSB], [https://www.ebi.ac.uk/pdbsum/3mf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mf9 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></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=3mf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mf9 OCA], [http://pdbe.org/3mf9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mf9 RCSB], [http://www.ebi.ac.uk/pdbsum/3mf9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mf9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q8GMV7_9ACTN Q8GMV7_9ACTN] |
| - | The field of computational protein design has experienced important recent success. However, the de novo computational design of high-affinity protein-ligand interfaces is still largely an open challenge. Using the Rosetta program, we attempted the in silico design of a high-affinity protein interface to a small peptide ligand. We chose the thermophilic endo-1,4-beta-xylanase from Nonomuraea flexuosa as the protein scaffold on which to perform our designs. Over the course of the study, 12 proteins derived from this scaffold were produced and assayed for binding to the target ligand. Unfortunately, none of the designed proteins displayed evidence of high-affinity binding. Structural characterization of four designed proteins revealed that although the predicted structure of the protein model was highly accurate, this structural accuracy did not translate into accurate prediction of binding affinity. Crystallographic analyses indicate that the lack of binding affinity is possibly due to unaccounted for protein dynamics in the 'thumb' region of our design scaffold intrinsic to the family 11 beta-xylanase fold. Further computational analysis revealed two specific, single amino acid substitutions responsible for an observed change in backbone conformation, and decreased dynamic stability of the catalytic cleft. These findings offer new insight into the dynamic and structural determinants of the beta-xylanase proteins.
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| - | Computational design of an endo-1,4-{beta}-xylanase ligand binding site.,Morin A, Kaufmann KW, Fortenberry C, Harp JM, Mizoue LS, Meiler J Protein Eng Des Sel. 2011 Feb 24. PMID:21349882<ref>PMID:21349882</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3mf9" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Acetomadura flexuosa krasil'nikov and agre 1964]] | + | [[Category: Large Structures]] |
| - | [[Category: Endo-1,4-beta-xylanase]] | + | [[Category: Thermopolyspora flexuosa]] |
| - | [[Category: Harp, J M]] | + | [[Category: Harp JM]] |
| - | [[Category: Morin, A]] | + | [[Category: Morin A]] |
| - | [[Category: Family 11]]
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| - | [[Category: Glycosidase]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Jelly-role]]
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| - | [[Category: Peptide binding]]
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| - | [[Category: Thumb]]
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| - | [[Category: Xylan degradation]]
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