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5rgd

From Proteopedia

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<StructureSection load='5rgd' size='340' side='right'caption='[[5rgd]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='5rgd' size='340' side='right'caption='[[5rgd]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5rgd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Theau Theau]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5RGD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5rgd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RGD FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NT:6-NITROBENZOTRIAZOLE'>6NT</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]] 1.6&#8491;</td></tr>
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<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6NT:6-NITROBENZOTRIAZOLE'>6NT</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://proteopedia.org/fgij/fg.htm?mol=5rgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgd OCA], [http://pdbe.org/5rgd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5rgd RCSB], [http://www.ebi.ac.uk/pdbsum/5rgd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgd 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=5rgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rgd OCA], [https://pdbe.org/5rgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rgd RCSB], [https://www.ebi.ac.uk/pdbsum/5rgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rgd 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/XYNA_THEAU XYNA_THEAU]
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The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M(-1)s(-1)). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M(-1)s(-1)) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.
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Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.,Broom A, Rakotoharisoa RV, Thompson MC, Zarifi N, Nguyen E, Mukhametzhanov N, Liu L, Fraser JS, Chica RA Nat Commun. 2020 Sep 23;11(1):4808. doi: 10.1038/s41467-020-18619-x. PMID:32968058<ref>PMID:32968058</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 5rgd" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Kemp eliminase|Kemp eliminase]]
*[[Kemp eliminase|Kemp eliminase]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Endo-1,4-beta-xylanase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Theau]]
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[[Category: Thermoascus aurantiacus]]
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[[Category: Broom, A]]
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[[Category: Broom A]]
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[[Category: Chica, R A]]
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[[Category: Chica RA]]
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[[Category: Fraser, J S]]
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[[Category: Fraser JS]]
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[[Category: Rakotoharisoa, R V]]
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[[Category: Rakotoharisoa RV]]
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[[Category: Thompson, M C]]
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[[Category: Thompson MC]]
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[[Category: Hydrolase]]
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Current revision

Crystal Structure of Kemp Eliminase HG3.14 with bound transition state analogue, 277K

PDB ID 5rgd

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