6c2c: Difference between revisions

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<StructureSection load='6c2c' size='340' side='right'caption='[[6c2c]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='6c2c' size='340' side='right'caption='[[6c2c]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6c2c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Achromobacter_georgiopolitanum Achromobacter georgiopolitanum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C2C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C2C FirstGlance]. <br>
<table><tr><td colspan='2'>[[6c2c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C2C FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.597&#8491;</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=6c2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c2c OCA], [http://pdbe.org/6c2c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c2c RCSB], [http://www.ebi.ac.uk/pdbsum/6c2c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c2c ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6c2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c2c OCA], [https://pdbe.org/6c2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c2c RCSB], [https://www.ebi.ac.uk/pdbsum/6c2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c2c ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Characterizing the adaptive landscapes that encompass the emergence of novel enzyme functions can provide molecular insights into both enzymatic and evolutionary mechanisms. Here, we combine ancestral protein reconstruction with biochemical, structural and mutational analyses to characterize the functional evolution of methyl-parathion hydrolase (MPH), an organophosphate-degrading enzyme. We identify five mutations that are necessary and sufficient for the evolution of MPH from an ancestral dihydrocoumarin hydrolase. In-depth analyses of the adaptive landscapes encompassing this evolutionary transition revealed that the mutations form a complex interaction network, defined in part by higher-order epistasis, that constrained the adaptive pathways available. By also characterizing the adaptive landscapes in terms of their functional activities towards three additional organophosphate substrates, we reveal that subtle differences in the polarity of the substrate substituents drastically alter the network of epistatic interactions. Our work suggests that the mutations function collectively to enable substrate recognition via subtle structural repositioning.
Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.,Yang G, Anderson DW, Baier F, Dohmen E, Hong N, Carr PD, Kamerlin SCL, Jackson CJ, Bornberg-Bauer E, Tokuriki N Nat Chem Biol. 2019 Nov;15(11):1120-1128. doi: 10.1038/s41589-019-0386-3. Epub, 2019 Oct 21. PMID:31636435<ref>PMID:31636435</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6c2c" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Achromobacter georgiopolitanum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Baier, F]]
[[Category: Pseudomonas sp]]
[[Category: Carr, P D]]
[[Category: Baier F]]
[[Category: Hong, N S]]
[[Category: Carr PD]]
[[Category: Jackson, C J]]
[[Category: Hong N-S]]
[[Category: Tokuriki, N]]
[[Category: Jackson CJ]]
[[Category: Yang, G]]
[[Category: Tokuriki N]]
[[Category: A xenobiotic degrading enzyme]]
[[Category: Yang G]]
[[Category: Directed evolution]]
[[Category: Hydrolase]]
[[Category: Phosphatase]]

Latest revision as of 17:25, 13 March 2024

The molecular basis for the functional evolution of an organophosphate hydrolysing enzymeThe molecular basis for the functional evolution of an organophosphate hydrolysing enzyme

Structural highlights

6c2c is a 2 chain structure with sequence from Pseudomonas sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.597Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

6c2c, resolution 1.60Å

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