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| | ==Crystal structure of the cyclohexadienyl dehydratase-like solute-binding protein SAR11_1068 from Candidatus Pelagibacter ubique.== | | ==Crystal structure of the cyclohexadienyl dehydratase-like solute-binding protein SAR11_1068 from Candidatus Pelagibacter ubique.== |
| - | <StructureSection load='5wjp' size='340' side='right' caption='[[5wjp]], [[Resolution|resolution]] 1.57Å' scene=''> | + | <StructureSection load='5wjp' size='340' side='right'caption='[[5wjp]], [[Resolution|resolution]] 1.57Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5wjp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_pelagibacter_ubique_htcc1062 Candidatus pelagibacter ubique htcc1062]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WJP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WJP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5wjp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Pelagibacter_ubique_HTCC1062 Candidatus Pelagibacter ubique HTCC1062]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WJP FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kkw|5kkw]]</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]] 1.57Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pheC, SAR11_1068 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=335992 Candidatus Pelagibacter ubique HTCC1062])</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=5wjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wjp OCA], [https://pdbe.org/5wjp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wjp RCSB], [https://www.ebi.ac.uk/pdbsum/5wjp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wjp ProSAT]</span></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=5wjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wjp OCA], [http://pdbe.org/5wjp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wjp RCSB], [http://www.ebi.ac.uk/pdbsum/5wjp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wjp ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q4FLR5_PELUB Q4FLR5_PELUB] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Candidatus pelagibacter ubique htcc1062]] | + | [[Category: Candidatus Pelagibacter ubique HTCC1062]] |
| - | [[Category: Clifton, B E]] | + | [[Category: Large Structures]] |
| - | [[Category: Jackson, C J]] | + | [[Category: Clifton BE]] |
| - | [[Category: Periplasmic binding protein]] | + | [[Category: Jackson CJ]] |
| - | [[Category: Solute-binding protein]]
| + | |
| - | [[Category: Transport protein]]
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| Structural highlights
Function
Q4FLR5_PELUB
Publication Abstract from PubMed
The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.
Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.,Clifton BE, Kaczmarski JA, Carr PD, Gerth ML, Tokuriki N, Jackson CJ Nat Chem Biol. 2018 Apr 23. pii: 10.1038/s41589-018-0043-2. doi:, 10.1038/s41589-018-0043-2. PMID:29686357[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Clifton BE, Kaczmarski JA, Carr PD, Gerth ML, Tokuriki N, Jackson CJ. Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Nat Chem Biol. 2018 Apr 23. pii: 10.1038/s41589-018-0043-2. doi:, 10.1038/s41589-018-0043-2. PMID:29686357 doi:http://dx.doi.org/10.1038/s41589-018-0043-2
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