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| | <StructureSection load='4ulx' size='340' side='right'caption='[[4ulx]], [[Resolution|resolution]] 2.35Å' scene=''> | | <StructureSection load='4ulx' size='340' side='right'caption='[[4ulx]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ulx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ULX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ULX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ulx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ULX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ULX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.35Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d27|4d27]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.7.1.4 4.7.1.4] </span></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=4ulx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ulx OCA], [https://pdbe.org/4ulx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ulx RCSB], [https://www.ebi.ac.uk/pdbsum/4ulx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ulx 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=4ulx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ulx OCA], [http://pdbe.org/4ulx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ulx RCSB], [http://www.ebi.ac.uk/pdbsum/4ulx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ulx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Thioredoxin|Thioredoxin]] | + | *[[Thioredoxin 3D structures|Thioredoxin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lyase]]
| + | [[Category: Synthetic construct]] |
| - | [[Category: Synthetic construct sequences]] | + | [[Category: Gavira JA]] |
| - | [[Category: Gavira, J A]] | + | [[Category: Ibarra-Molero B]] |
| - | [[Category: Ibarra-Molero, B]] | + | [[Category: Risso VA]] |
| - | [[Category: Risso, V A]] | + | [[Category: Sanchez-Ruiz JM]] |
| - | [[Category: Sanchez-Ruiz, J M]] | + | |
| - | [[Category: Ancestral]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to co-evolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and beta-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: energetic preference for an ancestral amino acid in a modern protein can be linked to re-organization upon mutation to the ancestral local structure around the mutated site. Lastly, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.
Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.,Risso VA, Manssour-Triedo F, Delgado-Delgado A, Arco R, Barroso-delJesus A, Ingles-Prieto A, Godoy-Ruiz R, Gavira JA, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM Mol Biol Evol. 2014 Nov 12. pii: msu312. PMID:25392342[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Risso VA, Manssour-Triedo F, Delgado-Delgado A, Arco R, Barroso-delJesus A, Ingles-Prieto A, Godoy-Ruiz R, Gavira JA, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Mol Biol Evol. 2014 Nov 12. pii: msu312. PMID:25392342 doi:http://dx.doi.org/10.1093/molbev/msu312
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