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| | <StructureSection load='5l9f' size='340' side='right'caption='[[5l9f]], [[Resolution|resolution]] 2.59Å' scene=''> | | <StructureSection load='5l9f' size='340' side='right'caption='[[5l9f]], [[Resolution|resolution]] 2.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5l9f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cholerae-suis"_smith_1894 "bacillus cholerae-suis" smith 1894]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L9F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L9F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5l9f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L9F FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <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]] 2.594Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hisA, AL032_11160, IN36_13675, IN69_03475, IN95_11755 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=28901 "Bacillus cholerae-suis" Smith 1894])</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=5l9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l9f OCA], [https://pdbe.org/5l9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l9f RCSB], [https://www.ebi.ac.uk/pdbsum/5l9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l9f 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/1-(5-phosphoribosyl)-5-_((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide_isomerase 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.16 5.3.1.16] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5l9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l9f OCA], [http://pdbe.org/5l9f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l9f RCSB], [http://www.ebi.ac.uk/pdbsum/5l9f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l9f ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/HIS4_SALTY HIS4_SALTY] |
| | <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: Bacillus cholerae-suis smith 1894]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Guo, X]] | + | [[Category: Salmonella enterica]] |
| - | [[Category: Selmer, M]] | + | [[Category: Guo X]] |
| - | [[Category: Soderholm, A]] | + | [[Category: Selmer M]] |
| - | [[Category: Hisa]] | + | [[Category: Soderholm A]] |
| - | [[Category: Iad model]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Protein evolution]]
| + | |
| - | [[Category: Trpf]]
| + | |
| Structural highlights
Function
HIS4_SALTY
Publication Abstract from PubMed
New genes can arise by duplication and divergence, but there is a fundamental gap in our understanding of the relationship between these genes, the evolving proteins they encode, and the fitness of the organism. Here we used crystallography, NMR dynamics, kinetics, and mass spectrometry to explain the molecular innovations that arose during a previous real-time evolution experiment. In that experiment, the (betaalpha)8 barrel enzyme HisA was under selection for two functions (HisA and TrpF), resulting in duplication and divergence of the hisA gene to encode TrpF specialists, HisA specialists, and bifunctional generalists. We found that selection affects enzyme structure and dynamics, and thus substrate preference, simultaneously and sequentially. Bifunctionality is associated with two distinct sets of loop conformations, each essential for one function. We observed two mechanisms for functional specialization: structural stabilization of each loop conformation and substrate-specific adaptation of the active site. Intracellular enzyme performance, calculated as the product of catalytic efficiency and relative expression level, was not linearly related to fitness. Instead, we observed thresholds for each activity above which further improvements in catalytic efficiency had little if any effect on growth rate. Overall, we have shown how beneficial substitutions selected during real-time evolution can lead to manifold changes in enzyme function and bacterial fitness. This work emphasizes the speed at which adaptive evolution can yield enzymes with sufficiently high activities such that they no longer limit the growth of their host organism, and confirms the (betaalpha)8 barrel as an inherently evolvable protein scaffold.
Structural and functional innovations in the real-time evolution of new (betaalpha)8 barrel enzymes.,Newton MS, Guo X, Soderholm A, Nasvall J, Lundstrom P, Andersson DI, Selmer M, Patrick WM Proc Natl Acad Sci U S A. 2017 Apr 17. pii: 201618552. doi:, 10.1073/pnas.1618552114. PMID:28416687[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Newton MS, Guo X, Soderholm A, Nasvall J, Lundstrom P, Andersson DI, Selmer M, Patrick WM. Structural and functional innovations in the real-time evolution of new (betaalpha)8 barrel enzymes. Proc Natl Acad Sci U S A. 2017 Apr 17. pii: 201618552. doi:, 10.1073/pnas.1618552114. PMID:28416687 doi:http://dx.doi.org/10.1073/pnas.1618552114
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