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| | <StructureSection load='6owy' size='340' side='right'caption='[[6owy]], [[Resolution|resolution]] 2.07Å' scene=''> | | <StructureSection load='6owy' size='340' side='right'caption='[[6owy]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6owy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OWY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6owy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OWY 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>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 2.07Å</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=6owy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owy OCA], [http://pdbe.org/6owy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6owy RCSB], [http://www.ebi.ac.uk/pdbsum/6owy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6owy ProSAT]</span></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>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=6owy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6owy OCA], [https://pdbe.org/6owy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6owy RCSB], [https://www.ebi.ac.uk/pdbsum/6owy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6owy ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI]] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref> | + | [https://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as approximately 12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.
| + | |
| - | | + | |
| - | Identifying dynamic, partially occupied residues using anomalous scattering.,Rocchio S, Duman R, El Omari K, Mykhaylyk V, Orr C, Yan Z, Salmon L, Wagner A, Bardwell JCA, Horowitz S Acta Crystallogr D Struct Biol. 2019 Dec 1;75(Pt 12):1084-1095. doi:, 10.1107/S2059798319014475. Epub 2019 Nov 19. PMID:31793902<ref>PMID:31793902</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6owy" style="background-color:#fffaf0;"></div>
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bardwell, J C.A]] | + | [[Category: Bardwell JCA]] |
| - | [[Category: Duman, R]] | + | [[Category: Duman R]] |
| - | [[Category: Horowitz, S]] | + | [[Category: El Omari K]] |
| - | [[Category: Mykhaylyk, V]] | + | [[Category: Horowitz S]] |
| - | [[Category: Omari, K El]] | + | [[Category: Mykhaylyk V]] |
| - | [[Category: Rocchio, S]] | + | [[Category: Rocchio S]] |
| - | [[Category: Wagner, A]] | + | [[Category: Wagner A]] |
| - | [[Category: Yan, Z]] | + | [[Category: Yan Z]] |
| - | [[Category: Chaperone]]
| + | |
| - | [[Category: Periplasmic]]
| + | |
| Structural highlights
Function
SPY_ECOLI An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).[1] [2] [3]
References
- ↑ Quan S, Koldewey P, Tapley T, Kirsch N, Ruane KM, Pfizenmaier J, Shi R, Hofmann S, Foit L, Ren G, Jakob U, Xu Z, Cygler M, Bardwell JC. Genetic selection designed to stabilize proteins uncovers a chaperone called Spy. Nat Struct Mol Biol. 2011 Feb 13. PMID:21317898 doi:10.1038/nsmb.2016
- ↑ Quan S, Wang L, Petrotchenko EV, Makepeace KA, Horowitz S, Yang J, Zhang Y, Borchers CH, Bardwell JC. Super Spy variants implicate flexibility in chaperone action. Elife. 2014;3:e01584. doi: 10.7554/eLife.01584. Epub 2014 Feb 4. PMID:24497545 doi:http://dx.doi.org/10.7554/eLife.01584
- ↑ Stull F, Koldewey P, Humes JR, Radford SE, Bardwell JC. Substrate protein folds while it is bound to the ATP-independent chaperone Spy. Nat Struct Mol Biol. 2016 Jan;23(1):53-8. doi: 10.1038/nsmb.3133. Epub 2015 Nov, 30. PMID:26619265 doi:http://dx.doi.org/10.1038/nsmb.3133
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