|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2r25' size='340' side='right'caption='[[2r25]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='2r25' size='340' side='right'caption='[[2r25]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2r25]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R25 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2r25]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R25 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qsp|1qsp]], [[1oxb|1oxb]], [[1oxk|1oxk]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YPD1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), SLN1, YPD2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=2r25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r25 OCA], [https://pdbe.org/2r25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r25 RCSB], [https://www.ebi.ac.uk/pdbsum/2r25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r25 ProSAT]</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=2r25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r25 OCA], [https://pdbe.org/2r25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r25 RCSB], [https://www.ebi.ac.uk/pdbsum/2r25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r25 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/YPD1_YEAST YPD1_YEAST]] Phosphorelay intermediate protein that is part of the branched SLN1-YPD1-SKN7/SSK1 two-component regulatory system, which controls activity of the HOG1 pathway and gene expression in response to changes in the osmolarity of the extracellular environment. Catalyzes the phosphoryl group transfer from the membrane-bound osmosensing histidine kinase SLN1 to two distinct response regulator proteins, SSK1 in the cytoplasm, and transcription factor SKN7 in the nucleus.<ref>PMID:11073911</ref> <ref>PMID:9843501</ref> [[https://www.uniprot.org/uniprot/SLN1_YEAST SLN1_YEAST]] Histidine kinase that acts as a osmosensor at the plasma membrane. Part of the bifurcated SLN1-YPD1-SKN7/SSK1 two-component regulatory system, which controls activity of the HOG1 pathway and gene expression in response to changes in the osmolarity of the extracellular environment. Under normal osmotic conditions, the histidine kinase autophosphorylates His-576. This phosphate is subsequently transferred to Asp-1144, from where it is relayed to 'His-64' of the phosphorelay intermediate protein YPD1. Under high osmolarity conditions, the histidine kinase is no longer active.<ref>PMID:8808622</ref> <ref>PMID:9843501</ref>
| + | [https://www.uniprot.org/uniprot/YPD1_YEAST YPD1_YEAST] Phosphorelay intermediate protein that is part of the branched SLN1-YPD1-SKN7/SSK1 two-component regulatory system, which controls activity of the HOG1 pathway and gene expression in response to changes in the osmolarity of the extracellular environment. Catalyzes the phosphoryl group transfer from the membrane-bound osmosensing histidine kinase SLN1 to two distinct response regulator proteins, SSK1 in the cytoplasm, and transcription factor SKN7 in the nucleus.<ref>PMID:11073911</ref> <ref>PMID:9843501</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 35: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| - | [[Category: Histidine kinase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Copeland, D M]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Soares, A S]] | + | [[Category: Copeland DM]] |
| - | [[Category: West, A H]] | + | [[Category: Soares AS]] |
| - | [[Category: Zhao, X]] | + | [[Category: West AH]] |
| - | [[Category: Alpha5-beta5]] | + | [[Category: Zhao X]] |
| - | [[Category: Cytoplasm]]
| + | |
| - | [[Category: Four helix bundle]]
| + | |
| - | [[Category: Glycoprotein]]
| + | |
| - | [[Category: Magnesium]]
| + | |
| - | [[Category: Membrane]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Nucleus]]
| + | |
| - | [[Category: Phosphorylation]]
| + | |
| - | [[Category: Response regulator]]
| + | |
| - | [[Category: Signaling protein-transferase complex]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transmembrane]]
| + | |
| - | [[Category: Two-component regulatory system]]
| + | |
| Structural highlights
Function
YPD1_YEAST Phosphorelay intermediate protein that is part of the branched SLN1-YPD1-SKN7/SSK1 two-component regulatory system, which controls activity of the HOG1 pathway and gene expression in response to changes in the osmolarity of the extracellular environment. Catalyzes the phosphoryl group transfer from the membrane-bound osmosensing histidine kinase SLN1 to two distinct response regulator proteins, SSK1 in the cytoplasm, and transcription factor SKN7 in the nucleus.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of the yeast SLN1 response regulator (RR) domain bound to both a phosphoryl analog [beryllium fluoride (BeF(3)(-))] and Mg(2+), in complex with its downstream phosphorelay signaling partner YPD1, has been determined at a resolution of 1.70 A. Comparisons between the BeF(3)(-)-activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1 x Mg(2+) x BeF(3)(-) structure from the complex provides evidence for the first time that the mechanism of phosphorylation-induced activation is highly conserved between bacterial RR domains and this example from a eukaryotic organism. Residues in and around the active site undergo slight rearrangements in order to form bonds with the essential divalent cation and fluorine atoms of BeF(3)(-). Two conserved switch-like residues (Thr1173 and Phe1192) occupy distinctly different positions in the apo versus BeF(3)(-)-bound structures, consistent with the "Y-T" coupling mechanism proposed for the activation of CheY and other bacterial RRs. Several loop regions and the alpha 4-beta 5-alpha 5 surface of the SLN1-R1 domain undergo subtle conformational changes ( approximately 1-3 A displacements relative to the apo structure) that lead to significant changes in terms of contacts that are formed with YPD1. Detailed structural comparisons of protein-protein interactions in the apo and BeF(3)(-)-bound complexes suggest at least a two-state equilibrium model for the formation of a transient encounter complex, in which phosphorylation of the RR promotes the formation of a phosphotransfer-competent complex. In the BeF(3)(-)-activated complex, the position of His64 from YPD1 needs to be within ideal distance of and in near-linear geometry with Asp1144 from the SLN1-R1 domain for phosphotransfer to occur. The ground-state structure presented here suggests that phosphoryl transfer will likely proceed through an associative mechanism involving the formation of a pentacoordinate phosphorus intermediate.
Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog.,Zhao X, Copeland DM, Soares AS, West AH J Mol Biol. 2008 Jan 25;375(4):1141-51. Epub 2007 Nov 22. PMID:18076904[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Janiak-Spens F, Sparling DP, West AH. Novel role for an HPt domain in stabilizing the phosphorylated state of a response regulator domain. J Bacteriol. 2000 Dec;182(23):6673-8. PMID:11073911
- ↑ Li S, Ault A, Malone CL, Raitt D, Dean S, Johnston LH, Deschenes RJ, Fassler JS. The yeast histidine protein kinase, Sln1p, mediates phosphotransfer to two response regulators, Ssk1p and Skn7p. EMBO J. 1998 Dec 1;17(23):6952-62. PMID:9843501 doi:http://dx.doi.org/10.1093/emboj/17.23.6952
- ↑ Zhao X, Copeland DM, Soares AS, West AH. Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog. J Mol Biol. 2008 Jan 25;375(4):1141-51. Epub 2007 Nov 22. PMID:18076904 doi:10.1016/j.jmb.2007.11.045
|
