2r25
From Proteopedia
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|PDB= 2r25 |SIZE=350|CAPTION= <scene name='initialview01'>2r25</scene>, resolution 1.70Å | |PDB= 2r25 |SIZE=350|CAPTION= <scene name='initialview01'>2r25</scene>, resolution 1.70Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <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> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span> |
|GENE= YPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), SLN1, YPD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]) | |GENE= YPD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), SLN1, YPD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1qsp|1QSP]], [[1oxb|1OXB]], [[1oxk|1OXK]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r25 OCA], [http://www.ebi.ac.uk/pdbsum/2r25 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2r25 RCSB]</span> | ||
}} | }} | ||
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[[Category: West, A H.]] | [[Category: West, A H.]] | ||
[[Category: Zhao, X.]] | [[Category: Zhao, X.]] | ||
| - | [[Category: BEF]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NA]] | ||
[[Category: alpha5-beta5]] | [[Category: alpha5-beta5]] | ||
[[Category: cytoplasm]] | [[Category: cytoplasm]] | ||
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[[Category: two-component regulatory system]] | [[Category: two-component regulatory system]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:55:46 2008'' |
Revision as of 01:55, 31 March 2008
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| , resolution 1.70Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | YPD1 (Saccharomyces cerevisiae), SLN1, YPD2 (Saccharomyces cerevisiae) | ||||||
| Activity: | Histidine kinase, with EC number 2.7.13.3 | ||||||
| Related: | 1QSP, 1OXB, 1OXK
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-
Overview
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.
About this Structure
2R25 is a Protein complex structure of sequences from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Mon Mar 31 04:55:46 2008
Categories: Histidine kinase | Protein complex | Saccharomyces cerevisiae | Copeland, D M. | Soares, A S. | West, A H. | Zhao, X. | Alpha5-beta5 | Cytoplasm | Four helix bundle | Glycoprotein | Histidine kinase (hk) | Histidine phosphotransfer (hpt) protein | Magnesium | Membrane | Metal-binding | Nucleus | Phosphorylation | Response regulator | Signaling protein/transferase complex | Transferase | Transmembrane | Two-component regulatory system
