2R25

Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3-

Summary for 2R25

• Entry DOI: 10.2210/pdb2r25/pdb
• Related: 1OXB 1OXK 1QSP
• Descriptor: Phosphorelay intermediate protein YPD1, Osmosensing histidine protein kinase SLN1, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: alpha5-beta5, response regulator, four helix bundle, histidine phosphotransfer (hpt) protein, histidine kinase (hk), cytoplasm, nucleus, phosphorylation, two-component regulatory system, glycoprotein, magnesium, membrane, metal-binding, transferase, transmembrane, signaling protein-transferase complex, signaling protein/transferase
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Cellular location: Cytoplasm: Q07688; Cell membrane ; Multi-pass membrane protein : P39928
• Total number of polymer chains: 2
• Total formula weight: 34251.29

Authors

Copeland, D.M.,Zhao, X.,Soares, A.S.,West, A.H. (deposition date: 2007-08-24, release date: 2008-01-15, Last modification date: 2023-08-30)

Primary citation

Zhao, X.,Copeland, D.M.,Soares, A.S.,West, A.H.
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., 375:1141-1151, 2008

PubMed Abstract: 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.

PubMed: 18076904
DOI: 10.1016/j.jmb.2007.11.045

Experimental method

X-RAY DIFFRACTION (1.7 Å)