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Title: Crystal Structure of a Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to a Phosphoryl Analog

Abstract

The crystal structure of the yeast SLN1 response regulator (RR) domain bound to both a phosphoryl analog [beryllium fluoride (BeF3 -)] and Mg2 +, in complex with its downstream phosphorelay signaling partner YPD1, has been determined at a resolution of 1.70 Angstroms. Comparisons between the BeF3 --activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1{center_dot}Mg2 +{center_dot}BeF3 - 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 BeF3 -. Two conserved switch-like residues (Thr1173 and Phe1192) occupy distinctly different positions in the apo versus BeF3 --bound structures, consistent with the 'Y-T' coupling mechanism proposed for the activation of CheY and other bacterial RRs. Several loop regions and the a4-{beta}5-a5 surface of the SLN1-R1 domain undergo subtle conformational changes ({approx} 1-3 Angstroms 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 inmore » the apo and BeF3 --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 BeF3 --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.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Brookhaven National Lab. (BNL), Upton, NY (United States). National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
959744
Report Number(s):
BNL-82730-2009-JA
Journal ID: ISSN 0022-2836; JMOBAK; TRN: US1005796
DOE Contract Number:  
DE-AC02-98CH10886
Resource Type:
Journal Article
Journal Name:
Journal of Molecular Biology
Additional Journal Information:
Journal Volume: 375; Journal Issue: 4; Journal ID: ISSN 0022-2836
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; ATOMS; BERYLLIUM; CATIONS; CONFORMATIONAL CHANGES; CRYSTAL STRUCTURE; FLUORIDES; FLUORINE; GEOMETRY; PHOSPHORUS; PHOSPHORYLATION; PROTEINS; RESIDUES; RESOLUTION; TRANSIENTS; YEASTS; national synchrotron light source

Citation Formats

Zhao, X, Copeland, D, Soares, A, and West, A. Crystal Structure of a Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to a Phosphoryl Analog. United States: N. p., 2008. Web. doi:10.1016/j.jmb.2007.11.045.
Zhao, X, Copeland, D, Soares, A, & West, A. Crystal Structure of a Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to a Phosphoryl Analog. United States. https://doi.org/10.1016/j.jmb.2007.11.045
Zhao, X, Copeland, D, Soares, A, and West, A. 2008. "Crystal Structure of a Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to a Phosphoryl Analog". United States. https://doi.org/10.1016/j.jmb.2007.11.045.
@article{osti_959744,
title = {Crystal Structure of a Complex Between the Phosphorelay Protein YPD1 and the Response Regulator Domain of SLN1 Bound to a Phosphoryl Analog},
author = {Zhao, X and Copeland, D and Soares, A and West, A},
abstractNote = {The crystal structure of the yeast SLN1 response regulator (RR) domain bound to both a phosphoryl analog [beryllium fluoride (BeF3 -)] and Mg2 +, in complex with its downstream phosphorelay signaling partner YPD1, has been determined at a resolution of 1.70 Angstroms. Comparisons between the BeF3 --activated complex and the unliganded (or apo) complex determined previously reveal modest but important differences. The SLN1-R1{center_dot}Mg2 +{center_dot}BeF3 - 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 BeF3 -. Two conserved switch-like residues (Thr1173 and Phe1192) occupy distinctly different positions in the apo versus BeF3 --bound structures, consistent with the 'Y-T' coupling mechanism proposed for the activation of CheY and other bacterial RRs. Several loop regions and the a4-{beta}5-a5 surface of the SLN1-R1 domain undergo subtle conformational changes ({approx} 1-3 Angstroms 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 BeF3 --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 BeF3 --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.},
doi = {10.1016/j.jmb.2007.11.045},
url = {https://www.osti.gov/biblio/959744}, journal = {Journal of Molecular Biology},
issn = {0022-2836},
number = 4,
volume = 375,
place = {United States},
year = {Tue Jan 01 00:00:00 EST 2008},
month = {Tue Jan 01 00:00:00 EST 2008}
}