2R25

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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, D.M.Soares, A.S.West, A.H.

(2008) J.Mol.Biol. 375: 1141-1151

  • DOI: 10.1016/j.jmb.2007.11.045
  • Also Cited By: 5KBX

  • 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 resolut ...

    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.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, OK 73019, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphorelay intermediate protein YPD1
A
167Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YPD1
Find proteins for Q07688 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07688
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Osmosensing histidine protein kinase SLN1
B
133Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SLN1 (YPD2)
EC: 2.7.13.3
Find proteins for P39928 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39928
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.013α = 90.00
b = 75.544β = 90.00
c = 98.392γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-3000data reduction
PHASERphasing
SCALEPACKdata scaling
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description