3Q15

Crystal Structure of RapH complexed with Spo0F

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.192 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural basis of response regulator dephosphorylation by Rap phosphatases.

Parashar, V., Mirouze, N., Dubnau, D.A., Neiditch, M.B.

(2011) Plos Biol. 9: e1000589-e1000589

  • DOI: 10.1371/journal.pbio.1000589

  • PubMed Abstract: 

    • Bacterial Rap family proteins have been most extensively studied in Bacillus subtilis, where they regulate activities including sporulation, genetic competence, antibiotic expression, and the movement of the ICEBs1 transposon. One subset of Rap prote ...

    Bacterial Rap family proteins have been most extensively studied in Bacillus subtilis, where they regulate activities including sporulation, genetic competence, antibiotic expression, and the movement of the ICEBs1 transposon. One subset of Rap proteins consists of phosphatases that control B. subtilis and B. anthracis sporulation by dephosphorylating the response regulator Spo0F. The mechanistic basis of Rap phosphatase activity was unknown. Here we present the RapH-Spo0F X-ray crystal structure, which shows that Rap proteins consist of a 3-helix bundle and a tetratricopeptide repeat domain. Extensive biochemical and genetic functional studies reveal the importance of the observed RapH-Spo0F interactions, including the catalytic role of a glutamine in the RapH 3-helix bundle that inserts into the Spo0F active site. We show that in addition to dephosphorylating Spo0F, RapH can antagonize sporulation by sterically blocking phosphoryl transfer to and from Spo0F. Our structure-function analysis of the RapH-Spo0F interaction identified Rap protein residues critical for Spo0F phosphatase activity. This information enabled us to assign Spo0F phosphatase activity to a Rap protein based on sequence alone, which was not previously possible. Finally, as the ultimate test of our newfound understanding of the structural requirements for Rap phosphatase function, a non-phosphatase Rap protein that inhibits the binding of the response regulator ComA to DNA was rationally engineered to dephosphorylate Spo0F. In addition to revealing the mechanistic basis of response regulator dephosphorylation by Rap proteins, our studies support the previously proposed T-loop-Y allostery model of receiver domain regulation that restricts the aromatic "switch" residue to an internal position when the β4-α4 loop adopts an active-site proximal conformation.

    Organizational Affiliation: 

    Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, New Jersey, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Response regulator aspartate phosphatase H
A, B
378Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: rapH (yeeH, yzqA)
EC: 3.1.-.-
Find proteins for Q59HN8 (Bacillus subtilis (strain 168))
Go to UniProtKB:  Q59HN8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sporulation initiation phosphotransferase F
C, D
126Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: spo0F
EC: 2.7.-.-
Find proteins for P06628 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P06628
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.192 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.064α = 90.00
b = 157.452β = 110.57
c = 84.715γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance