4S04

Crystal structure of Klebsiella pneumoniae PmrA in complex with PmrA box DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and dynamics of polymyxin-resistance-associated response regulator PmrA in complex with promoter DNA.

Lou, Y.C.Weng, T.H.Li, Y.C.Kao, Y.F.Lin, W.F.Peng, H.L.Chou, S.H.Hsiao, C.D.Chen, C.

(2015) Nat Commun 6: 8838-8838

  • DOI: 10.1038/ncomms9838
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PmrA, an OmpR/PhoB family response regulator, manages genes for antibiotic resistance. Phosphorylation of OmpR/PhoB response regulator induces the formation of a symmetric dimer in the N-terminal receiver domain (REC), promoting two C-terminal DNA-bi ...

    PmrA, an OmpR/PhoB family response regulator, manages genes for antibiotic resistance. Phosphorylation of OmpR/PhoB response regulator induces the formation of a symmetric dimer in the N-terminal receiver domain (REC), promoting two C-terminal DNA-binding domains (DBDs) to recognize promoter DNA to elicit adaptive responses. Recently, determination of the KdpE-DNA complex structure revealed an REC-DBD interface in the upstream protomer that may be necessary for transcription activation. Here, we report the 3.2-Å-resolution crystal structure of the PmrA-DNA complex, which reveals a similar yet different REC-DBD interface. However, NMR studies show that in the DNA-bound state, two domains tumble separately and an REC-DBD interaction is transiently populated in solution. Reporter gene analyses of PmrA variants with altered interface residues suggest that the interface is not crucial for supporting gene expression. We propose that REC-DBD interdomain dynamics and the DBD-DBD interface help PmrA interact with RNA polymerase holoenzyme to activate downstream gene transcription.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding transcriptional regulator BasR
A, B, E, F
232Klebsiella pneumoniae JM45Mutation(s): 2 
Find proteins for A0A0R4I965 (Klebsiella pneumoniae JM45)
Go to UniProtKB:  A0A0R4I965
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (25-MER)C,G25synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)D,H25synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 194.327α = 90.00
b = 250.761β = 90.00
c = 108.944γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Database references
  • Version 1.2: 2018-04-04
    Type: Advisory, Data collection
  • Version 1.3: 2018-04-18
    Type: Data collection