4S04

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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:  
    4S04, 4S05

  • 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-binding domains (DBDs) to recognize promoter DNA to elicit adaptive responses ...

    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

    Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding transcriptional regulator BasRABEF232Klebsiella pneumoniae JM45Mutation(s): 2 
Gene Names: N559_3529
Find proteins for A0A0R4I965 (Klebsiella pneumoniae JM45)
Explore A0A0R4I965 
Go to UniProtKB:  A0A0R4I965
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (25-MER)C, G25synthetic construct
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (25-MER)D, H25synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEF
Query on BEF

Download CCD File 
A, B, E, F
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.327α = 90
b = 250.761β = 90
c = 108.944γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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