6LXN

Crystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR in complex with F1-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for promoter DNA recognition by the response regulator OmpR.

Sadotra, S.Lou, Y.C.Tang, H.C.Chiu, Y.C.Hsu, C.H.Chen, C.

(2020) J Struct Biol 213: 107638-107638

  • DOI: 10.1016/j.jsb.2020.107638
  • Primary Citation of Related Structures:  
    6LXM, 6LXL, 6LXN

  • PubMed Abstract: 
  • OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp re ...

    OmpR, a response regulator of the EnvZ/OmpR two-component system (TCS), controls the reciprocal regulation of two porin proteins, OmpF and OmpC, in bacteria. During signal transduction, OmpR (OmpR-FL) undergoes phosphorylation at its conserved Asp residue in the N-terminal receiver domain (OmpRn) and recognizes the promoter DNA from its C-terminal DNA-binding domain (OmpRc) to elicit an adaptive response. Apart from that, OmpR regulates many genes in Escherichia coli and is important for virulence in several pathogens. However, the molecular mechanism of the regulation and the structural basis of OmpR-DNA binding is still not fully clear. In this study, we presented the crystal structure of OmpRc in complex with the F1 region of the ompF promoter DNA from E. coli. Our structural analysis suggested that OmpRc binds to its cognate DNA as a homodimer, only in a head-to-tail orientation. Also, the OmpRc apo-form showed a unique domain-swapped crystal structure under different crystallization conditions. Biophysical experimental data, such as NMR, fluorescent polarization and thermal stability, showed that inactive OmpR-FL (unphosphorylated) could bind to promoter DNA with a weaker binding affinity as compared with active OmpR-FL (phosphorylated) or OmpRc, and also confirmed that phosphorylation may only enhance DNA binding. Furthermore, the dimerization interfaces in the OmpRc-DNA complex structure identified in this study provide an opportunity to understand the regulatory role of OmpR and explore the potential for this "druggable" target.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. Electronic address: bmchinp@ibms.sinica.edu.tw.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulatory protein OmpRAB113Escherichia coliMutation(s): 0 
Gene Names: ompRNCTC10764_03768
Find proteins for A0A376JR14 (Escherichia coli)
Explore A0A376JR14 
Go to UniProtKB:  A0A376JR14
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (27-MER)C27Escherichia coli
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (27-MER)D27Escherichia coli K-12
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.178 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.753α = 90
b = 70.753β = 90
c = 165.344γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan108-2113-M-002-011
Ministry of Science and Technology (MoST, Taiwan)Taiwan108-2628-B-002-013

Revision History 

  • Version 1.0: 2020-12-23
    Type: Initial release