Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 42.88 kDa 
• Atom Count: 2817 
• Residue Count: 265 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

6LXN

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

• DOI: 10.2210/pdb6LXN/pdb
• NDB: 6LXN

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli, Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-11 Released: 2020-12-23 
• Deposition Author(s): Sadotra, S., Chen, C., Hsu, C.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

---

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 

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

• PubMed: 33152421 
• 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 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: [e-mail].

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein OmpR	A, B	113	Escherichia coli	Mutation(s): 0  Gene Names: ompR, NCTC10764_03768
Find proteins for A0A376JR14 (Escherichia coli) Explore A0A376JR14  Go to UniProtKB:  A0A376JR14

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	C	27	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	D	27	Escherichia coli K-12

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 70.753	α = 90
b = 70.753	β = 90
c = 165.344	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-02-11 
• Released Date: 2020-12-23 
Deposition Author(s): Sadotra, S., Chen, C., Hsu, C.H.

---

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	108-2113-M-002-011
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	108-2628-B-002-013

Revision History 

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