5DCL

Structure of a lantibiotic response regulator: N terminal domain of the nisin resistance regulator NsrR

• PDB DOI:  https://doi.org/10.2210/pdb5DCL/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Streptococcus agalactiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-24 Released: 2016-03-16 
• Deposition Author(s): Khosa, S., Kleinschrodt, D., Hoeppner, A., Smits, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.219 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Structure of the Response Regulator NsrR from Streptococcus agalactiae, Which Is Involved in Lantibiotic Resistance.

Khosa, S., Hoeppner, A., Gohlke, H., Schmitt, L., Smits, S.H.

(2016) PLoS One 11: e0149903-e0149903

• PubMed: 26930060 
• DOI: https://doi.org/10.1371/journal.pone.0149903
• Primary Citation of Related Structures:  
  5DCL, 5DCM


• PubMed Abstract: 
  

Lantibiotics are antimicrobial peptides produced by Gram-positive bacteria. Interestingly, several clinically relevant and human pathogenic strains are inherently resistant towards lantibiotics. The expression of the genes responsible for lantibiotic resistance is regulated by a specific two-component system consisting of a histidine kinase and a response regulator. Here, we focused on a response regulator involved in lantibiotic resistance, NsrR from Streptococcus agalactiae, and determined the crystal structures of its N-terminal receiver domain and C-terminal DNA-binding effector domain. The C-terminal domain exhibits a fold that classifies NsrR as a member of the OmpR/PhoB subfamily of regulators. Amino acids involved in phosphorylation, dimerization, and DNA-binding were identified and demonstrated to be conserved in lantibiotic resistance regulators. Finally, a model of the full-length NsrR in the active and inactive state provides insights into protein dimerization and DNA-binding.

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Organizational Affiliation: 

Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225, Duesseldorf, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 57.93 kDa 
• Atom Count: 2,155 
• Modelled Residue Count: 234 
• Deposited Residue Count: 486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PhoB family transcriptional regulator	A, B	243	Streptococcus agalactiae	Mutation(s): 0  Gene Names: DK41_05180, EN72_05470, graR, AX245_04450, C4618_08650, GE200_02475, NCTC6175_01356, RDF_0970
UniProt
Find proteins for X5JZS1 (Streptococcus agalactiae) Explore X5JZS1  Go to UniProtKB:  X5JZS1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.219 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.05	α = 90
b = 107.13	β = 90
c = 39.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Khosa, S., Kleinschrodt, D., Hoeppner, A., Smits, S.H.

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release