Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 45.10 kDa 
• Atom Count: 3350 
• Modelled Residue Count: 329 
• Deposited Residue Count: 342 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4U0Y

Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA

• PDB DOI: 10.2210/pdb4U0Y/pdb
• NDB: 4U0Y

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-14 Released: 2015-01-14 
• Deposition Author(s): Fillenberg, S.B., Muller, Y.A.
• Funding Organization(s): DFG

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.229 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Literature

Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR.

Fillenberg, S.B., Grau, F.C., Seidel, G., Muller, Y.A.

(2015) Nucleic Acids Res 43: 1283-1296

• PubMed: 25564531 
• DOI: 10.1093/nar/gku1374
• Primary Citation of Related Structures:  
  4U0V, 4U0W, 4U0Y, 4WWC


• PubMed Abstract: 
  

The uptake and metabolism of N-acetylglucosamine (GlcNAc) in Bacillus subtilis is controlled by NagR (formerly named YvoA), a member of the widely-occurring GntR/HutC family of transcription regulators. Upon binding to specific DNA operator sites (dre-sites) NagR blocks the transcription of genes for GlcNAc utilization and interaction of NagR with effectors abrogates gene repression. Here we report crystal structures of NagR in complex with operator DNA and in complex with the putative effector molecules glucosamine-6-phosphate (GlcN-6-P) and N-acetylglucosamine-6-phosphate (GlcNAc-6-P). A comparison of the distinct conformational states suggests that effectors are able to displace the NagR-DNA-binding domains (NagR-DBDs) by almost 70 Å upon binding. In addition, a high-resolution crystal structure of isolated NagR-DBDs in complex with palindromic double-stranded DNA (dsDNA) discloses both the determinants for highly sequence-specific operator dre-site recognition and for the unspecific binding of NagR to dsDNA. Extensive biochemical binding studies investigating the affinities of full-length NagR and isolated NagR-DBDs for either random DNA, dre-site-derived palindromic or naturally occurring non-palindromic dre-site sequences suggest that proper NagR function relies on an effector-induced fine-tuning of the DNA-binding affinities of NagR and not on a complete abrogation of its DNA binding.

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Organizational Affiliation: 

Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, D-91052 Erlangen, Germany [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional repressor YvoA	A, B, C, D	78	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: yvoA, BSU35030, nagR
UniProt
Find proteins for O34817 (Bacillus subtilis (strain 168)) Explore O34817  Go to UniProtKB:  O34817

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3')	E, F	15	Bacillus subtilis subsp. subtilis str. 168

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth B], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.229 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.554	α = 90
b = 48.554	β = 90
c = 153.941	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-07-14 
• Released Date: 2015-01-14 
Deposition Author(s): Fillenberg, S.B., Muller, Y.A.

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Funding Organization	Location	Grant Number
DFG	Germany	--

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-01-21
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Database references