4RAY

Crystal structure of Magnetospirillum gryphiswaldense MSR-1 Apo-Fur


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.

Deng, Z.Wang, Q.Liu, Z.Zhang, M.Machado, A.C.Chiu, T.P.Feng, C.Zhang, Q.Yu, L.Qi, L.Zheng, J.Wang, X.Huo, X.Qi, X.Li, X.Wu, W.Rohs, R.Li, Y.Chen, Z.

(--) Nat Commun 6: 7642-7642

  • DOI: 10.1038/ncomms8642
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution s ...

    Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution structures of Magnetospirillum gryphiswaldense MSR-1 Fur in four different states: apo-Fur, holo-Fur, the Fur-feoAB1 operator complex and the Fur-Pseudomonas aeruginosa Fur box complex. Apo-Fur is a transition metal ion-independent dimer whose binding induces profound conformational changes and confers DNA-binding ability. Structural characterization, mutagenesis, biochemistry and in vivo data reveal that Fur recognizes DNA by using a combination of base readout through direct contacts in the major groove and shape readout through recognition of the minor-groove electrostatic potential by lysine. The resulting conformational plasticity enables Fur binding to diverse substrates. Our results provide insights into metal ion activation and substrate recognition by Fur that suggest pathways to engineer magnetotactic bacteria and antipathogenic drugs.


    Organizational Affiliation

    State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)
A, B
145Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1)Mutation(s): 0 
Gene Names: Fur (fur)
Find proteins for V6F4Q0 (Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1))
Go to UniProtKB:  V6F4Q0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.192α = 90.00
b = 78.151β = 108.47
c = 66.316γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
HKL-2000data scaling
APEXdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release