4RB3

Crystal structure of Magnetospirillum gryphiswaldense MSR-1 Fur-Mn2+-feoAB1 operator

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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.

(null) Nat Commun 6: 7642-7642

  • DOI: 10.1038/ncomms8642
  • Primary Citation of Related Structures:  
    4RAY, 4RAZ, 4RB0, 4RB1, 4RB2, 4RB3

  • 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 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)C, D145Magnetospirillum gryphiswaldense MSR-1 v2Mutation(s): 3 
Gene Names: fur, MGMSRv2_3137
UniProt
Find proteins for V6F4Q0 (Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1))
Explore V6F4Q0 
Go to UniProtKB:  V6F4Q0
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (25-MER)A25N/A
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (25-MER)B25N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.995α = 90
b = 68.642β = 108.7
c = 83.995γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-09-12 
  • Released Date: 2015-07-15 
    • Deposition Author(s): Deng, Z., Chen, Z.

Revision History  (Full details and data files)

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