4RB2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report



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 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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)C, D145Magnetospirillum gryphiswaldense MSR-1 v2Mutation(s): 0 
Gene Names: furMGMSRv2_3137
Find proteins for V6F4Q0 (Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1))
Explore V6F4Q0 
Go to UniProtKB:  V6F4Q0
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (25-MER)A25N/A
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (25-MER)B25N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.301α = 90
b = 68.669β = 109.25
c = 82.646γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

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