4RB2

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

Summary for 4RB2

• Entry DOI: 10.2210/pdb4rb2/pdb
• Related: 4RAY 4RAZ 4RB0 4RB1 4RB3
• Descriptor: DNA (25-MER), DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family), MANGANESE (II) ION, ... (5 entities in total)
• Functional Keywords: ferric uptake regulator (fur), metal ion activation, operator recognition, cooperativity, broad substrate recognition, dna shape readout, metal binding protein-dna complex, metal binding protein/dna
• Biological source: Magnetospirillum gryphiswaldense
• Total number of polymer chains: 4
• Total formula weight: 49186.37

Authors

Deng, Z.,Chen, Z. (deposition date: 2014-09-12, release date: 2015-07-15, Last modification date: 2023-12-06)

Primary citation

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.
Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.
Nat Commun, 6:7642-7642,

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. 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.

PubMed: 26134419
DOI: 10.1038/ncomms8642

Experimental method

X-RAY DIFFRACTION (2.82 Å)