7DH7

Crystal structure of apo XcZur

Summary for 7DH7

• Entry DOI: 10.2210/pdb7dh7/pdb
• Descriptor: Transcriptional regulator fur family, ZINC ION, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: zinc perception, conformational change, zinc uptake regulator, dna binding, metal binding protein
• Biological source: Xanthomonas campestris pv. campestris (strain 8004)
• Total number of polymer chains: 4
• Total formula weight: 74752.31

Authors

Liu, F.M.,Su, Z.H.,Chen, P.,Tian, X.L.,Wu, L.J.,Tang, D.J.,Li, P.F.,Deng, H.T.,Tang, J.L.,Ming, Z.H. (deposition date: 2020-11-13, release date: 2021-06-09, Last modification date: 2024-05-29)

Primary citation

Liu, F.,Su, Z.,Chen, P.,Tian, X.,Wu, L.,Tang, D.J.,Li, P.,Deng, H.,Ding, P.,Fu, Q.,Tang, J.L.,Ming, Z.
Structural basis for zinc-induced activation of a zinc uptake transcriptional regulator.
Nucleic Acids Res., 49:6511-6528, 2021

PubMed Abstract: The zinc uptake regulator (Zur) is a member of the Fur (ferric uptake regulator) family transcriptional regulators that plays important roles in zinc homeostasis and virulence of bacteria. Upon zinc perception, Zur binds to the promoters of zinc responsive genes and controls their transcription. However, the mechanism underlying zinc-mediated Zur activation remains unclear. Here we report a 2.2-Å crystal structure of apo Zur from the phytopathogen Xanthomonas campestris pv. campestris (XcZur), which reveals the molecular mechanism that XcZur exists in a closed inactive state before regulatory zinc binding. Subsequently, we present a 1.9-Å crystal structure of holo XcZur, which, by contrast, adopts an open state that has enough capacity to bind DNA. Structural comparison and hydrogen deuterium exchange mass spectrometry (HDX-MS) analyses uncover that binding of a zinc atom in the regulatory site, formed by the hinge region, the dimerization domain and the DNA binding domain, drives a closed-to-open conformational change that is essential for XcZur activation. Moreover, key residues responsible for DNA recognition are identified by site-directed mutagenesis. This work provides important insights into zinc-induced XcZur activation and valuable discussions on the mechanism of DNA recognition.

PubMed: 34048589
DOI: 10.1093/nar/gkab432

Experimental method

X-RAY DIFFRACTION (2.2 Å)