3MWM image
Deposition Date 2010-05-06
Release Date 2011-03-16
Last Version Date 2023-11-01
Entry Detail
PDB ID:
3MWM
Keywords:
Title:
Graded expression of zinc-responsive genes through two regulatory zinc-binding sites in Zur
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Putative metal uptake regulation protein
Gene (Uniprot):SCC121.11
Chain IDs:A, B
Chain Length:139
Number of Molecules:2
Biological Source:Streptomyces coelicolor
Ligand Molecules
Primary Citation
Graded expression of zinc-responsive genes through two regulatory zinc-binding sites in Zur
Proc.Natl.Acad.Sci.USA 108 5045 5050 (2011)
PMID: 21383173 DOI: 10.1073/pnas.1017744108

Abstact

Zinc is one of the essential transition metals in cells. Excess or lack of zinc is detrimental, and cells exploit highly sensitive zinc-binding regulators to achieve homeostasis. In this article, we present a crystal structure of active Zur from Streptomyces coelicolor with three zinc-binding sites (C-, M-, and D-sites). Mutations of the three sites differentially affected sporulation and transcription of target genes, such that C- and M-site mutations inhibited sporulation and derepressed all target genes examined, whereas D-site mutations did not affect sporulation and derepressed only a sensitive gene. Biochemical and spectroscopic analyses of representative metal site mutants revealed that the C-site serves a structural role, whereas the M- and D-sites regulate DNA-binding activity as an on-off switch and a fine-tuner, respectively. Consistent with differential effect of mutations on target genes, zinc chelation by TPEN derepressed some genes (znuA, rpmF2) more sensitively than others (rpmG2, SCO7682) in vivo. Similar pattern of TPEN-sensitivity was observed for Zur-DNA complexes formed on different promoters in vitro. The sensitive promoters bound Zur with lower affinity than the less sensitive ones. EDTA-treated apo-Zur gained its DNA binding activity at different concentrations of added zinc for the two promoter groups, corresponding to free zinc concentrations of 4.5×10(-16) M and 7.9×10(-16) M for the less sensitive and sensitive promoters, respectively. The graded expression of target genes is a clever outcome of subtly modulating Zur-DNA binding affinities in response to zinc availability. It enables bacteria to detect metal depletion with improved sensitivity and optimize gene-expression pattern.

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