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Cited by 8Bacterial Genetics and BiotechnologyMetalloenzymes and iron-sulfur proteinsEnzyme Structure and Function

Characterization of the Zinc Uptake Repressor (Zur) from Acinetobacter baumannii

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Kim, Minyong, Le, My Tra, Fan, Lixin, Campbell, Courtney, Sen, Sambuddha, Capdevila, Daiana A., Stemmler, Timothy L., Giedroc, David P.·2024·Biochemistry
DOI 10.1021/acs.biochem.3c00679PMC PMC11019503
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Abstract

Bacterial cells tightly regulate the intracellular concentrations of essential transition metal ions by deploying a panel of metal-regulated transcriptional repressors and activators that bind to operator-promoter regions upstream of regulated genes. Like other zinc uptake regulator (Zur) proteins, Acinetobacter baumannii Zur represses transcription of its regulon when Zn II is replete and binds more weakly to DNA when Zn II is limiting. Previous studies established that Zur proteins are homodimeric and harbor at least two metal sites per protomer or four per dimer. Cd II X-ray absorption spectroscopy (XAS) of the Cd 2 Zn 2 Ab Zur metalloderivative with Cd II bound to the allosteric sites reveals a S(N/O) 3 first coordination shell. Site-directed mutagenesis suggests that H89 and C100 from the N-terminal DNA binding domain and H107 and E122 from the C-terminal dimerization domain comprise the regulatory metal site. K Zn for this allosteric site is 6.0 (±2.2) × 10 12 M –1 with a functional “division of labor” among the four metal ligands. N-terminal domain ligands H89 and C100 contribute far more to K Zn than H107 and E122, while C100S Ab Zur uniquely fails to bind to DNA tightly as measured by an in vitro transcription assay. The heterotropic allosteric coupling free energy, Δ G c, is negative, consistent with a higher K Zn for the Ab Zur-DNA complex and defining a bioavailable Zn II set-point of ≈6 × 10 –14 M. Small-angle X-ray scattering (SAXS) experiments reveal that only the wild-type Zn homodimer undergoes allosteric switching, while the C100S Ab Zur fails to switch. These data collectively suggest that switching to a high affinity DNA-binding conformation involves a rotation/translation of one protomer relative to the other in a way that is dependent on the integrity of C100. We place these findings in the context of other Zur proteins and Fur family repressors more broadly.

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  • Zur proteins sense Zn2+ sufficiency and the binding of Zn2+ is anywhere from 10- to 103-fold tighter when measured in the presence of DNA.

    “For example, Zur proteins sense Zn2+ sufficiency and the binding of Zn2+ is anywhere from 10- to 103-fold tighter when measured in the presence of DNA.25,27,28”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [27]

    The Results and Discussion section, “Zinc is a Positive Allosteric Effector of AbZur-DNA Binding” (page unavailable), supports that Zur responds to zinc and that zinc binding is tighter in the presence of DNA. But its measured value for Acinetobacter baumannii Zur is approximately 3-fold tighter than for the free protein, not within the claimed 10- to 10³-fold range. (LLM, conf=0.90)

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Authors
Kim, M., Le, M. T., Fan, L., Campbell, C., Sen, S., Capdevila, D. A., Stemmler, T. L., & Giedroc, D. P.
Affiliations
  • Indiana University Bloomington (US)
  • Frederick National Laboratory for Cancer Research (US)
  • Wayne State University (US)
  • Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
Corresponding author
Giedroc, David P.
ORCID
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
2024-02-22
Volume
63
Issue
5
Pages
660-670
ISSN
  • 0006-2960 (ISSN-L)
  • 1520-4995
DOI
10.1021/acs.biochem.3c00679
PMC
PMC11019503
OpenAlex
W4392038460
Cited by
8
References
9
Citations by year
2026: 1 · 2025: 4 · 2024: 3
FWCI
1.97
Type
journal article
Language
en
Open access
Licence
Locations
  • Biochemistry (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Conicet (submittedVersion, cc-by-nc-sa)
Funders
  • National Institute of Allergy and Infectious Diseases (R01 AI101171)
  • National Institute of General Medical Sciences (R35 GM118157)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
Acinetobacter baumannii, zinc homeostasis, allosteric regulation, zinc binding site, DNA binding affinity
MeSH terms
Bacterial Proteins, Binding Sites, Cadmium, DNA, Isoquinolines, Metals, Repressor Proteins, Sulfonamides, X-Ray Diffraction, Zinc, Protein Subunits, Acinetobacter baumannii, Scattering, Small Angle

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