Architecture of a Fur Binding Site: a Comparative Analysis
Open accessAbstract
Fur is an iron-binding transcriptional repressor that recognizes a 19-bp consensus site of the sequence 5′-GATAATGATAATCATTATC-3′. This site can be defined as three adjacent hexamers of the sequence 5′-GATAAT-3′, with the third being slightly imperfect (an F-F-F configuration), or as two hexamers in the forward orientation separated by one base pair from a third hexamer in the reverse orientation (an F-F-x-R configuration). Although Fur can bind synthetic DNA sequences containing the F-F-F arrangement, most natural binding sites are variations of the F-F-x-R arrangement. The studies presented here compared the ability of Fur to recognize synthetic DNA sequences containing two to four adjacent hexamers with binding to sequences containing variations of the F-F-x-R arrangement (including natural operator sequences from the entS and fepB promoter regions of Escherichia coli ). Gel retardation assays showed that the F-F-x-R architecture was necessary for high-affinity Fur-DNA interactions and that contiguous hexamers were not recognized as effectively. In addition, the stoichiometry of Fur at each binding site was determined, showing that Fur interacted with its minimal 19-bp binding site as two overlapping dimers. These data confirm the proposed overlapping-dimer binding model, where the unit of interaction with a single Fur dimer is two inverted hexamers separated by a C:G base pair, with two overlapping units comprising the 19-bp consensus binding site required for the high-affinity interaction with two Fur dimers.
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Fur can bind DNA targets at different ratios.
“Combined with the findings from the gel shift assay ( Fig. 1b , lanes 3–6) and a previous report 22 , these results suggest that Fur can bind DNA targets at different ratios.”
From Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator (2015) · cites this paper as [22]
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- Authors
- Lavrrar, J. L., & McIntosh, M. A.
- Affiliations
- University of Missouri (US)
- Corresponding author
- McIntosh, Mark A.
- Venue
- Journal of Bacteriology
- Publisher
- American Society for Microbiology
- Published
- 2003-04
- Volume
- 185
- Issue
- 7
- Pages
- 2194-2202
- ISSN
- 0021-9193 (ISSN-L)
- 1098-5530
- PMC
- PMC151488
- OpenAlex
- W2104610389
- Cited by
- 95
- References
- 45
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 2 · 2023: 1 · 2021: 4 · 2020: 2 · 2019: 2 · 2018: 5 · 2017: 4 · 2016: 5 · 2015: 4 · 2014: 9 · 2013: 5 · 2012: 3
- FWCI
- 4.58
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Bacteriology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Health and Human Services
- National Institutes of Health (5r01gm054243-04)
- National Institute of General Medical Sciences (GM 54243)
- National Institute of Allergy and Infectious Diseases (T32AI007276, 5-T32-AI07276)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- Fur repressor, Escherichia coli, synthetic DNA sequences, gel retardation
- MeSH terms
- Bacterial Proteins, Base Sequence, Binding Sites, DNA, Models, Molecular, Repressor Proteins, Dimerization, Base Pairing, Electrophoretic Mobility Shift Assay, Membrane Transport Proteins, Escherichia coli Proteins, Periplasmic Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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