Zinc fingers: DNA binding and protein-protein interactions

A second-site mutation that restored DNA binding to ADR1 mutants altered at different positions in the two zinc fingers was identified. This mutation (called IS1) was a conservative change of arginine 91 to lysine in a region amino terminal to the two zinc fingers and known from previous experiments to be necessary for DNA binding. IS1 increased binding to the UAS1 sequence two- to sevenfold for various ADR1 mutants and twofold for wild-type ADR1. The change of arginine 91 to glycine decreased binding twofold, suggesting that this arginine is involved in DNA binding in the wild-type protein. The increase in binding by IS1 did not involve protein-protein interactions between the two ADR1 monomers, nor did it require the presence of the sequences flanking UAS1. However, the effect of IS1 was influenced by the sequence of the first finger, suggesting that interactions between the region amino terminal to the fingers and the fingers themselves could exist. A model for the role of the amino-terminal region based on these results and sequence homologies with other DNA-binding motifs is proposed.

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A mutation outside the two zinc fingers of ADR1 can suppress defects in either finger.

Molecular and Cellular Biology ◽

10.1128/mcb.12.12.5758 ◽

1992 ◽

Vol 12 (12) ◽

pp. 5758-5767 ◽

Cited By ~ 9

Author(s):

S Camier ◽

N Kacherovsky ◽

E T Young

Keyword(s):

Dna Binding ◽

Protein Interactions ◽

Zinc Fingers ◽

Wild Type ◽

Protein Protein Interactions ◽

Site Mutation ◽

Binding Motifs ◽

Amino Terminal ◽

Sequence Homologies ◽

In The Wild

A second-site mutation that restored DNA binding to ADR1 mutants altered at different positions in the two zinc fingers was identified. This mutation (called IS1) was a conservative change of arginine 91 to lysine in a region amino terminal to the two zinc fingers and known from previous experiments to be necessary for DNA binding. IS1 increased binding to the UAS1 sequence two- to sevenfold for various ADR1 mutants and twofold for wild-type ADR1. The change of arginine 91 to glycine decreased binding twofold, suggesting that this arginine is involved in DNA binding in the wild-type protein. The increase in binding by IS1 did not involve protein-protein interactions between the two ADR1 monomers, nor did it require the presence of the sequences flanking UAS1. However, the effect of IS1 was influenced by the sequence of the first finger, suggesting that interactions between the region amino terminal to the fingers and the fingers themselves could exist. A model for the role of the amino-terminal region based on these results and sequence homologies with other DNA-binding motifs is proposed.

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Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

Nature Communications ◽

10.1038/s41467-021-22253-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Christopher R. Horne ◽

Hariprasad Venugopal ◽

Santosh Panjikar ◽

David M. Wood ◽

Amy Henrickson ◽

...

Keyword(s):

Sialic Acid ◽

Dna Binding ◽

Protein Interactions ◽

Acid Metabolism ◽

Environmental Changes ◽

Dna Interaction ◽

Protein Protein Interactions ◽

Nutrient Source ◽

Cryo Electron Microscopy ◽

Close Proximity

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.

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Transactivation Functions of the N-Terminal Domains of Nuclear Hormone Receptors: Protein Folding and Coactivator Interactions

Molecular Endocrinology ◽

10.1210/me.2002-0258 ◽

2003 ◽

Vol 17 (1) ◽

pp. 1-10 ◽

Cited By ~ 125

Author(s):

Raj Kumar ◽

E. Brad Thompson

Keyword(s):

Dna Binding ◽

Protein Interactions ◽

Hormone Receptors ◽

Nuclear Hormone Receptor ◽

Binding Domain ◽

Dna Binding Domain ◽

Protein Protein Interactions ◽

Carboxy Terminal ◽

And Function ◽

Terminal Domains

Abstract The N-terminal domains (NTDs) of many members of the nuclear hormone receptor (NHR) family contain potent transcription-activating functions (AFs). Knowledge of the mechanisms of action of the NTD AFs has lagged, compared with that concerning other important domains of the NHRs. In part, this is because the NTD AFs appear to be unfolded when expressed as recombinant proteins. Recent studies have begun to shed light on the structure and function of the NTD AFs. Recombinant NTD AFs can be made to fold by application of certain osmolytes or when expressed in conjunction with a DNA-binding domain by binding that DNA-binding domain to a DNA response element. The sequence of the DNA binding site may affect the functional state of the AFs domain. If properly folded, NTD AFs can bind certain cofactors and primary transcription factors. Through these, and/or by direct interactions, the NTD AFs may interact with the AF2 domain in the ligand binding, carboxy-terminal portion of the NHRs. We propose models for the folding of the NTD AFs and their protein-protein interactions.

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An unusual arrangement of 13 zinc fingers in the vertebrate gene Z13

Biochemical Journal ◽

10.1042/bj3110219 ◽

1995 ◽

Vol 311 (1) ◽

pp. 219-224 ◽

Cited By ~ 7

Author(s):

T C Schulz ◽

B Hopwood ◽

P D Rathjen ◽

J R Wells

Keyword(s):

Dna Binding ◽

Zinc Finger ◽

Protein Interactions ◽

Structural Organization ◽

Zinc Fingers ◽

Binding Activity ◽

Protein Domain ◽

Nucleic Acid Binding ◽

C Terminus ◽

Wide Range

The zinc finger is a protein domain that imparts specific nucleic acid-binding activity on a wide range of functionally important proteins. In this paper we report the molecular cloning and characterization of a novel murine zinc-finger gene, mZ13. Analysis of mZ13 cDNAs revealed that the gene expresses a 794-amino-acid protein encoded by a 2.7 kb transcript. The protein has an unusual arrangement of 13 zinc fingers into a ‘hand’ of 12 tandem fingers and a single isolated finger near the C-terminus. This structural organization is conserved with the probable chicken homologue, cZ13. mZ13 also contained an additional domain at the N-terminus which has previously been implicated in the regulation of zinc-finger transcription factor DNA-binding, via protein-protein interactions. mZ13 expression was detected in a wide range of murine embryonic and adult tissues. The structural organization of mZ13 and its expression profile suggest that it may function as a housekeeping DNA-binding protein that regulates the expression of specific genes.

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Functional redundancy of the zinc fingers of A20 for inhibition of NF-κB activation and protein-protein interactions

FEBS Letters ◽

10.1016/s0014-5793(01)02504-2 ◽

2001 ◽

Vol 498 (1) ◽

pp. 93-97 ◽

Cited By ~ 62

Author(s):

Marco Klinkenberg ◽

Sofie Van Huffel ◽

Karen Heyninck ◽

Rudi Beyaert

Keyword(s):

Protein Interactions ◽

Zinc Fingers ◽

Functional Redundancy ◽

Protein Protein Interactions

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Dof DNA-Binding Domains of Plant Transcription Factors Contribute to Multiple Protein-Protein Interactions

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1997.0403a.x ◽

1997 ◽

Vol 250 (2) ◽

pp. 403-410 ◽

Cited By ~ 58

Author(s):

Shuichi Yanagisawa

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Protein Interactions ◽

Protein Protein Interactions ◽

Dna Binding Domains ◽

Binding Domains ◽

Multiple Protein

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Domain swapping reveals the modular nature of Fos, Jun, and CREB proteins.

Molecular and Cellular Biology ◽

10.1128/mcb.10.9.4565 ◽

1990 ◽

Vol 10 (9) ◽

pp. 4565-4573 ◽

Cited By ~ 21

Author(s):

L J Ransone ◽

P Wamsley ◽

K L Morley ◽

I M Verma

Keyword(s):

Dna Binding ◽

Protein Interactions ◽

Leucine Zipper ◽

Chimeric Protein ◽

Domain Swapping ◽

Amino Terminus ◽

Protein Protein Interactions ◽

Amino Terminal ◽

Nih 3T3 ◽

Basic Region

The products of the Jun and Fos proto-oncogenes form a heterodimer that binds to and activates transcription from 12-O-tetradecanoylphorbol-13-acetate-responsive promoter elements (TGACTCA) and AP-1-binding sites (TGACATCA). These two proteins belong to a family of related transcription factors which contain similar domains required for protein dimerization and DNA binding but display different protein and DNA binding specificities. The basic region, required for DNA binding, is followed by a leucine zipper structure, a domain that mediates protein-protein interactions. To assess the role of these two domains in three related proteins, Fos, Jun, and CREB, we carried out extensive domain-swapping analysis. We found that (i) dimers formed by two Jun leucine zipper-containing proteins were unable to bind DNA as efficiently as a Fos-Jun combination, regardless of the source of the basic region; (ii) the Fos leucine zipper was unable to form either homo- or heterodimers with a chimeric protein containing a Fos leucine zipper; (iii) the Fos basic region was capable of binding to an AP-1 site; (iv) replacement of the Jun amino terminus with that of CREB had little effect on dimerization, whereas replacement with the amino terminus of Fos disrupted both protein-protein and protein-DNA interactions; (v) changes in relative affinities of the Fos and Jun basic regions for the AP-1 element were dependent on the secondary contributions of amino-terminal residues; and (vi) the Fos-Jun chimeric constructs cooperated in transcriptional transactivation of the Jun promoter in NIH 3T3 cells.

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