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Results for “Zinc-binding domain”

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PubMed2026

A novel DNA-protective function of Escherichia coli thioredoxin 2 mediated by its N-terminal zinc-binding domain.

Thioredoxins are ubiquitous thiol-disulfide oxidoreductases that maintain intracellular redox homeostasis. In addition to its conserved catalytic domain, Escherichia coli thioredoxin 2 (EcTrx2) possesses a unique N-terminal zinc-binding domain whose physiological function remains largely unknown. Here, we identify a previously unrecognized DNA-binding activity of EcTrx2 and demonstrate its role in protecting DNA during oxidative stress. Electrophoretic mobility shift assays showed that EcTrx2 bound plasmid DNA in a concentration-dependent and GST-tag-independent manner, whereas EcTrx1 exhibited no detectable DNA-binding activity. DNA binding was abolished by deletion of the N-terminal zinc-binding domain and was blocked by zinc occupancy, indicating that this unique domain is essential for DNA interaction. Consistent with these findings, EcTrx2 significantly protected plasmid DNA from DNase I digestion and hydroxyl radical-mediated oxidative damage in vitro. Furthermore, EcTrx2 enhanced bacterial tolerance to the DNA-damaging agents zeocin and diamide, supporting the physiological relevance of its DNA-binding activity. Our results reveal a DNA-binding role for EcTrx2 and identify its N-terminal zinc-binding domain as a key determinant of DNA binding and protection against oxidative DNA damage.

DNA binding↗

PubMed1978

Three-dimensional structures of aspartate carbamoyltransferase from Escherichia coli and of its complex with cytidine triphosphate.

X-ray diffraction studies to nominal resolutions of 3.0 A for unliganded aspartate carbamolytransferase (EC 2.1.3.2)(R32 crystal symmetry) and of 2.8 A for the complex of aspartate carbamoyltransferase with cytidine triphosphate (P321 crystal symmetry) have yielded traces of the polypeptide chains of the catalytic (C) and regulatory (R) chains in the hexameric C6R6 molecules. The independent molecular structures of the liganded and unliganded forms of the enzyme are very nearly identical. In the regulatory chain there is a CTP-binding domain that interacts with an adjacent regulatory subunit and a zinc-binding domain that interacts with the catalytic subunit. In the catalytic chain a polar domain shows interactions between adjacent pairs of C chains to form each trimer C3 while an equatorial domain shows intramolecular C3--C3 interactions. The active site is at or near the interface between adjacent C chains within the trimers. Probably each active center involves amino acid residues from adjacent C chains.

Aspartate Carbamoyltransferase↗

PubMed2025

Analysis of novel zinc-binding proteins in the cell wall of Corynebacterium diphtheriae.

UNLABELLED: Zinc is a critical nutrient for all living organisms, including bacterial pathogens such as Corynebacterium diphtheriae, the causative agent of the severe human respiratory disease diphtheria. As such, zinc acquisition is essential for many pathogens to cause disease. We previously showed that the zinc-regulated ABC transporter encoded by the znu locus is one of several zinc uptake systems that support the growth of C. diphtheriae in zinc-limited medium. In this study, we examine the function and cellular localization of components encoded by the znu gene cluster, which includes the ZnuABC transporter and the novel membrane and cell wall proteins ZnuE, ZnuF, and ZnuG. Deletion of znuE results in reduced growth in zinc-limited media, suggesting a role in zinc uptake. While the growth of znuF and znuG mutants was not affected in zinc-limited medium, deletion of these two genes in a mutant also lacking the znuABC transporter restored growth to wild-type levels, suggesting that ZnuF and ZnuG exert an unusual modulating effect on zinc import. ZnuE, ZnuF, and ZnuG possess a unique motif that is associated with Zn binding as demonstrated by thermal shift assays, targeted mutagenesis, and structural analysis. Although ZnuF and ZnuG are both present in the cell wall, only ZnuG contains a sortase recognition signal that is critical for localizing proteins to the cell wall. Furthermore, ZnuF localization does not require any of the six known sortase enzymes in C. diphtheriae, suggesting a novel localization mechanism. IMPORTANCE: Zinc is a critical nutrient required by many bacterial pathogens. While the function of multiple zinc importer systems has been previously characterized in Corynebacterium diphtheriae, the transporter encoded by the znu gene cluster includes components not found in other metal transport systems. In this report, we examined the roles of three components of the znu gene cluster, ZnuE, ZnuF, and ZnuG, and show that these proteins all possess a putative zinc-binding domain and have varying effects on growth in zinc-limited medium. Additionally, ZnuF uses a novel mechanism for cell wall localization. This study further expands our understanding of C. diphtheriae zinc import and points to a potentially novel mechanism for the localization of cell wall proteins.

Corynebacterium diphtheriae↗

PubMed1977

Differences between alcohol dehydrogenases. Structural properties and evolutionary aspects.

Comparisons of the primary structures of yeast and horse liver alcohol dehydrogenases reveal that the enzymes are homologous but distantly related. The overall positional identity is 25% between common regions, and several deletions/insertions occur in either enzyme, the longest apparently corresponding to 21 residues, showing that the different subunit sizes are largely explained by internal differences. Variabilities in the structural similarities can be coupled with functional requirements but not directly with whole domains in the previously known tertiary structure of the horse protein. The two most similar regions of the enzymes affect active-site segments and the two most dissimilar regions seem to affect a loop structure without known function, and a segment participating in subunit interactions. The dissimilarities may probably be correlated with changes in zinc-binding properties and quaternary structures. The extra region corresponding to the large internal chain-length difference shows an apparent coincidence in sequence to a following segment of the horse enzyme, and additional elements of internal coincidences, or superficial similarities with other dehydrogenases, are noticed. These characteristics are not fully distinguishable from chance distributions but in view of the extensive species variations in alcohol dehydrogenases some evolutionary considerations may not be excluded, in which case a model relating all regions of these and associated enzymes to a common ancestor is shown to be compatible with all known observations.

Alcohol Oxidoreductases↗

PubMed2025

DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.

BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive. To dissect these, we performed genotype-phenotype correlations of 92 affected individuals harboring a pathogenic or likely pathogenic BCL11B variant, followed by immune phenotyping, analysis of chromatin immunoprecipitation DNA-sequencing data, dual-luciferase reporter assays, and molecular modeling. These integrative analyses enabled us to define three clinical subtypes of BCL11B-related disorders. It is likely that gene-disruptive BCL11B variants and missense variants affecting zinc-binding cysteine and histidine residues cause mild to moderate neurodevelopmental delay with increased propensity for behavioral and dental anomalies, allergies and asthma, and reduced type 2 innate lymphoid cells. Missense variants within C2H2-ZnF DNA-contacting α helices cause highly variable clinical presentations ranging from multisystem anomalies with demise in the first years of life to late-onset, hyperkinetic movement disorder with poor fine motor skills. Those not in direct DNA contact cause a milder phenotype through reduced, target-specific transcriptional activity. However, missense variants affecting C2H2-ZnFs, DNA binding, and "specificity residues" impair BCL11B transcriptional activity in a target-specific, dominant-negative manner along with aberrant regulation of alternative DNA targets, resulting in more severe and unpredictable clinical outcomes. Taken together, we suggest that the phenotypic severity and variability is largely dependent on the DNA-binding affinity and specificity of altered BCL11B proteins.

Adolescent↗

PubMed2026

Genome-wide analysis of the plant-specific PLATZ gene family in Taraxacum kok-saghyz and its roles in response to drought and salt tolerance.

Abiotic stress severely limits plant growth and productivity. Taraxacum kok-saghyz Rodin (TKS), known for its environmental resilience, represents a valuable resource for identifying stress-tolerant genes to improve stress-adaptive crops. Plant AT-rich protein and zinc-binding protein (PLATZ) transcription factors serve as core regulators of plant growth, developmental processes, and adaptive responses to various stress conditions; however, they remain uncharacterized in TKS. Here, we identified 10 TksPLATZ genes through a whole-genome analysis. Phylogenetically, these genes were grouped into five distinct evolutionary branches. Promoter sequence analysis revealed multiple types of cis-acting regulatory elements that are connected with hormonal signal responses and environmental stress adaptation. Integrated analysis of transcriptome datasets and RT-qPCR validation demonstrated that TksPLATZ genes display tissue-specific expression profiles and show distinct responsive patterns to drought and salt stress treatments. Among them, TksPLATZ1, TksPLATZ2 and TksPLATZ7 were markedly induced under both stressors and were selected for further functional study. We demonstrated that TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively. Phenotypic data from overexpression experiments in plants confirm that heterologous expression of TksPLATZ1, TksPLATZ2, and TksPLATZ7 enhances the tolerance of Arabidopsis to salt and osmotic stress. These findings provide valuable genetic resources for improving plant tolerance to environmental stresses.

Salt Tolerance↗