ArticlePloS one2011
Minimal functional sites allow a classification of zinc sites in proteins.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- The first and second zinc finger domains from Poly-ADP-ribose polymerase 1 (PARP1) are modified by hydrogen sulfide.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2026Article
- Integrated analysis of the redoxome and zinc proteome links ribosomal protein oxidation to zinc homeostasis.Redox biology · 2026Article
- Master of Metals2: a graph neural network based architecture for the prediction of zinc binding sites in protein structures.Briefings in bioinformatics · 2026Article
- A bioinformatics approach to design minimal biomimetic metal-binding peptides.Communications chemistry · 2025Article
- PinMyMetal: a hybrid learning system to accurately model transition metal binding sites in macromolecules.Nature communications · 2025Article
- Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?Life (Basel, Switzerland) · 2025Article
- Zinc and RNA Binding Is Linked to the Conformational Flexibility of ZRANB2: A CCCC-Type Zinc Finger Protein.Biochemistry · 2025Article
- Roles of zinc and zinc transporters in development, progression, and treatment of inflammatory bowel disease (IBD).Frontiers in nutrition · 2025Review
- Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population.BMC genomics · 2024Article
- PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules.Research square · 2024Article
- Hunting down zinc(II)-binding sites in proteins with distance matrices.Bioinformatics (Oxford, England) · 2023Article
- In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Zinc in Cognitive Impairment and Aging.Biomolecules · 2022Review
- Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications.International journal of molecular sciences · 2022Review
- Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies.Chemphyschem : a European journal of chemical physics and physical chemistry · 2021Article
- Dengue virus replication enhances labile zinc pools by modulation of ZIP8.Cellular microbiology · 2021Article
- Unravelling the Structure of the Tetrahedral Metal-Binding Site in METP3 through an Experimental and Computational Approach.Molecules (Basel, Switzerland) · 2021Article
- Cadmium Exchange with Zinc in the Non-Classical Zinc Finger Protein Tristetraprolin.Inorganic chemistry · 2021Article
- InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information.Journal of proteome research · 2021Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design.
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