MetalMine: a database of functional metal-binding sites in proteins

Nakamura, Kensuke; Hirai, Atsuko; Altaf‐Ul‐Amin, Md.; Takahashi, Hiroki

doi:10.5511/plantbiotechnology.26.517

Cited by 4 publications

(4 citation statements)

References 32 publications

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“…We designed a workflow for the systematic detection of interactions between trace elements and protein-coding genes that display differential expression in glaucoma. To this end, we retrieved the trace element-binding proteins' interactions from databases like MINAS [31], MetalPDB [32], RCSB [33], and MetalMine [34]. To integrate the information contained in the databases, we formulated a score, in which.…”

Section: Methodsmentioning

confidence: 99%

Glaucoma-TrEl: A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma

et al. 2022

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Objective Glaucoma is a chronic neurological disease that is associated with high intraocular pressure (IOP), causes gradual damage to retinal ganglion cells, and often culminates in vision loss. Recent research suggests that glaucoma is a complex multifactorial disease in which multiple interlinked genes and pathways play a role during onset and development. Also, differential availability of trace elements seems to play a role in glaucoma pathophysiology, although their mechanism of action is unknown. The aim of this work is to disseminate a web-based repository on interactions between trace elements and protein-coding genes linked to glaucoma pathophysiology. Results In this study, we present Glaucoma-TrEl, a web database containing information about interactions between trace elements and protein-coding genes that are linked to glaucoma. In the database, we include interactions between 437 unique genes and eight trace elements. Our analysis found a large number of interactions between trace elements and protein-coding genes mutated or linked to the pathophysiology of glaucoma. We associated genes interacting with multiple trace elements to pathways known to play a role in glaucoma. The web-based platform provides an easy-to-use and interactive tool, which serves as an information hub facilitating future research work on trace elements in glaucoma.

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Section: Methodsmentioning

confidence: 99%

Glaucoma-TrEl: A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma

et al. 2022

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“…MEDB presents quantitative information on metal-binding sites in protein structures and can be used for the identification of trends or patterns in the metal-binding sites [ 42 ]. MetalMine automatically collects and categorizes different types of metal-binding sites that derived from the structures of protein-metal-ion complexes [ 43 ]. Metal-MACiE gathers all available metalloenzymes and includes structural and functional information of metal ions in the context of the catalytic mechanisms of these metalloenzymes [ 44 ].…”

Section: Public Databases For Metal Bindingmentioning

confidence: 99%

A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level

Zhou

Liang

et al. 2022

BioMed Research International

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Clear evidence has shown that metal ions strongly connect and delicately tune the dynamic homeostasis in living bodies. They have been proved to be associated with protein structure, stability, regulation, and function. Even small changes in the concentration of metal ions can shift their effects from natural beneficial functions to harmful. This leads to degenerative diseases, malignant tumors, and cancers. Accurate characterizations and predictions of metalloproteins at the residue level promise informative clues to the investigation of intrinsic mechanisms of protein-metal ion interactions. Compared to biophysical or biochemical wet-lab technologies, computational methods provide open web interfaces of high-resolution databases and high-throughput predictors for efficient investigation of metal-binding residues. This review surveys and details 18 public databases of metal-protein binding. We collect a comprehensive set of 44 computation-based methods and classify them into four categories, namely, learning-, docking-, template-, and meta-based methods. We analyze the benchmark datasets, assessment criteria, feature construction, and algorithms. We also compare several methods on two benchmark testing datasets and include a discussion about currently publicly available predictive tools. Finally, we summarize the challenges and underlying limitations of the current studies and propose several prospective directions concerning the future development of the related databases and methods.

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“…without any other protein residue being involved. We narrowed these hits to tri-Asp sites in proteins at three-fold symmetry axes and combined them with hits from other searches using MIPS 26 , MetalS3 27 , and Metalmine 28 resulting in 14 sites, including LarE (Fig. 3).…”

Section: Crystallographic Characterization Of Metal Binding To the Trmentioning

confidence: 99%

Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE

Fellner

Huizenga

Hausinger

et al. 2020

Sci Rep

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Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the threefold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds ca 2+ , Mn 2+ , Fe 2+ /fe 3+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and cd 2+ , but not monovalent metal ions, Cr 3+ , Mg 2+ , Y 3+ , Sr 2+ or Ba 2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of triaspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization. Metals are essential components of many biological macromolecules, especially proteins. About a third 1,2 of the protein structures in the PDB 3 contain one or more metal atoms. The atomic structures of metal-containing cofactors and other metal-binding sites often provide insights into molecular mechanisms and/or reveal critical structural roles. Ten metal cations Mg 2+ , K + , Ca 2+ , Mn 2+ , Fe 2+ , Co 2+ , Ni 2+ , Cu 2+/+ , and Zn 2+ are commonly associated with proteins 4 , but other elements also may play important roles in catalysis or are associated with toxic effects 1. Because of their unique spectroscopic characteristics, some transition metals have been used to study structural and dynamics properties of macromolecules 5-7. In this study, we present a crystallographic analysis of a recently discovered 8 tri-Asp metal-binding site on the threefold symmetry axis of the hexameric LarE protein from Lactobacillus plantarum. LarE 8,9 , a member of the PP-loop ATP pyrophosphatase family 10 , in conjunction with LarB 11,12 and LarC 13 , participates in the synthesis of the nickel-pincer nucleotide cofactor of lactate racemase 14-17. Our crystallographic studies indicated binding specificity towards certain divalent or trivalent metal ions. An extensive database search for similar metal binding sites in other proteins resulted in only 13 hits and structural comparison among these sites revealed the uniqueness of the tri-Asp site in LarE. Given its rarity in protein structures, we propose that such a metal binding site can be engineered into macromolecules 18,19 of interest to facilitate structural and biophysical characterization.

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MetalMine: a database of functional metal-binding sites in proteins

Cited by 4 publications

References 32 publications

Glaucoma-TrEl: A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma

Glaucoma-TrEl: A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma

A Comprehensive Review of Computation-Based Metal-Binding Prediction Approaches at the Residue Level

Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE

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