InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information.

Józef Ba Tran,Artur Krężel

doi:10.1021/acs.jproteome.0c00906

Abstract

InterMetalDB is a free-of-charge database and browser of intermolecular metal binding sites that are present on the interfaces of macromolecules forming larger assemblies based on structural information deposited in Protein Data Bank (PDB). It can be found and freely used at https://intermetaldb.biotech.uni.wroc.pl/. InterMetalDB collects the interfacial binding sites with involvement of metal ions and clusters them on the basis of 50% sequence similarity and the nearest metal environment (5 Å radius). The data are available through the web interface where they can be queried, viewed, and downloaded. Complexity of the query depends on the user, because the questions in the query are connected with each other by a logical AND. InterMetalDB offers several useful options for filtering records including searching for structures by particular parameters such as structure resolution, structure description, and date of deposition. Records can be filtered by coordinated metal ion, number of bound amino acid residues, coordination sphere, and other features. InterMetalDB is regularly updated and will continue to be regularly updated with new content in the future. InterMetalDB is a useful tool for all researchers interested in metalloproteins, protein engineering, and metal-driven oligomerization.

Highlights

Every macromolecule in living organisms needs to interact either in a transient or permanent way with another macromolecule to fulfill its function
In addition to developing our knowledge of intermolecular metal ion binding, it is worth noting that the tool we provide can be used for the construction or improvement of existing models that predict metal ion binding by macromolecules
Structures containing metal elements were acquired from the RCSB Protein Data Bank (PDB),[22] querying for the relevant metal element via RCSB PDB Search application programming interface (API) using the chemical component identifier rcsb_chem_comp_container_identifiers.comp_id, which is an exact search attribute, and returns only structures that contain a standalone metal ion, not metal bound by any kind of molecule; i.e., structures containing iron in heme or iron−sulfur clusters are not returned

Summary

Introduction

Every macromolecule in living organisms needs to interact either in a transient or permanent way with another macromolecule to fulfill its function. It was described in an extensive review paper in 2014,3 few preceding reviews mentioned intermolecular zinc binding.[7,8] It is possible that the presence of metal ions on macromolecules’ interfaces has not attracted much attention because of the rarity or instability of this type of interaction, but it might be due to the great difficulty in testing and investigating intermolecularly bound metal ions, especially with transient character. In addition to developing our knowledge of intermolecular metal ion binding, it is worth noting that the tool we provide can be used for the construction or improvement of existing models that predict metal ion binding by macromolecules. We believe that our very recent contribution in the field of interfacial metal binding together with the presented resource will help researchers to expand knowledge about factors determining interfacial metal binding and its role in biological systems.[10]

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Results

Conclusion