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Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics
Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881497/ https://www.ncbi.nlm.nih.gov/pubmed/27153067 http://dx.doi.org/10.3390/ijms17050671 |
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author | Rosato, Antonio Valasatava, Yana Andreini, Claudia |
author_facet | Rosato, Antonio Valasatava, Yana Andreini, Claudia |
author_sort | Rosato, Antonio |
collection | PubMed |
description | Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity. |
format | Online Article Text |
id | pubmed-4881497 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-48814972016-05-27 Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics Rosato, Antonio Valasatava, Yana Andreini, Claudia Int J Mol Sci Review Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity. MDPI 2016-05-04 /pmc/articles/PMC4881497/ /pubmed/27153067 http://dx.doi.org/10.3390/ijms17050671 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Review Rosato, Antonio Valasatava, Yana Andreini, Claudia Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics |
title | Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics |
title_full | Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics |
title_fullStr | Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics |
title_full_unstemmed | Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics |
title_short | Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics |
title_sort | minimal functional sites in metalloproteins and their usage in structural bioinformatics |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881497/ https://www.ncbi.nlm.nih.gov/pubmed/27153067 http://dx.doi.org/10.3390/ijms17050671 |
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