Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family

Abstract Divalent d-block metal cations (DDMCs), such as Fe, Zn and Mn, participate in many biological processes. Understanding how specific DDMCs are transported to and within the cell and what controls their binding selectivity to different proteins is crucial for defining the mechanisms of metall...

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Autores principales:	Shiran Barber-Zucker, Boaz Shaanan, Raz Zarivach
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c38ed71c89164a9d8ad0c27f978fd06d
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spelling	oai:doaj.org-article:c38ed71c89164a9d8ad0c27f978fd06d2021-12-02T15:18:52ZTransition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family10.1038/s41598-017-16777-52045-2322https://doaj.org/article/c38ed71c89164a9d8ad0c27f978fd06d2017-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-16777-5https://doaj.org/toc/2045-2322Abstract Divalent d-block metal cations (DDMCs), such as Fe, Zn and Mn, participate in many biological processes. Understanding how specific DDMCs are transported to and within the cell and what controls their binding selectivity to different proteins is crucial for defining the mechanisms of metalloproteins. To better understand such processes, we scanned the RCSB Protein Data Bank, performed a de novo structural-based comprehensive analysis of seven DDMCs and found their amino acid binding and coordination geometry propensities. We then utilized these results to characterize the correlation between metal selectivity, specific binding site composition and phylogenetic classification of the cation diffusion facilitator (CDF) protein family, a family of DDMC transporters found throughout evolution and sharing a conserved structure, yet with different members displaying distinct metal selectivity. Our analysis shows that DDMCs differ, at times significantly, in terms of their binding propensities, and that in each CDF clade, the metal selectivity-related binding site has a unique and conserved sequence signature. However, only limited correlation exists between the composition of the DDMC binding site in each clade and the metal selectivity shown by its proteins.Shiran Barber-ZuckerBoaz ShaananRaz ZarivachNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shiran Barber-Zucker Boaz Shaanan Raz Zarivach Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
description	Abstract Divalent d-block metal cations (DDMCs), such as Fe, Zn and Mn, participate in many biological processes. Understanding how specific DDMCs are transported to and within the cell and what controls their binding selectivity to different proteins is crucial for defining the mechanisms of metalloproteins. To better understand such processes, we scanned the RCSB Protein Data Bank, performed a de novo structural-based comprehensive analysis of seven DDMCs and found their amino acid binding and coordination geometry propensities. We then utilized these results to characterize the correlation between metal selectivity, specific binding site composition and phylogenetic classification of the cation diffusion facilitator (CDF) protein family, a family of DDMC transporters found throughout evolution and sharing a conserved structure, yet with different members displaying distinct metal selectivity. Our analysis shows that DDMCs differ, at times significantly, in terms of their binding propensities, and that in each CDF clade, the metal selectivity-related binding site has a unique and conserved sequence signature. However, only limited correlation exists between the composition of the DDMC binding site in each clade and the metal selectivity shown by its proteins.
format	article
author	Shiran Barber-Zucker Boaz Shaanan Raz Zarivach
author_facet	Shiran Barber-Zucker Boaz Shaanan Raz Zarivach
author_sort	Shiran Barber-Zucker
title	Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
title_short	Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
title_full	Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
title_fullStr	Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
title_full_unstemmed	Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
title_sort	transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/c38ed71c89164a9d8ad0c27f978fd06d
work_keys_str_mv	AT shiranbarberzucker transitionmetalbindingselectivityinproteinsanditscorrelationwiththephylogenomicclassificationofthecationdiffusionfacilitatorproteinfamily AT boazshaanan transitionmetalbindingselectivityinproteinsanditscorrelationwiththephylogenomicclassificationofthecationdiffusionfacilitatorproteinfamily AT razzarivach transitionmetalbindingselectivityinproteinsanditscorrelationwiththephylogenomicclassificationofthecationdiffusionfacilitatorproteinfamily
_version_	1718387473096114176

Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family

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