Data mining of metal ion environments present in protein structures

Zheng, Heping; Chruszcz, M.; Lasota, Piotr; Lebioda, Lukasz; Minor, Władek

doi:10.1016/j.jinorgbio.2008.05.006

Cited by 286 publications

(365 citation statements)

References 20 publications

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“…This atom has been assigned as a Mg 2ϩ ion due to the coordination geometry, the nature of the coordinated ligands, the average bond distance of 2.3 Å (Table 3), and the refined electron density. These geometric parameters correspond well with those found for crystallographically refined Mg 2ϩ ions in other protein structures (40,41). The metal-binding residues Asp 284 and Thr 288 are conserved across the ApbE structural homologs.…”

Section: Purification and Biophysical Properties Of The Proteins-re-supporting

confidence: 80%

The TP0796 Lipoprotein of Treponema pallidum Is a Bimetal-dependent FAD Pyrophosphatase with a Potential Role in Flavin Homeostasis

Deka

Brautigam

Liu

et al. 2013

Journal of Biological Chemistry

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Background:The TP0796 lipoprotein of Treponema pallidum belongs to the poorly characterized ApbE superfamily. Results: TP0796 hydrolyzed FAD into FMN and AMP, consistent with the general enzymatic mechanism of an FAD pyrophosphatase. Conclusion: This novel metal-dependent enzyme probably plays an essential role in flavin homeostasis in T. pallidum. Significance: This is the first description of a metal-dependent FAD pyrophosphatase in bacteria.

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Section: Purification and Biophysical Properties Of The Proteins-re-supporting

confidence: 80%

The TP0796 Lipoprotein of Treponema pallidum Is a Bimetal-dependent FAD Pyrophosphatase with a Potential Role in Flavin Homeostasis

Deka

Brautigam

Liu

et al. 2013

Journal of Biological Chemistry

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“…Methionine is rarely found in binding sites for most metals, with the notable exception of copper (27,28). However, the putative metal-binding site in the iron exporter ferroportin contains a methionine (29), suggesting a strategy similar to Nramps' for selective transition metal transport.…”

Section: Wtmentioning

confidence: 99%

Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters

Bozzi

Bane

Weihofen

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

110

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Natural resistance-associated macrophage protein (Nramp) family transporters catalyze uptake of essential divalent transition metals like iron and manganese. To discriminate against abundant competitors, the Nramp metal-binding site should favor softer transition metals, which interact either covalently or ionically with coordinating molecules, over hard calcium and magnesium, which interact mainly ionically. The metal-binding site contains an unusual, but conserved, methionine, and its sulfur coordinates transition metal substrates, suggesting a vital role in their transport. Using a bacterial Nramp model system, we show that, surprisingly, this conserved methionine is dispensable for transport of the physiological manganese substrate and similar divalents iron and cobalt, with several small amino acid replacements still enabling robust uptake. Moreover, the methionine sulfur's presence makes the toxic metal cadmium a preferred substrate. However, a methionine-to-alanine substitution enables transport of calcium and magnesium. Thus, the putative evolutionary pressure to maintain the Nramp metal-binding methionine likely exists because it-more effectively than any other amino acid-increases selectivity for low-abundance transition metal transport in the presence of high-abundance divalents like calcium and magnesium.transition metals | MntH | divalent metal transporter DMT1 | hard-soft acid-base theory | ion selectivity filters A ll organisms require transition metal ions as cofactors in proteins that perform a variety of essential cellular tasks. Through evolution, organisms have developed mechanisms to acquire, transport, and safely store essential metals such as manganese, iron, cobalt, and zinc. The natural resistance-associated macrophage protein (Nramp) family of metal transporters represents a common transition metal acquisition strategy conserved across all kingdoms of life (1). The first discovered mammalian Nramp (Nramp1) is expressed in phagosomal membranes and likely extracts essential metals to help kill engulfed pathogens (2, 3). Mammals use Nramp2, an essential gene also called DMT1, to absorb dietary iron into the enterocytes that line the small intestine (4) and to extract iron from transferrin-containing endosomes in all tissues. Bacteria express their own Nramp homologs, which they typically use to scavenge manganese and other first row divalent transition metals (5, 6). Last, most plants have several Nramp homologs that take up iron and manganese, the essential cofactor in photosystem II, from the soil or vacuolar stores (7,8).Nramps are generally thought to function as metal-proton symporters (1) and are able to bind and/or transport a wide range of divalent transition metal substrates, including the biologically useful metals Mn 2+ , Fe 2+ , Co 2+ , Ni 2+ , Cu 2+ , and Zn 2+ , as well as the toxic heavy metals Cd 2+ , Pb 2+ , and Hg 2+ (4, 9-13). Nramps do discriminate against the divalent alkaline earth metal ions Mg 2+ and Ca 2+ (9, 14), which are typically several orders of magnitude mor...

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“…During the investigation of metal ion-binding architectures in proteins (Zheng et al , 2008, 2014), we successfully employed the bond-valence model to check the quality of metal-binding site modeling in low-resolution structures. Initially, we used reference literature values for bond-valence ( R 0 ) parameters, which were derived two decades ago from manually curated structures and extrapolated linear relationships between bond-valence contributions (Brese & O’Keeffe, 1991; Brown & Altermatt, 1985).…”

Section: Introductionmentioning

confidence: 99%

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

Zheng

Langner

Shields

et al. 2017

Acta Crystallogr D Struct Biol

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The bond-valence model is a reliable way to validate assumed oxidation states based on structural data. It has successfully been employed for analyzing metal-binding sites in macromolecule structures. However, inconsistent results for heme-based structures suggest that some widely used bond-valence R0 parameters may need to be adjusted in certain cases. Given the large number of experimental crystal structures gathered since these initial parameters were determined and the similarity of binding sites in organic compounds and macromolecules, the Cambridge Structural Database (CSD) is a valuable resource for refining metal–organic bond-valence parameters. R0 bond-valence parameters for iron(II), iron(III) and other metals have been optimized based on an automated processing of all CSD crystal structures. Almost all R0 bond-valence parameters were reproduced, except for iron–nitrogen bonds, for which distinct R0 parameters were defined for two observed subpopulations, corresponding to low-spin and high-spin states, of iron in both oxidation states. The significance of this data-driven method for parameter discovery, and how the spin state affects the interpretation of heme-containing proteins and iron-binding sites in macromolecular structures, are discussed.

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Data mining of metal ion environments present in protein structures

Cited by 286 publications

References 20 publications

The TP0796 Lipoprotein of Treponema pallidum Is a Bimetal-dependent FAD Pyrophosphatase with a Potential Role in Flavin Homeostasis

The TP0796 Lipoprotein of Treponema pallidum Is a Bimetal-dependent FAD Pyrophosphatase with a Potential Role in Flavin Homeostasis

Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

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