Diversity of structures and functions of oxo-bridged non-heme diiron proteins

Nogueira, Maria Luiza Caldas; Pastore, Anthony J.; Davidson, Victor L.

doi:10.1016/j.abb.2021.108917

Cited by 18 publications

(6 citation statements)

References 100 publications

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“…Since potassium ferricyanide was previously shown to liberate O 2 from hemerythrin to form met-hemerythrin ( 38 ), the change in the protein spectra was most likely due to this reaction. The as-isolated PG_0686 spectra most likely represented oxy-hemerythrin and the sodium dithionite-treated protein spectra represented the deoxy-hemeythrin ( 39 ). The met-hemerythrin was not produced by treatment with potassium ferrocyanide.…”

Section: Resultsmentioning

confidence: 99%

The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase

et al. 2023

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Section: Resultsmentioning

confidence: 99%

The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase

et al. 2023

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“…Localized orbital bonding analysis 76 (LOBA) using Pipek-Mezey orbitals 77,78 as implemented with default settings in Multiwfn 75 was used to analyze oxidation states of the iron center. We removed the active site models resulting from proteins that have a di-iron or di-nuclear site, such as is common with two iron atoms bridged by a glutamate or μ-oxo bridge 79 as the oxidation state and spin assignment would likely not be valid if only considering one of the metals in this site. These checks brought our 372 initial calculations down to 182 for final analysis.…”

Section: Density Functional Theory Calculationsmentioning

confidence: 99%

Protein3D: Enabling analysis and extraction of metal‐containing sites from the Protein Data Bank with molSimplify

Edholm,

Nandy,

Reinhardt

et al. 2023

J Comput Chem

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Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non‐heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high‐throughput study of metal‐containing active sites in proteins.

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“…Mononuclear iron dioxygenases, such as lipoxygenases, utilize dioxygen (O 2 ) for the oxidation of their substrate. Ribonucleotide reductase, belonging to the class of oxo-bridged diiron proteins [ 11 ], catalyzes the conversion of ribonucleotides into deoxyribonucleotides and thereby facilitates DNA synthesis. Iron is stored intracellularly in a complex with ferritin, which is another oxo-bridged diiron protein [ 12 ], and transported through the blood plasma via transferrin, a glycoprotein with two binding sites for ferric iron ions (Fe 3+ ) [ 13 ].…”

Section: Metabolism Of Iron In the Skinmentioning

confidence: 99%

Iron Metabolism of the Skin: Recycling versus Release

Surbek,

Sukseree,

Eckhart

2023

Metabolites

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The skin protects the body against exogenous stressors. Its function is partially achieved by the permanent regeneration of the epidermis, which requires high metabolic activity and the shedding of superficial cells, leading to the loss of metabolites. Iron is involved in a plethora of important epidermal processes, including cellular respiration and detoxification of xenobiotics. Likewise, microorganisms on the surface of the skin depend on iron, which is supplied by the turnover of epithelial cells. Here, we review the metabolism of iron in the skin with a particular focus on the fate of iron in epidermal keratinocytes. The iron metabolism of the epidermis is controlled by genes that are differentially expressed in the inner and outer layers of the epidermis, establishing a system that supports the recycling of iron and counteracts the release of iron from the skin surface. Heme oxygenase-1 (HMOX1), ferroportin (SLC40A1) and hephaestin-like 1 (HEPHL1) are constitutively expressed in terminally differentiated keratinocytes and allow the recycling of iron from heme prior to the cornification of keratinocytes. We discuss the evidence for changes in the epidermal iron metabolism in diseases and explore promising topics of future studies of iron-dependent processes in the skin.

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Diversity of structures and functions of oxo-bridged non-heme diiron proteins

Cited by 18 publications

References 100 publications

The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase

The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase

Protein3D: Enabling analysis and extraction of metal‐containing sites from the Protein Data Bank with molSimplify

Iron Metabolism of the Skin: Recycling versus Release

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