{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,20]],"date-time":"2026-05-20T01:57:12Z","timestamp":1779242232557,"version":"3.51.4"},"reference-count":41,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2023,1,12]],"date-time":"2023-01-12T00:00:00Z","timestamp":1673481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country","award":["BG2019"],"award-info":[{"award-number":["BG2019"]}]},{"name":"The Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country","award":["BG2021"],"award-info":[{"award-number":["BG2021"]}]},{"name":"The Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country","award":["RTI2018-101269-B-I00"],"award-info":[{"award-number":["RTI2018-101269-B-I00"]}]},{"name":"The Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country","award":["SEV-2016-0644"],"award-info":[{"award-number":["SEV-2016-0644"]}]},{"name":"The Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country","award":["1U01 AA026817"],"award-info":[{"award-number":["1U01 AA026817"]}]},{"name":"The Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country","award":["777377"],"award-info":[{"award-number":["777377"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n (Spain)","award":["BG2019"],"award-info":[{"award-number":["BG2019"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n (Spain)","award":["BG2021"],"award-info":[{"award-number":["BG2021"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n (Spain)","award":["RTI2018-101269-B-I00"],"award-info":[{"award-number":["RTI2018-101269-B-I00"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n (Spain)","award":["SEV-2016-0644"],"award-info":[{"award-number":["SEV-2016-0644"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n (Spain)","award":["1U01 AA026817"],"award-info":[{"award-number":["1U01 AA026817"]}]},{"name":"Agencia Estatal de Investigaci\u00f3n (Spain)","award":["777377"],"award-info":[{"award-number":["777377"]}]},{"name":"Severo Ochoa Excellence Accreditation","award":["BG2019"],"award-info":[{"award-number":["BG2019"]}]},{"name":"Severo Ochoa Excellence Accreditation","award":["BG2021"],"award-info":[{"award-number":["BG2021"]}]},{"name":"Severo Ochoa Excellence Accreditation","award":["RTI2018-101269-B-I00"],"award-info":[{"award-number":["RTI2018-101269-B-I00"]}]},{"name":"Severo Ochoa Excellence Accreditation","award":["SEV-2016-0644"],"award-info":[{"award-number":["SEV-2016-0644"]}]},{"name":"Severo Ochoa Excellence Accreditation","award":["1U01 AA026817"],"award-info":[{"award-number":["1U01 AA026817"]}]},{"name":"Severo Ochoa Excellence Accreditation","award":["777377"],"award-info":[{"award-number":["777377"]}]},{"name":"National Institute of Health","award":["BG2019"],"award-info":[{"award-number":["BG2019"]}]},{"name":"National Institute of Health","award":["BG2021"],"award-info":[{"award-number":["BG2021"]}]},{"name":"National Institute of Health","award":["RTI2018-101269-B-I00"],"award-info":[{"award-number":["RTI2018-101269-B-I00"]}]},{"name":"National Institute of Health","award":["SEV-2016-0644"],"award-info":[{"award-number":["SEV-2016-0644"]}]},{"name":"National Institute of Health","award":["1U01 AA026817"],"award-info":[{"award-number":["1U01 AA026817"]}]},{"name":"National Institute of Health","award":["777377"],"award-info":[{"award-number":["777377"]}]},{"name":"Innovative Medicines Initiative (IMI2) Program of the European Union","award":["BG2019"],"award-info":[{"award-number":["BG2019"]}]},{"name":"Innovative Medicines Initiative (IMI2) Program of the European Union","award":["BG2021"],"award-info":[{"award-number":["BG2021"]}]},{"name":"Innovative Medicines Initiative (IMI2) Program of the European Union","award":["RTI2018-101269-B-I00"],"award-info":[{"award-number":["RTI2018-101269-B-I00"]}]},{"name":"Innovative Medicines Initiative (IMI2) Program of the European Union","award":["SEV-2016-0644"],"award-info":[{"award-number":["SEV-2016-0644"]}]},{"name":"Innovative Medicines Initiative (IMI2) Program of the European Union","award":["1U01 AA026817"],"award-info":[{"award-number":["1U01 AA026817"]}]},{"name":"Innovative Medicines Initiative (IMI2) Program of the European Union","award":["777377"],"award-info":[{"award-number":["777377"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Life"],"abstract":"<jats:p>(1) Background: Human frataxin is an iron binding protein that participates in the biogenesis of iron sulfur clusters and enhances ferrochelatase activity. While frataxin association to other proteins has been extensively characterized up to the structural level, much less is known about the putative capacity of frataxin to interact with functionally related metabolites. In turn, current knowledge about frataxin\u2019s capacity to coordinate metal ions is limited to iron (II and III); (2) Methods: here, we used NMR spectroscopy, Molecular Dynamics, and Docking approaches to demonstrate new roles of frataxin; (3) Results: We demonstrate that frataxin also binds Zn2+ in a structurally similar way to Fe2+, but with lower affinity. In turn, both Fe2+-loaded and Zn2+-loaded frataxins specifically associate to protoporphyrin IX with micromolar affinity, while apo-frataxin does not bind to the porphyrin. Protoporphyrin IX association to metal-loaded frataxin shares the binding epitope with ferrochelatase; and (4) Conclusions: these findings expand the plethora of relevant molecular targets for frataxin and may help to elucidate the yet unknown different roles that this protein exerts in iron regulation and metabolism.<\/jats:p>","DOI":"10.3390\/life13010222","type":"journal-article","created":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T02:05:52Z","timestamp":1673575552000},"page":"222","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Protoporphyrin IX Binds to Iron(II)-Loaded and to Zinc-Loaded Human Frataxin"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1372-3844","authenticated-orcid":false,"given":"Ganeko","family":"Bernardo-Seisdedos","sequence":"first","affiliation":[{"name":"ATLAS Molecular Pharma, Bizkaia Science and Technology Park, 48160 Derio, Spain"},{"name":"Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Schedlbauer","sequence":"additional","affiliation":[{"name":"Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1753-7387","authenticated-orcid":false,"given":"Tania","family":"Pereira-Ortuzar","sequence":"additional","affiliation":[{"name":"Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e9 M.","family":"Mato","sequence":"additional","affiliation":[{"name":"Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain"},{"name":"Biomedical Research Network on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8748-4105","authenticated-orcid":false,"given":"Oscar","family":"Millet","sequence":"additional","affiliation":[{"name":"ATLAS Molecular Pharma, Bizkaia Science and Technology Park, 48160 Derio, Spain"},{"name":"Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160 Derio, Spain"},{"name":"Biomedical Research Network on Hepatic and Digestive Diseases (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/S0969-2126(00)00158-1","article-title":"Towards a structural understanding of Friedreich\u2019s ataxia: Solution structure of frataxin","volume":"8","author":"Musco","year":"2000","journal-title":"Structure"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"16254","DOI":"10.1021\/bi0488193","article-title":"Yeast frataxin solution structure, iron binding, and ferrochelatase interaction","volume":"43","author":"He","year":"2004","journal-title":"Biochemistry"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.1021\/acs.biochem.6b01304","article-title":"The Iron Chaperone Protein CyaY from Vibrio cholerae Is a Heme-Binding Protein","volume":"56","author":"Uchida","year":"2017","journal-title":"Biochemistry"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"11887","DOI":"10.1074\/jbc.M115.701128","article-title":"The structure of the complex between yeast frataxin and ferrochelatase: Characterization and pre-steady state reaction of ferrous iron delivery and heme synthesis","volume":"291","author":"Gillam","year":"2016","journal-title":"J. Biol. Chem."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1080\/10409230600846058","article-title":"The Structure and Function of Frataxin","volume":"41","author":"Bencze","year":"2006","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"13468","DOI":"10.1073\/pnas.0806762105","article-title":"Mitochondrial localization of human frataxin is necessary but processing is not for rescuing frataxin deficiency in Trypanosoma brucei","volume":"105","author":"Long","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/ng0897-345","article-title":"Studies of human, mouse and yeast homologues indicate a mitochondrial function for frataxin","volume":"16","author":"Koutnikova","year":"1997","journal-title":"Nat. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1007\/s12311-012-0383-5","article-title":"Friedreich\u2019s ataxia causes redistribution of iron, copper, and zinc in the dentate nucleus","volume":"11","author":"Koeppen","year":"2012","journal-title":"Cerebellum"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1007\/s00109-009-0565-x","article-title":"The ins and outs of mitochondrial iron-loading: The metabolic defect in Friedreich\u2019s ataxia","volume":"88","author":"Richardson","year":"2010","journal-title":"J. Mol. Med."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fnins.2019.00075","article-title":"The role of iron in Friedreich\u2019s ataxia: Insights from studies in human tissues and cellular and animal models","volume":"13","author":"Llorens","year":"2019","journal-title":"Front. Neurosci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1159\/000380967","article-title":"Dysregulated iron metabolism in patients on hemodialysis","volume":"185","author":"Nakanishi","year":"2015","journal-title":"Contrib. Nephrol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.amjcard.2016.04.024","article-title":"Abundance and Significance of Iron, Zinc, Copper, and Calcium in the Hearts of Patients With Friedreich Ataxia","volume":"118","author":"Kruger","year":"2016","journal-title":"Am. J. Cardiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3787","DOI":"10.1093\/hmg\/ddi393","article-title":"Frataxin deficiency alters heme pathway transcripts and decreases mitochondrial heme metabolites in mammalian cells","volume":"14","author":"Schoenfeld","year":"2005","journal-title":"Hum. Mol. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"7767","DOI":"10.1021\/bi060424r","article-title":"Monomeric yeast frataxin is an iron-binding protein","volume":"45","author":"Cook","year":"2006","journal-title":"Biochemistry"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"6078","DOI":"10.1021\/ja027967i","article-title":"Iron-sulfur cluster biosynthesis. Characterization of frataxin as an iron donor for assembly of [2Fe-2S] clusters in ISU-type proteins","volume":"125","author":"Yoon","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.jinorgbio.2018.03.007","article-title":"Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly","volume":"183","author":"Cai","year":"2018","journal-title":"J. Inorg. Biochem."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"140254","DOI":"10.1016\/j.bbapap.2019.07.007","article-title":"BBA\u2014Proteins and Proteomics Exploring iron-binding to human frataxin and to selected Friedreich ataxia mutants by means of NMR and EPR spectroscopies","volume":"1867","author":"Bellanda","year":"2019","journal-title":"BBA Proteins Proteom."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3680","DOI":"10.1111\/j.1742-4658.2008.06512.x","article-title":"Dynamics, stability and iron-binding activity of frataxin clinical mutants","volume":"275","author":"Correia","year":"2008","journal-title":"FEBS J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"26737","DOI":"10.1074\/jbc.R110.118679","article-title":"Frataxin and mitochondrial FeS cluster biogenesis","volume":"285","author":"Stemmler","year":"2010","journal-title":"J. Biol. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1039\/C7MT00089H","article-title":"Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers","volume":"9","author":"Galeano","year":"2017","journal-title":"Metallomics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-09989-y","article-title":"Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism","volume":"10","author":"Fox","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Perfitt, T.L., and Martelli, A. (2022). Mitochondrial De Novo Assembly of Iron\u2013Sulfur Clusters in Mammals: Complex Matters in a Complex That Matters. Inorganics, 10.","DOI":"10.3390\/inorganics10030031"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1798","DOI":"10.1039\/B703195E","article-title":"Human frataxin: Iron and ferrochelatase binding surface","volume":"1","author":"Bencze","year":"2007","journal-title":"Chem. Commun."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"25943","DOI":"10.1074\/jbc.C400107200","article-title":"Frataxin-mediated iron delivery to ferrochelatase in the final step of heme biosynthesis","volume":"279","author":"Yoon","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Mielcarek, A., Blauenburg, B., Miethke, M., and Marahiel, M.A. (2015). Molecular insights into frataxin-mediated iron supply for heme biosynthesis in Bacillus subtilis. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0122538"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1093\/hmg\/ddg096","article-title":"Iron use for haeme synthesis is under control of the yeast frataxin homologue (Yfh1)","volume":"12","author":"Lesuisse","year":"2003","journal-title":"Hum. Mol. Genet."},{"key":"ref_27","first-page":"93","article-title":"Ferrochelatase","volume":"Volume 12","author":"Dailey","year":"2003","journal-title":"The Porphyrin Handbook"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Medlock, A.E., Shiferaw, M.T., Marcero, J.R., Vashisht, A.A., Wohlschlegel, J.A., Phillips, J.D., and Dailey, H.A. (2015). Identification of the mitochondrial heme metabolism complex. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0135896"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.pep.2005.01.016","article-title":"Protein production by auto-induction in high density shaking cultures","volume":"41","author":"Studier","year":"2005","journal-title":"Protein Expr. Purif."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"13051","DOI":"10.1074\/jbc.RA119.009367","article-title":"Hereditary tyrosinemia type I-associated mutations in fumarylacetoacetate hydrolase reduce the enzyme stability and increase its aggregation rate","volume":"294","author":"MacIas","year":"2019","journal-title":"J. Biol. Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1073\/pnas.1800235115","article-title":"Structural basis and energy landscape for the Ca2+ gating and calmodulation of the Kv7.2 K+ channel","volume":"115","author":"Malo","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data","volume":"34","author":"Huang","year":"2013","journal-title":"J. Comput. Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1007\/s10858-010-9430-z","article-title":"Nitrogen-detected CAN and CON experiments as alternative experiments for main chain NMR resonance assignments","volume":"47","author":"Takeuchi","year":"2010","journal-title":"J. Biomol. NMR"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1093\/hmg\/11.3.217","article-title":"Assembly and iron-binding properties of human frataxin, the protein dificient in Friedreich ataxia","volume":"11","author":"Cavadini","year":"2002","journal-title":"Hum. Mol. Genet."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1042\/BJ20060345","article-title":"Conformational stability of human frataxin and effect of Friedreich\u2019s ataxia-related mutations on protein folding","volume":"398","author":"Correia","year":"2006","journal-title":"Biochem. J."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2409","DOI":"10.1021\/acs.biochem.2c00434","article-title":"ALAD Inhibition by Porphobilinogen Rationalizes the Accumulation of  \u03b4-Aminolevulinate in Acute Porphyrias","volume":"61","author":"Cendoya","year":"2022","journal-title":"Biochemistry"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"eaat7467","DOI":"10.1126\/scitranslmed.aat7467","article-title":"Repurposing ciclopirox as a pharmacological chaperone in a model of congenital erythropoietic porphyria","volume":"10","author":"Urquiza","year":"2018","journal-title":"Sci. Transl. Med."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Poli, A., Schmitt, C., Moulouel, B., Mirmiran, A., Puy, H., Lef\u00e8bvre, T., and Gouya, L. (2021). Iron, Heme Synthesis and Erythropoietic Porphyrias: A Complex Interplay. Metabolites, 11.","DOI":"10.3390\/metabo11120798"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1016\/j.ymgme.2019.01.006","article-title":"The mitochondrial heme metabolon: Insights into the complex(ity) of heme synthesis and distribution","volume":"128","author":"Piel","year":"2019","journal-title":"Mol. Genet. Metab."}],"container-title":["Life"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2075-1729\/13\/1\/222\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:04:38Z","timestamp":1760119478000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2075-1729\/13\/1\/222"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,12]]},"references-count":41,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,1]]}},"alternative-id":["life13010222"],"URL":"https:\/\/doi.org\/10.3390\/life13010222","relation":{},"ISSN":["2075-1729"],"issn-type":[{"value":"2075-1729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,12]]}}}