A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria

Nicolas Grosjean, Estella F. Yee, Desigan Kumaran, Kriti Chopra, Macon Abernathy, Sandeep Biswas, James Byrnes, Dale F. Kreitler, Jan-Fang Cheng, Agnidipta Ghosh, Steven C. Almo, Masakazu Iwai, Krishna K. Niyogi, Himadri B. Pakrasi, Ritimukta Sarangi, Hubertus Dam, Lin Yang, Ian K. Blaby and Crysten E. Blaby-Haas ()
Additional contact information
Nicolas Grosjean: Brookhaven National Laboratory
Estella F. Yee: Brookhaven National Laboratory
Desigan Kumaran: Brookhaven National Laboratory
Kriti Chopra: Brookhaven National Laboratory
Macon Abernathy: SLAC National Accelerator Laboratory
Sandeep Biswas: Washington University
James Byrnes: Brookhaven National Laboratory
Dale F. Kreitler: Brookhaven National Laboratory
Jan-Fang Cheng: Lawrence Berkeley National Laboratory
Agnidipta Ghosh: Albert Einstein College of Medicine
Steven C. Almo: Albert Einstein College of Medicine
Masakazu Iwai: University of California
Krishna K. Niyogi: University of California
Himadri B. Pakrasi: Washington University
Ritimukta Sarangi: SLAC National Accelerator Laboratory
Hubertus Dam: Brookhaven National Laboratory
Lin Yang: Brookhaven National Laboratory
Ian K. Blaby: Lawrence Berkeley National Laboratory
Crysten E. Blaby-Haas: Brookhaven National Laboratory

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: Abstract Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.

Date: 2024
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DOI: 10.1038/s41467-024-47486-z

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