8GF4

Crystal structure of Domain Related to Iron (DRI) in complex with heme

Summary for 8GF4

• Entry DOI: 10.2210/pdb8gf4/pdb
• Descriptor: Ssr1698 protein, ZINC ION, PROTOPORPHYRIN IX CONTAINING FE, ... (4 entities in total)
• Functional Keywords: heme binding protein, dri-heme complex, duf2470 domain, iron homeostasis, metal binding protein
• Biological source: Synechocystis sp. PCC 6803
• Total number of polymer chains: 4
• Total formula weight: 46721.47

Authors

Kumaran, D.,Blaby, E.C. (deposition date: 2023-03-07, release date: 2024-03-13, Last modification date: 2024-04-24)

Primary citation

Grosjean, N.,Yee, E.F.,Kumaran, D.,Chopra, K.,Abernathy, M.,Biswas, S.,Byrnes, J.,Kreitler, D.F.,Cheng, J.F.,Ghosh, A.,Almo, S.C.,Iwai, M.,Niyogi, K.K.,Pakrasi, H.B.,Sarangi, R.,van Dam, H.,Yang, L.,Blaby, I.K.,Blaby-Haas, C.E.
A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria.
Nat Commun, 15:3167-3167, 2024

PubMed 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.

PubMed: 38609367
DOI: 10.1038/s41467-024-47486-z

Experimental method

X-RAY DIFFRACTION (3 Å)