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TitleCommensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.
Journal, issue, pagesEMBO J, Vol. 44, Issue 21, Page 6226-6252, Year 2025
Publish dateSep 12, 2025
AuthorsArnab Kumar Nath / Ronivaldo Rodrigues da Silva / Colin C Gauvin / Emmanuel Akpoto / Mensur Dlakić / C Martin Lawrence / Jennifer L DuBois /
PubMed AbstractIron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu ...Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.
External linksEMBO J / PubMed:40940422 / PubMed Central
MethodsEM (single particle)
Resolution2.55 - 2.6 Å
Structure data

46483

9d26

EMDB-46483, PDB-9d26:
A widespread heme dechelatase in healthy and pathogenic human microbiomes.
Method: EM (single particle) / Resolution: 2.6 Å

71280

9p4s

EMDB-71280, PDB-9p4s:
HmuS heme dechelatase: disordered domain 1, heme free.
Method: EM (single particle) / Resolution: 2.55 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

Source
  • bacteroides thetaiotaomicron (bacteria)
  • bacteroides (bacteria)
KeywordsMETAL TRANSPORT / Iron / Microbiome / Heme

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