9VWB

HamA, a Heme-Oxygenase-Like Enzyme

Summary for 9VWB

• Entry DOI: 10.2210/pdb9vwb/pdb
• Descriptor: DUF3050 domain-containing protein, FE (III) ION, ACETIC ACID, ... (6 entities in total)
• Functional Keywords: 2-oxoglutarate-dependent hydroxylase, metal binding protein
• Biological source: Burkholderia cenocepacia H111
• Total number of polymer chains: 1
• Total formula weight: 30476.22

Authors

Su, B.B.,Zhang, T.T.,Yu, Y.,Liu, H.P. (deposition date: 2025-07-16, release date: 2025-11-12)

Primary citation

Su, B.,Zhang, T.,Yu, Y.,Liu, H.
Structural basis of a 2-oxoglutarate-dependent heme-oxygenase-like enzyme HamA in fragin biosynthesis.
Rsc Adv, 15:38502-38509, 2025

PubMed Abstract: The fungicide fragin, which contains a diazeniumdiolate moiety, exhibits a broad spectrum of biological activities. HamA, the key enzyme responsible for forming the nitrogen-nitrogen bond in this moiety, was investigated in this study. We determined the crystal structure of HamA at 2.0 Å resolution, revealing a mononuclear iron center in the active site coordinated by both the "2His-1Glu" motif and an acetate group. Notably, HamA adopts a heme oxygenase-like fold, forming a hydrophobic cavity within a helical bundle that likely accommodates the substrate. Structural data confirmed the presence of an acetate and a formate group near the active site and microscale thermophoresis (MST) experiments further demonstrated HamA's ability to bind 2-oxoglutarate (2OG) with a dissociation constant ( ) of 208 ± 1.42 μM. In summary, this study elucidates the 2OG-dependent heme-oxygenase-like enzyme HamA with a monoiron active center, providing critical structural insights into the mechanistic formation of the diazeniumdiolate moiety in fragin.

PubMed: 41103923
DOI: 10.1039/d5ra05203c

Experimental method

X-RAY DIFFRACTION (2 Å)