9VYC

The crystal structure of PaiB from Bacillus stearothermophilus bound to HEM

Summary for 9VYC

• Entry DOI: 10.2210/pdb9vyc/pdb
• Descriptor: PaiB, PROTOPORPHYRIN IX CONTAINING FE (3 entities in total)
• Functional Keywords: transcriptional repressor of sporulation and degradative enzymes production, transcription
• Biological source: Geobacillus kaustophilus HTA426
• Total number of polymer chains: 2
• Total formula weight: 48216.61

Authors

Zhang, Z.M.,Huang, H.S. (deposition date: 2025-07-20, release date: 2026-04-01)

Primary citation

Huang, H.,Wang, L.,Chen, P.,Yang, T.,Zhu, C.,Li, S.,Zhou, Y.,Tan, Y.,Li, Z.,Zhang, H.,Chen, J.,Zhang, Z.M.
Structural insights into heme-iron dependent N-N bond formation enzyme LnzB.
Commun Chem, 8:344-344, 2025

PubMed Abstract: Nitrogen-nitrogen (N-N) bond formation is integrated into the biosynthetic pathways of various classes of natural products, some of which exhibit intriguing biological activities. While recent studies have identified several distinct groups of enzymes responsible for N-N bond formation, the underlying catalytic mechanisms are largely unknown. Here, we report the dimeric structure of the N-N bond forming enzyme LnzB (Streptomyces spp.), which relies on a heme-iron to catalyze the formation of intramolecular N-N bonds using N-hydroxyornithine as a substrate. The structure reveals the molecular architecture of its active sites and heme-interacting pocket. In combination with MD simulation, site-directed mutagenesis, and kinetic activity assays, we have identified key residues responsible for ligand binding and N-N bond formation activity. Phylogenetic analysis and structural comparison reveal that LnzB and its homologues may have evolved from the transcriptional regulator PaiB by altering the substrate binding pocket. Our study extends the limited knowledge of N-N bond formation catalyzed by a heme iron-dependent enzyme in natural products.

PubMed: 41214184
DOI: 10.1038/s42004-025-01724-7

Experimental method

X-RAY DIFFRACTION (2.42122719099 Å)