27DQ

Crystal structure of HPO from Pseudomonas

Summary for 27DQ

• Entry DOI: 10.2210/pdb27dq/pdb
• Descriptor: 2,5-DHP dioxygenase, FE (III) ION (3 entities in total)
• Functional Keywords: hpo, catalysis, biosynthetic protein
• Biological source: Pseudomonas putida (strain DSM 28022 / S16)
• Total number of polymer chains: 6
• Total formula weight: 226918.79

Authors

Cheng, Z.Y.,Han, X.,Li, Q.,Wei, H.L.,Hu, H.Y.,Xu, P.,Liu, W.,Tang, H.Z. (deposition date: 2026-05-27, release date: 2026-10-14, Last modification date: 2026-11-04)

Primary citation

Cheng, Z.,Han, X.,Wei, H.,Hu, H.,Xu, P.,Liu, W.,Tang, H.
Structural and catalytic characterization of the 2,5-dihydroxypyridine ring-cleaving dioxygenase Hpo from Pseudomonas putida S16.
Appl.Environ.Microbiol., :e0146726-e0146726, 2026

PubMed Abstract: 2,5-Dihydroxypyridine (2,5-DHP) is a potentially carcinogenic intermediate in pyridine catabolism. Hpo, a non-heme Fe(II)-dependent dioxygenase from S16, catalyzes ring cleavage of 2,5-DHP, yet its structure has remained uncharacterized. We determined the crystal structure of Hpo at 2.56 Å resolution, revealing a catalytic Fe center coordinated by His257, His310, and Asp312 in a conserved 2-His-1-carboxylate motif, with Ser294 positioned directly below the iron and essential for iron binding. The substrate-binding pocket, formed primarily by Phe94, Phe97, Phe186, Phe188, and Arg285, incorporates potential hydrogen-bonding interactions from Glu169 and His181. Hpo employs a distinctive Phe94-Leu95-Leu96-Phe97 motif for substrate recognition, contrasting with the Met102-Leu103-Leu104-His105 motif in the isoenzyme NicX. Molecular dynamics simulations spanning 200 ns demonstrated that Phe94 and Phe97 mutations destabilized substrate binding, confirming their role in substrate recognition, and explaining the corresponding loss of catalytic activity. These findings reveal the active-site architecture and substrate engagement mechanism of Hpo, advancing our understanding of pyridine ring-cleaving non-heme Fe(II)-dependent dioxygenases.IMPORTANCEPyridine compounds are common environmental contaminants that pose risks to human health. The microbial degradation of pyridine compounds generates toxic intermediates, including 2,5-dihydroxypyridine (2,5-DHP), which require enzymatic detoxification. Prior to this study, only one 2,5-DHP dioxygenase had been structurally characterized, leaving the structural basis of this rare enzyme subgroup unresolved. By determining the Hpo crystal structure and identifying residues critical for iron coordination and catalysis, this work addresses a significant knowledge gap and establishes a structural framework for understanding pyridine ring-cleaving non-heme Fe(II)-dependent dioxygenases and may also provide an enzymatic perspective on the removal of pyridine contaminants from the environment.

PubMed: 42873482
DOI: 10.1128/aem.01467-26

Experimental method

X-RAY DIFFRACTION (2.56 Å)