6VNA

Pden_1323

Summary for 6VNA

• Entry DOI: 10.2210/pdb6vna/pdb
• Descriptor: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding protein (2 entities in total)
• Functional Keywords: heme, metal binding protein
• Biological source: Paracoccus denitrificans (strain Pd 1222)
• Total number of polymer chains: 3
• Total formula weight: 52106.91

Authors

Isiorho, E.A.,Mansoorabadi, S.O. (deposition date: 2020-01-29, release date: 2021-02-03, Last modification date: 2024-04-03)

Primary citation

Li, S.,Isiorho, E.A.,Owens, V.L.,Donnan, P.H.,Odili, C.L.,Mansoorabadi, S.O.
A noncanonical heme oxygenase specific for the degradation of c-type heme.
J.Biol.Chem., 296:100666-100666, 2021

PubMed Abstract: Heme oxygenases (HOs) play a critical role in recouping iron from the labile heme pool. The acquisition and liberation of heme iron are especially important for the survival of pathogenic bacteria. All characterized HOs, including those belonging to the HugZ superfamily, preferentially cleave free b-type heme. Another common form of heme found in nature is c-type heme, which is covalently linked to proteinaceous cysteine residues. However, mechanisms for direct iron acquisition from the c-type heme pool are unknown. Here we identify a HugZ homolog from the oligopeptide permease (opp) gene cluster of Paracoccus denitrificans that lacks any observable reactivity with heme b and show that it instead rapidly degrades c-type hemopeptides. This c-type heme oxygenase catalyzes the oxidative cleavage of the model substrate microperoxidase-11 at the β- and/or δ-meso position(s), yielding the corresponding peptide-linked biliverdin, CO, and free iron. X-ray crystallographic analysis suggests that the switch in substrate specificity from b-to c-type heme involves loss of the N-terminal α/β domain and C-terminal loop containing the coordinating histidine residue characteristic of HugZ homologs, thereby accommodating a larger substrate that provides its own iron ligand. These structural features are also absent in certain heme utilization/storage proteins from human pathogens that exhibit low or no HO activity with free heme. This study thus expands the scope of known iron acquisition strategies to include direct oxidative cleavage of heme-containing proteolytic fragments of c-type cytochromes and helps to explain why certain oligopeptide permeases show specificity for the import of heme in addition to peptides.

PubMed: 33862082
DOI: 10.1016/j.jbc.2021.100666

Experimental method

X-RAY DIFFRACTION (2.2 Å)