A noncanonical heme oxygenase specific for the degradation of c-type heme

Shuxin Li,Eta A Isiorho,Victoria L Owens,Patrick H Donnan,Chidinma L Odili,Steven O Mansoorabadi

doi:10.1016/j.jbc.2021.100666

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.

Highlights

Bound ferrous state) [4]
The HemS homolog HmuS from Yersinia pseudotuberculosis was found to convert heme to a mixture of β- and δ-biliverdins, analogous to the reaction catalyzed by PigA (Fig. 1) [21]
The purified enzyme was tested for its ability to oxidize pyridoxamine 50phosphate (PMP) and pyridoxine 50-phosphate (PNP), but no activity was observed with either substrate using FMN, FAD, F420, or 8-hydroxy-5-deazaflavin (Fo)

Summary

Introduction

Bound ferrous state) [4]. in many hosts, including humans, iron is predominantly found complexed with protoporphyrin IX in the form of heme. We show that Pden_1323 is an unusual HO that shows specificity for the degradation of c-type heme instead of b-type heme, differentiating it from all previously characterized HOs. The crystal structure of Pden_1323 contains only a partial active site relative to HugZ, suggesting that it can accommodate a c-type hemopeptide substrate that provides its own histidine ligand.

Results

Conclusion