6ERC image
Deposition Date 2017-10-17
Release Date 2017-12-27
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6ERC
Keywords:
Title:
Peroxidase A from Dictyostelium discoideum (DdPoxA)
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 31 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peroxinectin A
Gene (Uniprot):poxA
Chain IDs:A, B
Chain Length:511
Number of Molecules:2
Biological Source:Dictyostelium discoideum
Primary Citation
Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role.
J. Biol. Chem. 293 1330 1345 (2018)
PMID: 29242189 DOI: 10.1074/jbc.RA117.000463

Abstact

Oxidation of halides and thiocyanate by heme peroxidases to antimicrobial oxidants is an important cornerstone in the innate immune system of mammals. Interestingly, phylogenetic and physiological studies suggest that homologous peroxidases are already present in mycetozoan eukaryotes such as Dictyostelium discoideum This social amoeba kills bacteria via phagocytosis for nutrient acquisition at its single-cell stage and for antibacterial defense at its multicellular stages. Here, we demonstrate that peroxidase A from D. discoideum (DdPoxA) is a stable, monomeric, glycosylated, and secreted heme peroxidase with homology to mammalian peroxidases. The first crystal structure (2.5 Å resolution) of a mycetozoan peroxidase of this superfamily shows the presence of a post-translationally-modified heme with one single covalent ester bond between the 1-methyl heme substituent and Glu-236. The metalloprotein follows the halogenation cycle, whereby compound I oxidizes iodide and thiocyanate at high rates (>108 m-1 s-1) and bromide at very low rates. It is demonstrated that DdPoxA is up-regulated and likely secreted at late multicellular development stages of D. discoideum when migrating slugs differentiate into fruiting bodies that contain persistent spores on top of a cellular stalk. Expression of DdPoxA is shown to restrict bacterial contamination of fruiting bodies. Structure and function of DdPoxA are compared with evolutionary-related mammalian peroxidases in the context of non-specific immune defense.

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