6ERC

Peroxidase A from Dictyostelium discoideum (DdPoxA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role.

Nicolussi, A.Dunn, J.D.Mlynek, G.Bellei, M.Zamocky, M.Battistuzzi, G.Djinovic-Carugo, K.Furtmuller, P.G.Soldati, T.Obinger, C.

(2018) J Biol Chem 293: 1330-1345

  • DOI: 10.1074/jbc.RA117.000463
  • Primary Citation of Related Structures:  
    6ERC

  • PubMed Abstract: 
  • 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 ...

    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 (>10 8 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.


    Organizational Affiliation

    From the Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria, christian.obinger@boku.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peroxinectin AA, B511Dictyostelium discoideumMutation(s): 0 
Gene Names: poxADDB_G0277275
EC: 1.11.1.7
UniProt
Find proteins for Q6TMK4 (Dictyostelium discoideum)
Explore Q6TMK4 
Go to UniProtKB:  Q6TMK4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
F [auth A], M [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], N [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download Ideal Coordinates CCD File 
H [auth A]beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MRD
Query on MRD

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O [auth B](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A], P [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
CA
Query on CA

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G [auth A], L [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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K [auth A], Q [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.253α = 90
b = 128.253β = 90
c = 146.015γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaW1224

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.2: 2018-02-07
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary