4CIT

Crystal structure of the first bacterial vanadium dependant iodoperoxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Bacterial Vanadium Iodoperoxidase from the Marine Flavobacteriaceae Zobellia Galactanivorans Reveals Novel Molecular and Evolutionary Features of Halide Specificity in This Enzyme Family.

Fournier, J.B.Rebuffet, E.Delage, L.Grijol, R.Meslet-Cladiere, L.Rzonca, J.Potin, P.Michel, G.Czjzek, M.Leblanc, C.

(2014) Appl Environ Microbiol 80: 7561

  • DOI: 10.1128/AEM.02430-14
  • Primary Citation of Related Structures:  
    4USZ, 4CIT

  • PubMed Abstract: 
  • Vanadium haloperoxidases (VHPO) are key enzymes that oxidize halides and are involved in the biosynthesis of organo-halogens. Until now, only chloroperoxidases (VCPO) and bromoperoxidases (VBPO) have been characterized structurally, mainly from eukaryotic species ...

    Vanadium haloperoxidases (VHPO) are key enzymes that oxidize halides and are involved in the biosynthesis of organo-halogens. Until now, only chloroperoxidases (VCPO) and bromoperoxidases (VBPO) have been characterized structurally, mainly from eukaryotic species. Three putative VHPO genes were predicted in the genome of the flavobacterium Zobellia galactanivorans, a marine bacterium associated with macroalgae. In a phylogenetic analysis, these putative bacterial VHPO were closely related to other VHPO from diverse bacterial phyla but clustered independently from eukaryotic algal VBPO and fungal VCPO. Two of these bacterial VHPO, heterogeneously produced in Escherichia coli, were found to be strictly specific for iodide oxidation. The crystal structure of one of these vanadium-dependent iodoperoxidases, Zg-VIPO1, was solved by multiwavelength anomalous diffraction at 1.8 Å, revealing a monomeric structure mainly folded into α-helices. This three-dimensional structure is relatively similar to those of VCPO of the fungus Curvularia inaequalis and of Streptomyces sp. and is superimposable onto the dimeric structure of algal VBPO. Surprisingly, the vanadate binding site of Zg-VIPO1 is strictly conserved with the fungal VCPO active site. Using site-directed mutagenesis, we showed that specific amino acids and the associated hydrogen bonding network around the vanadate center are essential for the catalytic properties and also the iodide specificity of Zg-VIPO1. Altogether, phylogeny and structure-function data support the finding that iodoperoxidase activities evolved independently in bacterial and algal lineages, and this sheds light on the evolution of the VHPO enzyme family.


    Organizational Affiliation

    Sorbonne Universités, UPMC Université Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique, Roscoff, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique, Roscoff, France catherine.leblanc@sb-roscoff.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VANADIUM-DEPENDENT HALOPEROXIDASEA458Zobellia galactanivoransMutation(s): 0 
Gene Names: zobellia_1262
EC: 1.11.1 (PDB Primary Data), 1.11.1.8 (PDB Primary Data)
Find proteins for G0LAH5 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij))
Explore G0LAH5 
Go to UniProtKB:  G0LAH5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
AL-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.8α = 90
b = 84.4β = 90
c = 117.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-11-26
    Changes: Database references
  • Version 1.2: 2020-06-03
    Changes: Advisory, Derived calculations, Other