6FL2

Crystal structure of a dye-decolorizing peroxidase D143A variant from Klebsiella pneumoniae (KpDyP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.116 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage.

Pfanzagl, V.Nys, K.Bellei, M.Michlits, H.Mlynek, G.Battistuzzi, G.Djinovic-Carugo, K.Van Doorslaer, S.Furtmuller, P.G.Hofbauer, S.Obinger, C.

(2018) J Biol Chem 293: 14823-14838

  • DOI: https://doi.org/10.1074/jbc.RA118.004773
  • Primary Citation of Related Structures:  
    6FIY, 6FKS, 6FKT, 6FL2

  • PubMed Abstract: 

    Dye-decolorizing peroxidases (DyPs) represent the most recently classified hydrogen peroxide-dependent heme peroxidase family. Although widely distributed with more than 5000 annotated genes and hailed for their biotechnological potential, detailed biochemical characterization of their reaction mechanism remains limited. Here, we present the high-resolution crystal structures of WT B-class DyP from the pathogenic bacterium Klebsiella pneumoniae ( Kp DyP) (1.6 Å) and the variants D143A (1.3 Å), R232A (1.9 Å), and D143A/R232A (1.1 Å). We demonstrate the impact of elimination of the DyP-typical, distal residues Asp-143 and Arg-232 on (i) the spectral and redox properties, (ii) the kinetics of heterolytic cleavage of hydrogen peroxide, (iii) the formation of the low-spin cyanide complex, and (iv) the stability and reactivity of an oxoiron(IV)porphyrin π-cation radical (Compound I). Structural and functional studies reveal that the distal aspartate is responsible for deprotonation of H 2 O 2 and for the poor oxidation capacity of Compound I. Elimination of the distal arginine promotes a collapse of the distal heme cavity, including blocking of one access channel and a conformational change of the catalytic aspartate. We also provide evidence of formation of an oxoiron(IV)-type Compound II in Kp DyP with absorbance maxima at 418, 527, and 553 nm. In summary, a reaction mechanism of the peroxidase cycle of B-class DyPs is proposed. Our observations challenge the idea that peroxidase activity toward conventional aromatic substrates is related to the physiological roles of B-class DyPs.


  • Organizational Affiliation

    Chemistry and Geology, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy, and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-dependent peroxidase
A, B
303Klebsiella pneumoniaeMutation(s): 1 
Gene Names: 
EC: 1.11.1
UniProt
Find proteins for A0A0W8ATM9 (Klebsiella pneumoniae)
Explore A0A0W8ATM9 
Go to UniProtKB:  A0A0W8ATM9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0W8ATM9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

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

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO2
Query on NO2

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.114 
  • R-Value Observed: 0.116 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.76α = 90
b = 76.69β = 107.79
c = 76.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaW1224
Austrian Science FundAustriaG005416N

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description