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PDBsum entry 6fkt
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Oxidoreductase
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PDB id
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6fkt
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Crystal structure of a dye-decolorizing peroxidase r232a variant from klebsiella pneumoniae (kpdyp)
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Structure:
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Iron-dependent peroxidase. Chain: a, b. Synonym: peroxidase,putative deferrochelatase/peroxidase yfex. Engineered: yes
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Source:
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Klebsiella pneumoniae. Organism_taxid: 573. Variant: r232a. Gene: yfex, agg09_21550, b1727_13990, b8011_07420, bl102_0001560, bn49_3985, bvx91_12125, ceo55_07245, cit28_09840, cp905_14695, pmk1_00271, samea3531778_01640, sm57_03027. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768
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Resolution:
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1.86Å
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R-factor:
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0.170
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R-free:
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0.207
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Authors:
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V.Pfanzagl,S.Hofbauer,G.Mlynek
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Key ref:
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V.Pfanzagl
et al.
(2018).
Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage.
J Biol Chem,
293,
14823-14838.
PubMed id:
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Date:
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24-Jan-18
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Release date:
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08-Aug-18
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PROCHECK
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Headers
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References
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A0A0W8ATM9
(A0A0W8ATM9_KLEPN) -
Deferrochelatase/peroxidase YfeX from Klebsiella pneumoniae
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Seq:
Struc:
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299 a.a.
299 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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J Biol Chem
293:14823-14838
(2018)
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PubMed id:
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Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage.
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V.Pfanzagl,
K.Nys,
M.Bellei,
H.Michlits,
G.Mlynek,
G.Battistuzzi,
K.Djinovic-Carugo,
S.Van Doorslaer,
P.G.Furtmüller,
S.Hofbauer,
C.Obinger.
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ABSTRACT
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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
(KpDyP) (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 H2O2 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 KpDyP 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.
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