› 6fks

X-ray diffraction
1.6Å resolution

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

Released:
DOI: 10.2210/pdb6fks/pdb
PDB entry 6fks coloured by chain, front view.
PDB entry 6fks coloured by chain, side view.
PDB entry 6fks coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
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, Furtmüller PG, Hofbauer S, Obinger C
J Biol Chem 293 14823-14838 (2018)
PMID: 30072383

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-102791 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peroxidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 303 amino acids
Theoretical weight: 33.45 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: A0A0W8ATM9 (Residues: 1-299; Coverage: 100%)
Gene names: B5L96_13025, BANRA_01434, BL124_00002915, DW281_04425, EAO17_06045, G4V31_13870, GJJ08_007500, GJJ13_006675, GJJ18_14085, GNF00_21995, NCTC5047_01851, NCTC5052_04810, NCTC5053_06042, NCTC8849_04436, NCTC9128_06528, NCTC9617_05926, NCTC9645_04146, NCTC9661_02271, QIG75_11925, SAMEA3499874_02682, SAMEA3499901_02278, SAMEA3538658_00805, SAMEA3538828_02330, SAMEA3673026_00719, SAMEA3720909_00279, SAMEA4364603_01449, SAMEA4370542_04012, SAMEA4873597_02071, SAMEA4873632_02324, VKR_01427, yfeX
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand HEM 2 x HEM
Ligand GOL 4 x GOL
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 50.52Å b: 75.85Å c: 75.64Å
α: 90° β: 107.86° γ: 90°
R-values:
R R work R free
0.13 0.128 0.167
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

3 review citations

Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives.
Lee et al. (2019)
2 more

8 mentions without citation

Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of FeIV = O formation in bacterial dye-decolorizing peroxidases.
Lučić et al. (2021)
7 more