7DLK

Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol.

Dhankhar, P.Dalal, V.Singh, V.Sharma, A.K.Kumar, P.

(2021) Int J Biol Macromol 193: 601-608

  • DOI: https://doi.org/10.1016/j.ijbiomac.2021.10.100
  • Primary Citation of Related Structures:  
    7DLK

  • PubMed Abstract: 

    Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s -1 , followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (k cat ) of 0.07 s -1 and 0.07 s -1 , respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.


  • Organizational Affiliation

    Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deferrochelatase/peroxidase
A, B, C, D, E
A, B, C, D, E, F
363Bacillus subtilisMutation(s): 0 
Gene Names: efeBGS595_16230
EC: 1.11.1 (PDB Primary Data), 4.98.1.1 (UniProt)
UniProt
Find proteins for P39597 (Bacillus subtilis (strain 168))
Explore P39597 
Go to UniProtKB:  P39597
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39597
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
EA [auth E]
G [auth A]
KA [auth F]
O [auth B]
S [auth C]
EA [auth E],
G [auth A],
KA [auth F],
O [auth B],
S [auth C],
Z [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
EPE (Subject of Investigation/LOI)
Query on EPE

Download Ideal Coordinates CCD File 
MA [auth F]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
VOH (Subject of Investigation/LOI)
Query on VOH

Download Ideal Coordinates CCD File 
GA [auth E],
U [auth C]
Veratryl alcohol
C9 H12 O3
OEGPRYNGFWGMMV-UHFFFAOYSA-N
MPD (Subject of Investigation/LOI)
Query on MPD

Download Ideal Coordinates CCD File 
I [auth A],
V [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

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N [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL (Subject of Investigation/LOI)
Query on GOL

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BA [auth D]
HA [auth E]
IA [auth E]
J [auth A]
K [auth A]
BA [auth D],
HA [auth E],
IA [auth E],
J [auth A],
K [auth A],
L [auth A],
NA [auth F],
OA [auth F],
PA [auth F],
Q [auth B],
QA [auth F],
W [auth C],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

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CA [auth D]
DA [auth D]
JA [auth E]
M [auth A]
R [auth B]
CA [auth D],
DA [auth D],
JA [auth E],
M [auth A],
R [auth B],
RA [auth F],
SA [auth F],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
AA [auth D]
FA [auth E]
H [auth A]
LA [auth F]
P [auth B]
AA [auth D],
FA [auth E],
H [auth A],
LA [auth F],
P [auth B],
T [auth C]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.988α = 87.84
b = 102.108β = 76.45
c = 105.47γ = 83.22
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaDBT-1088-BIO

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description