6A6Q

Crystal strcuture of a lignin peroxidase isozyme H8 variant that is stable at very acidic pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

In silico-designed lignin peroxidase fromPhanerochaete chrysosporiumshows enhanced acid stability for depolymerization of lignin.

Pham, L.T.M.Seo, H.Kim, K.J.Kim, Y.H.

(2018) Biotechnol Biofuels 11: 325-325

  • DOI: 10.1186/s13068-018-1324-4

  • PubMed Abstract: 
  • The lignin peroxidase isozyme H8 from the white-rot fungus <i>Phanerochaete chrysosporium </i> (LiPH8) demonstrates a high redox potential and can efficiently catalyze the oxidation of veratryl alcohol, as well as the degradation of recalcitrant lig ...

    The lignin peroxidase isozyme H8 from the white-rot fungus Phanerochaete chrysosporium (LiPH8) demonstrates a high redox potential and can efficiently catalyze the oxidation of veratryl alcohol, as well as the degradation of recalcitrant lignin. However, native LiPH8 is unstable under acidic pH conditions. This characteristic is a barrier to lignin depolymerization, as repolymerization of phenolic products occurs simultaneously at neutral pH. Because repolymerization of phenolics is repressed at acidic pH, a highly acid-stable LiPH8 could accelerate the selective depolymerization of recalcitrant lignin.


    Organizational Affiliation

    2School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-gu, Daegu, 41566 Republic of Korea.,1School of Energy and Chemical Engineering, UNIST, 50 UNIST-gil, Ulju-gun, Ulsan, 44919 Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ligninase H8
A
351Phanerochaete chrysosporiumMutation(s): 3 
Gene Names: LPOA
EC: 1.11.1.14
Find proteins for P06181 (Phanerochaete chrysosporium)
Go to UniProtKB:  P06181
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEB
Query on HEB

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Download CCD File 
A
HEME B/C
HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-ICENSXKYDL
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HTR
Query on HTR
A
L-PEPTIDE LINKINGC11 H12 N2 O3TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.212α = 90.00
b = 99.621β = 113.86
c = 48.322γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release