1QPA

LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of lignin peroxidase at 1.70 A resolution reveals a hydroxy group on the cbeta of tryptophan 171: a novel radical site formed during the redox cycle.

Choinowski, T.Blodig, W.Winterhalter, K.H.Piontek, K.

(1999) J.Mol.Biol. 286: 809-827

  • DOI: 10.1006/jmbi.1998.2507
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of lignin peroxidase (LiP) from the white rot fungus Phanerochaete chrysosporium was refined to an R-factor of 16.2 % utilizing synchrotron data in the resolution range from 10 to 1.7 A. The final model comprises all 343 amino a ...

    The crystal structure of lignin peroxidase (LiP) from the white rot fungus Phanerochaete chrysosporium was refined to an R-factor of 16.2 % utilizing synchrotron data in the resolution range from 10 to 1.7 A. The final model comprises all 343 amino acid residues, 370 water molecules, the heme, four carbohydrates, and two calcium ions. Lignin peroxidase shows the typical peroxidase fold and the heme has a close environment as found in other peroxidases. During refinement of the LiP model an unprecedented modification of an amino acid was recognized. The surface residue tryptophan 171 in LiP is stereospecifically hydroxylated at the Cbeta atom due to an autocatalytic process. We propose that during the catalytic cycle of LiP a transient radical at Trp171 occurs that is different from those previously assumed for this type of peroxidase. Recently, the existence of a second substrate-binding site centered at Trp171 has been reported, by us which is different from the "classical heme edge" site found in other peroxidases. Here, we report evidence for a radical formation at Trp171 using spin trapping, which supports the concept of Trp171 being a redox active amino acid and being involved in the oxidation of veratryl alcohol. On the basis of our current model, an electron pathway from Trp171 to the heme is envisaged, relevant for the oxidation of veratryl alcohol and possibly lignin. Beside the opening leading to the heme edge, which can accommodate small aromatic substrate molecules, a smaller channel giving access to the distal heme pocket was identified that is large enough for molecules such as hydrogen peroxide. Furthermore, it was found that in LiP the bond between the heme iron and the Nepsilon2 atom of the proximal histidine residue is significantly longer than in cytochrome c peroxidase (CcP). The weaker Fe-N bond in LiP renders the heme more electron deficient and destabilizes high oxidation states, which could explain the higher redox potential of LiP as compared to CcP.


    Related Citations: 
    • Do Carbohydrates Play a Role in the Lignin Peroxidase Cycle? Redox Catalysis in the Endergonic Region of the Driving Force
      Schoemaker, H.E.,Lundell, T.K.,Floris, R.,Glumoff, T.,Winterhalter, K.H.,Piontek, K.
      (1994) Bioorg.Med.Chem. 2: 509
    • The Oxidation of Veratryl Alcohol, Dimeric Lignin Models and Lignin by Lignin Peroxidase: The Redox Cycle Revisited
      Schoemaker, H.E.,Lundell, T.K.,Hatakka, A.I.,Piontek, K.
      (1994) Fems Microbiol.Rev. 13: 321
    • Low Ph Crystal Structure of Glycosylated Lignin Peroxidase from Phanerochaete Chrysosporium at 2.5 A Resolution
      Piontek, K.,Glumoff, T.,Winterhalter, K.
      (1993) FEBS Lett. 315: 119


    Organizational Affiliation

    Laboratorium für Biochemie I, Eidgenössische Technische Hochschule, Universitätstrasse 16, Zürich, CH-8092, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIGNIN PEROXIDASE
A, B
345Phanerochaete chrysosporiumMutation(s): 0 
Gene Names: GLG4 (LIP2)
EC: 1.11.1.14
Find proteins for P11542 (Phanerochaete chrysosporium)
Go to UniProtKB:  P11542
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HTR
Query on HTR
A, B
L-PEPTIDE LINKINGC11 H12 N2 O3TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.790α = 90.00
b = 94.020β = 106.47
c = 81.260γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance