1QPA

LIGNIN PEROXIDASE ISOZYME LIP4.65 (PI 4.65)

Summary for 1QPA

• Entry DOI: 10.2210/pdb1qpa/pdb
• Descriptor: LIGNIN PEROXIDASE, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose, ... (8 entities in total)
• Functional Keywords: oxidoreductase, lignin degradation, heme, glycoprotein
• Biological source: Phanerochaete chrysosporium
• Total number of polymer chains: 2
• Total formula weight: 76850.37

Authors

Choinowski, T.H.,Piontek, K. (deposition date: 1996-10-08, release date: 1997-01-11, Last modification date: 2020-07-29)

Primary citation

Choinowski, T.,Blodig, W.,Winterhalter, K.H.,Piontek, K.
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.
J.Mol.Biol., 286:809-827, 1999

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 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.

PubMed: 10024453
DOI: 10.1006/jmbi.1998.2507

Experimental method

X-RAY DIFFRACTION (1.8 Å)