PDBsum entry 1qpa

Oxidoreductase

PDB id: 1qpa

Contents

Protein chains

344 a.a. *

Ligands

NAG-NAG-FUC

MAN-MAN

NAG

MAN ×5

HEM ×2

Metals

_CA ×4

Waters ×464

* Residue conservation analysis

PDB id:

1qpa

Name:

Oxidoreductase

Title:

Lignin peroxidase isozyme lip4.65 (pi 4.65)

Structure:

Lignin peroxidase. Chain: a, b. Other_details: isozyme lip4.65

Source:

Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: bkm-f1267. Atcc: 24725

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.162

Authors:

T.H.Choinowski,K.Piontek

Key ref:

T.Choinowski et al. (1999). 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. PubMed id: 10024453 DOI: 10.1006/jmbi.1998.2507

Date:

08-Oct-96 Release date: 11-Jan-97

Protein chains

P11542  (LIG4_PHACH) -  Ligninase H2 from Phanerodontia chrysosporium

Seq: 372 a.a.

Struc: 344 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.11.1.14 - lignin peroxidase.
• Reaction:
  1. 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol + H2O2 = 3,4-dimethoxybenzaldehyde + guaiacol + glycolaldehyde + H2O
  2. 2 (3,4-dimethoxyphenyl)methanol + H2O2 = 2 (3,4- dimethoxyphenyl)methanol radical + 2 H2O

1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol + H2O2 = 3,4-dimethoxybenzaldehyde (Bound ligand (Het Group name = MAN) matches with 64.29% similarity) + guaiacol (Bound ligand (Het Group name = NAG) matches with 53.33% similarity) + glycolaldehyde (Bound ligand (Het Group name = FUC) matches with 40.00% similarity) + H2O

• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1006/jmbi.1998.2507

J Mol Biol 286:809-827 (1999)

PubMed id: 10024453

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.

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

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.

Selected figure(s)

Figure 6.
Figure 6. Stereoscopic view of the (a) proximal and (b) distal calcium-binding sites in LiP415. Both difference omit maps are contoured at 15σ. The bonds are shown as broken lines and the liganding residues and bond lengths are labelled.

Figure 15.
Figure 15. The molecular surface charge distribution of LiP415 showing the “back side” of the protein. The negative potentials on the surface are shaded in red and the positive potentials in blue. The heme, and several hydrophobic surface residues at the vicinity of Trp171 are depicted by bonds. The picture was generated using the program GRASP [Nicholls 1993].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 286, 809-827) copyright 1999.

Figures were selected by an automated process.