PDBsum entry 1b80

Oxidoreductase

PDB id: 1b80

Contents

Protein chains

349 a.a. *

Ligands

HEM ×2

Metals

_CA ×4

Waters ×573

* Residue conservation analysis

PDB id:

1b80

Name:

Oxidoreductase

Title:

Rec. Lignin peroxidase h8 oxidatively processed

Structure:

Protein (recombinant lignin peroxidase h8). Chain: a, b. Fragment: mature protein plus 7-residue prosequence. Engineered: yes. Other_details: heme containing, trp171 is hydroxylated at its cbeta atom

Source:

Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: bkm 1767. Variant: wild type. Gene: lip h8. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: recombinant expression in e. Coli

Biol. unit:

Tetramer (from PQS)

Resolution:

1.73Å R-factor: 0.170 R-free: 0.208

Authors:

W.Blodig,A.T.Smith,W.A.Doyle,K.Piontek

Key ref:

W.Blodig et al. (2001). Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism. J Mol Biol, 305, 851-861. PubMed id: 11162097 DOI: 10.1006/jmbi.2000.4346

Date:

03-Feb-99 Release date: 09-Feb-99

Protein chains

P06181  (LIG8_PHACH) -  Ligninase H8 from Phanerodontia chrysosporium

Seq: 372 a.a.

Struc: 349 a.a.*

* PDB and UniProt seqs differ at 2 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
• 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.2000.4346

J Mol Biol 305:851-861 (2001)

PubMed id: 11162097

Crystal structures of pristine and oxidatively processed lignin peroxidase expressed in Escherichia coli and of the W171F variant that eliminates the redox active tryptophan 171. Implications for the reaction mechanism.

W.Blodig, A.T.Smith, W.A.Doyle, K.Piontek.

ABSTRACT

The heme enzyme lignin peroxidase (LiP) from the white rot fungus Phanerochaete chrysosporium contains a solvent exposed redox active tryptophan residue (Trp171) that carries a unique hydroxy group stereo-specifically attached to its C(beta) atom. A Trp171Phe mutant has no activity at all towards the substrate veratryl alcohol. The mechanism of veratryl alcohol oxidation involving beta-hydroxy-Trp171 is largely unknown. Here, we present the first crystal structures of LiP isozyme H8 at high resolution in its pristine non-hydroxylated form, of the C(beta)-hydroxylated form, and of the Trp171Phe mutant using recombinantly expressed and refolded protein produced from Escherichia coli. As a consequence, all structures are unglycosylated. Structural changes in response to the mutation are marginal and allow us to attribute the complete lack of activity exclusively to the absence of the redox active indole side-chain. The origin of the stereospecificity of the Trp171 hydroxylation can be explained on structural grounds. A reaction mechanism involving Trp171 is proposed and the possible function of the modification is discussed. Another important result regarding the ongoing debate on the co-ordination state of the heme iron in the resting state is that the iron is six co-ordinate in all cases the data being collected at room temperature. The mean distance from the iron to the distal water ligand is 2.18(+/-0.08) A. The radical scavenger orcinol was found to decrease radiation damage to the crystals, during data collection at room temperature.

Selected figure(s)

Figure 3.
Figure 3. Difference omit maps of (a) the LiPH8-H[2]O[2]structure and (b) the pristine LiPH8 structure for residue Trp171 at 1.73 and 1.8 Å resolution, respectively. The maps in cyan are (2F[o] -F[c])exp(ia[c]) electron densities contoured at 2 s where all atoms of Trp171 were omitted for phase calculation. In red a (F[o] -F[c])exp(ia[c]) electron density map is shown, contoured at 8 s where only the hydroxy group was omitted. The picture was produced with O [Jones et al 1991].

Figure 5.
Figure 5. Difference omit map ((F[o] -F[c])exp(ia[c])) at 1.85 Å resolution of the W171F mutant structure of recombinant LiPH8 for residue Phe171 contoured at 7s. The water molecule (Wat417) which hydrogen bonds to the hydroxy group at the C^b atom of Trp171 in the LiP-H[2]O[2] structure is shown as a red asterisk (see also Figure 4). The picture was produced with O [Jones et al 1991].

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 305, 851-861) copyright 2001.

Figures were selected by an automated process.