3FU8

Melanocarpus albomyces laccase crystal soaked (10 sec) with 2,6-dimethoxyphenol

Summary for 3FU8

• Entry DOI: 10.2210/pdb3fu8/pdb
• Related: 2q9o
• Descriptor: Laccase-1, GLYCEROL, alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (11 entities in total)
• Functional Keywords: laccase, multicopper oxidase, complex structure, 2, 6-dimethoxyphenol, oxidation of phenolic compounds, glycoprotein, lignin degradation, metal-binding, oxidoreductase
• Biological source: Melanocarpus albomyces
• Total number of polymer chains: 2
• Total formula weight: 130975.31

Authors

Kallio, J.P.,Hakulinen, N.,Rouvinen, J. (deposition date: 2009-01-14, release date: 2009-09-22, Last modification date: 2020-07-29)

Primary citation

Kallio, J.P.,Auer, S.,Janis, J.,Andberg, M.,Kruus, K.,Rouvinen, J.,Koivula, A.,Hakulinen, N.
Structure-Function Studies of a Melanocarpus albomyces Laccase Suggest a Pathway for Oxidation of Phenolic Compounds.
J.Mol.Biol., 392:895-909, 2009

PubMed Abstract: Melanocarpus albomyces laccase crystals were soaked with 2,6-dimethoxyphenol, a common laccase substrate. Three complex structures from different soaking times were solved. Crystal structures revealed the binding of the original substrate and adducts formed by enzymatic oxidation of the substrate. The dimeric oxidation products were identified by mass spectrometry. In the crystals, a 2,6-dimethoxy-p-benzoquinone and a C-O dimer were observed, whereas a C-C dimer was the main product identified by mass spectrometry. Crystal structures demonstrated that the substrate and/or its oxidation products were bound in the pocket formed by residues Ala191, Pro192, Glu235, Leu363, Phe371, Trp373, Phe427, Leu429, Trp507 and His508. Substrate and adducts were hydrogen-bonded to His508, one of the ligands of type 1 copper. Therefore, this surface-exposed histidine most likely has a role in electron transfer by laccases. Based on our mutagenesis studies, the carboxylic acid residue Glu235 at the bottom of the binding site pocket is also crucial in the oxidation of phenolics. Glu235 may be responsible for the abstraction of a proton from the OH group of the substrate and His508 may extract an electron. In addition, crystal structures revealed a secondary binding site formed through weak dimerization in M. albomyces laccase molecules. This binding site most likely exists only in crystals, when the Phe427 residues are packed against each other.

PubMed: 19563811
DOI: 10.1016/j.jmb.2009.06.053

Experimental method

X-RAY DIFFRACTION (1.8 Å)