4HOV

DypB N246A in complex with manganese

Summary for 4HOV

• Entry DOI: 10.2210/pdb4hov/pdb
• Related: 3VEE
• Descriptor: DypB, PROTOPORPHYRIN IX CONTAINING FE, CHLORIDE ION, ... (7 entities in total)
• Functional Keywords: peroxidase, lignin, heme, dyp, oxidoreductase
• Biological source: Rhodococcus jostii
• Total number of polymer chains: 3
• Total formula weight: 114742.38

Authors

Grigg, J.C.,Singh, R.,Eltis, L.D.,Murphy, M.E.P. (deposition date: 2012-10-22, release date: 2013-01-16, Last modification date: 2023-09-20)

Primary citation

Singh, R.,Grigg, J.C.,Qin, W.,Kadla, J.F.,Murphy, M.E.,Eltis, L.D.
Improved Manganese-Oxidizing Activity of DypB, a Peroxidase from a Lignolytic Bacterium.
Acs Chem.Biol., 8:700-706, 2013

PubMed Abstract: DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn(2+)), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine increased the enzyme's apparent k(cat) and k(cat)/K(m) values for Mn(2+) by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn(2+) to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different from that of another bacterial Mn(2+)-oxidizing peroxidase. The first coordination sphere was entirely composed of solvent, consistent with the variant's high K(m) for Mn(2+) (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin.

PubMed: 23305326
DOI: 10.1021/cb300608x

Experimental method

X-RAY DIFFRACTION (2.2 Å)