3qns | pdb_00003qns
DyPB from Rhodococcus jostii RHA1, crystal form 2
Structural highlights
Publication Abstract from PubMedThe soil bacterium Rhodococcus jostii RHA1 contains two dye-decolorizing peroxidases (DyPs) named according to the subfamily they represent: DypA, predicted to be periplasmic, and DypB, implicated in lignin degradation. Steady-state kinetic studies of these enzymes revealed that they have much lower peroxidase activities than C- and D-type DyPs. Nevertheless, DypA showed 6-fold greater apparent specificity for the anthraquinone dye Reactive Blue 4 (k(cat)/K(m) = 12800 +/- 600 M(-1) s(-1)) than either ABTS or pyrogallol, consistent with previously characterized DyPs. By contrast, DypB showed the greatest apparent specificity for ABTS (k(cat)/K(m) = 2000 +/- 100 M(-1) s(-1)) and also oxidized Mn(II) (k(cat)/K(m) = 25.1 +/- 0.1 M(-1) s(-1)). Further differences were detected using electron paramagnetic resonance (EPR) spectroscopy: while both DyPs contained high-spin (S = (5)/(2)) Fe(III) in the resting state, DypA had a rhombic high-spin signal (g(y) = 6.32, g(x) = 5.45, and g(z) = 1.97) while DypB had a predominantly axial signal (g(y) = 6.09, g(x) = 5.45, and g(z) = 1.99). Moreover, DypA reacted with H(2)O(2) to generate an intermediate with features of compound II (Fe(IV) horizontal lineO). By contrast, DypB reacted with H(2)O(2) with a second-order rate constant of (1.79 +/- 0.06) x 10(5) M(-1) s(-1) to generate a relatively stable green-colored intermediate (t(1/2) approximately 9 min). While the electron absorption spectrum of this intermediate was similar to that of compound I of plant-type peroxidases, its EPR spectrum was more consistent with a poorly coupled protein-based radical than with an [Fe(IV) horizontal lineO Por(*)](+) species. The X-ray crystal structure of DypB, determined to 1.4 A resolution, revealed a hexacoordinated heme iron with histidine and a solvent species occupying axial positions. A solvent channel potentially provides access to the distal face of the heme for H(2)O(2). A shallow pocket exposes heme propionates to the solvent and contains a cluster of acidic residues that potentially bind Mn(II). Insight into the structure and function of DypB facilitates its engineering for the improved degradation of lignocellulose. Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1.,Roberts JN, Singh R, Grigg JC, Murphy ME, Bugg TD, Eltis LD Biochemistry. 2011 Jun 14;50(23):5108-19. Epub 2011 May 19. PMID:21534572[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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