The crystal structure of peanut peroxidase

Schüller, David; Ban, Nenad; Huystee, Robert B. van; McPherson, Alexander; Poulos, T.L.

doi:10.1016/s0969-2126(96)00035-4

Cited by 269 publications

(222 citation statements)

References 53 publications

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“…Hence, a detailed comparison of the crystal structures of LiP [10,12,13] with that of C. cinereus peroxidase\A. ramosus [47] as well as those from the class III peroxidases HRP [15] and peanut peroxidase [14] may well suggest mutational strategies to achieve an alkali-stable LIP variant.…”

Section: Re-activation and Stabilization Of Lip H2 With Ca 2 +mentioning

confidence: 99%

“…However, LiP H2 has four disulphide bridges (between cysteine residues 3-15, 14-285, 34-120 and 249-317) that are located differently with respect to the four disulphides in HRP. Importantly for the present paper, LiP possesses both proximal and distal calcium sites, but lacks additional structural elements between helices F and G that occur in the class III peroxidases [12][13][14][15] (see also [16] for a review).…”

Section: Introductionmentioning

confidence: 99%

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Reversible alkaline inactivation of lignin peroxidase involves the release of both the distal and proximal site calcium ions and bishistidine co-ordination of the haem

George

Kvaratskhelia

Dilworth

et al. 1999

Biochemical Journal

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Phanerochaete chrysosporium lignin peroxidase isoenzyme H2 (LiP H2) exhibits a transition to a stable, inactive form at pH 9.0 with concomitant spectroscopic changes. The So$ ret peak intensity decreases some 55 % with a red shift from 408 to 412 nm ; the bands at 502 nm and 638 nm disappear and the peak at 536 nm increases. The EPR spectrum changes from a signal typical of high spin ferric haem to an exclusively low spin spectrum with g l 2.92, 2.27, 1.50. These data indicate that the active pentacoordinated haem is converted into a hexaco-ordinated species at alkaline pH. Room temperature near-IR MCD data coupled with the EPR spectrum allow us to assign the haem co-ordination of alkali-inactivated enzyme as bishistidine. Re-acidification of the alkali-inactivated enzyme to pH 6 induces further spectroscopic changes and generates an irreversibly inactivated species. By contrast, a pH shift from 9.0 to 6.0 with simultaneous addition of 50 mM CaCl # results in the recovery of the initial

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Section: Re-activation and Stabilization Of Lip H2 With Ca 2 +mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Reversible alkaline inactivation of lignin peroxidase involves the release of both the distal and proximal site calcium ions and bishistidine co-ordination of the haem

George

Kvaratskhelia

Dilworth

et al. 1999

Biochemical Journal

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“…plant and fungal peroxidases (23,(28)(29)(30)(31). All of the catalytic residues, including the distal His and Arg and proximal His and Asp, are conserved in MnP, LiP, cytochrome c peroxidase, horseradish peroxidase (HRP), and Coprinus cinereus peroxidase (CiP)/Arthromyces ramosus peroxidase (ArP) (2,(28)(29)(30)(32)(33)(34)(35).…”

mentioning

confidence: 99%

Formation of a Bis(histidyl) Heme Iron Complex in Manganese Peroxidase at High pH and Restoration of the Native Enzyme Structure by Calcium

et al. 2000

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Manganese peroxidase (MnP) from Phanerochaete chrysosporium undergoes a pH-dependent conformational change evidenced by changes in the electronic absorption spectrum. This high-to lowspin alkaline transition occurs at ∼2 pH units lower in an F190I mutant MnP when compared to the wild-type enzyme. Herein, we provide evidence that these spectral changes are attributable to the formation of a bis(histidyl) heme iron complex in both proteins at high pH. The resonance Raman (RR) spectra of both ferric proteins at high pH are similar, indicating similar heme environments in both proteins, and resemble that of ferric cytochrome b 558 , a protein that contains a bis-His iron complex. Upon reduction with dithionite at high pH, the visible spectra of both the wild-type and F190I MnP exhibit absorption maxima at 429, 529, and 558 nm, resembling the absorption spectrum of ferrous cytochrome b 558 . RR spectra of the reduced wild-type and F190I mutant proteins at high pH are also similar to the RR spectrum of ferrous cytochrome b 558 , further suggesting that the alkaline low-spin species is a bis(histidyl) heme derivative. No shift in the low-frequency RR bands was observed in 75% 18 O-labeled water, indicating that the low-spin species is most likely not a hydroxo-heme derivative. Electronic and RR spectra also indicate that addition of Ca 2+ to either the ferric or ferrous enzymes at high pH completely restores the high-spin pentacoordinate species. Other divalent metals, such as Mn 2+ , Mg 2+ , Zn 2+ , or Cd 2+ , do not restore the enzyme under the conditions studied.Manganese peroxidase (MnP) 1 is an extracellular heme protein produced by virtually all lignin-degrading white-rot fungi (1-3). Sequences have been determined for mnp cDNA (4, 5) and genomic clones (6-8) encoding three MnP isozymes from Phanerochaete chrysosporium, the beststudied lignin-degrading fungus. These sequences and spectroscopic studies of the native and oxidized enzyme intermediates indicate that the heme environment of MnP is similar to that of other plant and fungal peroxidases (4,(9)(10)(11)(12)(13)(14). Kinetic and spectroscopic studies of the purified enzyme indicate a typical peroxidase reaction catalytic cycle:However, MnP is unique in its ability to efficiently oxidize Mn 2+ to Mn 3+ (9,15,16). The released Mn 3+ is stabilized by organic acid chelators, such as oxalate and malonate, which are secreted by the fungus (16, 17). The Mn 3+ -chelator complex is capable of diffusing from the enzyme to oxidize terminal substrates including lignin substructures, phenolic compounds, and pollutants (2, 3 and references therein, 18).The three amino acid residues believed to bind Mn 2+ , D179, E35, and E39, were investigated by site-directed mutagenesis of recombinant MnP homologously expressed in P. chrysosporium (19)(20)(21)(22). These studies, combined with X-ray crystal structure analyses of the proteins (23,24), confirmed that the side-chain carboxylates of D179, E35, and E39 form the only apparent Mn 2+ -binding site in MnP from P. chry...

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“…Class II includes the lignin-degrading, manganese-dependent (MnP), and Coprinus peroxidases (synonymous with Arthromyces ramosus peroxidase). Class III includes the classic horseradish peroxidase (HRP C); peanut peroxidase (PNP), for which the first crystal structure of a class III peroxidase was solved (9); and the major peroxidase from barley grain (BP 1).…”

mentioning

confidence: 99%

Structure of Barley Grain Peroxidase Refined at 1.9-Å Resolution

Henriksen

Welinder

Gajhede

1998

Journal of Biological Chemistry

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The crystal structure of the major peroxidase of barley grain (BP 1) has been solved by molecular replacement and phase combination and refined to an R-factor of 19.2% for all data between 38 and 1.9 Å. The refined model includes amino acid residues 1-309, one calcium ion, one sodium ion, iron-protoporphyrin IX, and 146 solvent molecules. BP 1 has the apparently unique property of being unable to catalyze the reaction with the primary substrate hydrogen peroxide to form compound I at pH values > 5, a feature investigated by obtaining crystal structure data at pH 5.5, 7.5, and 8.5. Structural comparison shows that the overall fold of inactive barley grain peroxidase at these pH values resembles that of both horseradish peroxidase C and peanut peroxidase. The key differences between the structures of active horseradish peroxidase C and inactive BP 1 include the orientation of the catalytic distal histidine, disruption of a hydrogen bond between this histidine and a conserved asparagine, and apparent substitution of calcium at the distal cation binding site with sodium at pH 7.5. These profound changes are a result of a dramatic structural rearrangement to the loop region between helices B and C. This is the first time that structural rearrangements linked to active site chemistry have been observed by crystallography in the peroxidase domain distal to heme.All living organisms utilize peroxidases in a variety of biosynthetic or degradable processes and in defense against pathogens or oxidative pressure. The majority of known peroxidases belong to the plant peroxidase superfamily, which is characterized by a central heme group sandwiched between a distal and a proximal protein domain. The plant peroxidase superfamily is subdivided into three classes based on structural divergence (1). Class I constitutes intracellular peroxidases of prokaryotic origin, and class I peroxidases are found in yeast (cytochrome c peroxidase; CCP), 1 plants (pea cytosolic ascorbate peroxidase), and bacteria. Class II and III peroxidases are found in fungi and plants, respectively, and are largely extracellular. Both class II and class III peroxidases contain two conserved calcium ions, one in each of the distal and proximal domains. Class II includes the lignin-degrading, manganese-dependent (MnP), and Coprinus peroxidases (synonymous with Arthromyces ramosus peroxidase). Class III includes the classic horseradish peroxidase (HRP C); peanut peroxidase (PNP), for which the first crystal structure of a class III peroxidase was solved (9); and the major peroxidase from barley grain (BP 1).In common with other heme-containing peroxidases, BP 1 catalyzes the following multistep reaction.Still, with its unique pH and calcium dependent activity profile (2, 3), BP 1 is the most interesting and atypical of the class III peroxidases. In the presence of calcium and following a pHinduced conformational change with a pK a Ͻ 3.7, BP 1 has a rate constant for compound I formation comparable with the rate constant for HRP C. The similarities between BP ...

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The crystal structure of peanut peroxidase

Cited by 269 publications

References 53 publications

Reversible alkaline inactivation of lignin peroxidase involves the release of both the distal and proximal site calcium ions and bishistidine co-ordination of the haem

Reversible alkaline inactivation of lignin peroxidase involves the release of both the distal and proximal site calcium ions and bishistidine co-ordination of the haem

Formation of a Bis(histidyl) Heme Iron Complex in Manganese Peroxidase at High pH and Restoration of the Native Enzyme Structure by Calcium

Structure of Barley Grain Peroxidase Refined at 1.9-Å Resolution

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