Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1·9 Å resolution

Kunishima, N.; Fukuyama, Keiichi; Matsubara, Hiroshi; Hatanaka, Haruyo; Shibano, Yuji; Amachi, Teruo

doi:10.1016/s0022-2836(05)80037-3

Cited by 202 publications

(166 citation statements)

References 36 publications

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“…The conformation of the protein mole- cule shows little change, whereas the solvent molecules around the distal side of the heme show marked rearrangement. Electron density, clearly seen at the sixth position of the heme iron at pH 7.5 [7], is absent in the low pH form. The heme iron of ARP at a low pH has typical pentacoordinated geometry.…”

Section: Coordination To the Heme Ironmentioning

confidence: 90%

“…In brief, the position of the water molecule on the distal side of the heme in peroxidases appears to be dominated by the orientation of the imidazole ring rather than by interaction with the heme. The different orientation of the imidazole ring in ARP [7,8] causes marked deviation of the water molecule from the 6th position of the heme. Generally in peroxidases the interaction between the water molecule and the heme iron appears to be weak, which is consistent with the spectroscopic evidence for CcP [10,11] and LiP [12,13].…”

Section: Coordination To the Heme Ironmentioning

confidence: 99%

“…rorhizus peroxidases were characterized by Kjalke et al [6]. Crystal structures of the native ARP, its cyanide-and triiodidebound forms, and C. cinereus peroxidase have been obtained at high resolution [7][8][9].…”

Section: Introductionmentioning

confidence: 99%

“…Crystallographic analyses of CcP, LiP, MnP, and ascorbate peroxidase have shown that the water molecule is located at the sixth coordination position of each heme [14][15][16][17]. In the case of ARP, structural analysis of crystals grown at pH 7.5 with ammonium sulfate as the precipitant showed significant electron density at the sixth coordination position of the heme [7]. Moreover, the color of the ARP crystals showed marked pH dependence, being reddish-brown at a high pH and brown at a low one.…”

Section: Introductionmentioning

confidence: 99%

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Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 Å resolution crystallographic study at pH 4.5

Kunishima¹,

Amada²,

Fukuyama³

et al. 1996

FEBS Letters

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In the presence of ammonium sulfate the absorption spectra of a peroxidase from the fungus Arthromyces ramosus (ARP) showed that the low-spin component increased as the pH increased from 6.0 to 9.0, whereas in its absence ARP remained in the high-spin state in the pH range investigated. The crystal structure of ARP at pH 4.5 in the presence of ammonium sulfate at 1.8 A resolution showed that the electron density at the 6th position of the heine iron seen at pH 7.5 had disappeared and that the iron atom deviated markedly from the heme plane. These observations strongly suggest that under physiological conditions the heine of ARP is in the pentacoordinated high-spin state and that at a high pH the heine iron is able to bind ammonia, forming the low-spin state. The location of the water molecule at the distal side of the heme in peroxidases is also discussed.

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Section: Coordination To the Heme Ironmentioning

confidence: 90%

Section: Coordination To the Heme Ironmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 Å resolution crystallographic study at pH 4.5

Kunishima¹,

Amada²,

Fukuyama³

et al. 1996

FEBS Letters

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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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Refinement of 3D models of horseradish peroxidase isoenzyme C: Predictions of 2D NMR assignments and substrate binding sites

et al. 1996

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In this study, two alternative three-dimensional (3D) models of horseradish peroxidase (HRP-C)-differing mainly in the structure of a long untemplated insertion-were refined, systematically assessed, and used to make predictions that can both guide and be tested by future experimental studies. A key first step in the model-building process was a procedure for multiple sequence alignment based on structurally conserved regions and key conserved residues, including those side chains providing ligands to the two Ca2+ binding sites. The model refinements reported here include (1) optimization of side-chain conformations; (3) addition of structural waters using a template-independent procedure; (2) structural refinement of the untemplated 34 amino acid insertion located between the F and G helices, using both energy criteria and NMR data; (4) unconstrained energy optimization of the refined models. Using these procedures, two refined structures of HRP-C were obtained, differing mainly in the conformation of this long insertion. The presence of residues in this insertion that could potentially interact with bound substrates suggests a functional role that may be related to the general ability of class III peroxidases to form stable 1:1 complexes with a variety of substrates. The structural validity of the models was systematically assessed by a variety of criteria. Most notably, the ProsaII z scores and Profiles 3D scores of the two HRP-C models indicated that they are significantly better than would be obtained by simple amino acid replacement, using any of the known structures as a template. These two 3D HRP-C models, were then used to predict candidate residues for the assignment of NOESY cross-peaks previously noted in 2D-NMR studies. Specifically, the residues known as Ile X, Phe A, Phe B, aliphatic residue Q, and Ile T. Candidate substrate binding sites were also identified and compared with experimentally based predictions. This work is timely because new X-ray structures are anticipated that will facilitate the validation of these procedures.

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Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1·9 Å resolution

Cited by 202 publications

References 36 publications

Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 Å resolution crystallographic study at pH 4.5

Pentacoordination of the heme iron of Arthromyces ramosus peroxidase shown by a 1.8 Å resolution crystallographic study at pH 4.5

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

Refinement of 3D models of horseradish peroxidase isoenzyme C: Predictions of 2D NMR assignments and substrate binding sites

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