• Prosthetic group features
• Active site residues
• Fungal, plant and bacterial haem peroxidases in enzyme databases
• Fungal, plant and bacterial haem peroxidases in motif databases
• Fungal, plant and bacterial haem peroxidases in alignment databases
• Fungal, plant and bacterial haem peroxidases in 3­D databases
• References

Haem type	Haem iron coordination	Axial iron ligand(s)	Formal iron oxidation/spin states
Haem b	Pentacoordinate / Hexacoordinate	NHis; (H2O or OH¯)	FeII (S=2); FeIII (S=5/2)
	Hexacoordinate	NHis; H2O, H2O2 or O2	FeII (S=0); FeIII (S=1/2)
	Hexacoordinate	NHis; O (O·)	FeIV (S=1)

Peroxidases are haem­containing enzymes that use hydrogen peroxide (H₂O₂) as the electron acceptor to catalyse a number of oxidative reactions [1]. Peroxidases are found in bacteria, fungi, plants and animals. On the basis of sequence similarity, fungal, plant and bacterial peroxidases can be viewed as members of a superfamily consisting of three major classes [2].

Class I, the intracellular peroxidases, includes: yeast cytochrome c peroxidase (CCP), a soluble protein found in the mitochondrial electron transport chain, where it probably protects against toxic peroxides; ascorbate peroxidase (AP), the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants [3]; and bacterial catalase­peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase­peroxidase provides protection to cells under oxidative stress [4].

Class II consists of secretory fungal peroxidases: ligninases, or lignin peroxidases (LiPs), and manganese­dependent peroxidases (MnPs). These are monomeric glycoproteins involved in the degradation of lignin. In MnP, Mn²⁺ serves as the reducing substrate [5]. Class II proteins contain four conserved disulphide bridges and two conserved calcium­binding sites.

Class III consists of the secretory plant peroxidases, which have multiple tissue­specific functions: e.g., removal of hydrogen peroxide from chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the cell wall; defence responses towards wounding; indole­3­acetic acid (IAA) catabolism; ethylene biosynthesis; and so on [6]. Class III peroxidases are also monomeric glycoproteins, containing four conserved disulphide bridges and two calcium ions, although the placement of the disulphides differs from class II enzymes.

The 3­D structures of several peroxidases have been determined, including yeast CCP [7], Phanerochaete chrysosporium LiP [8] and MnP [9], Arthromyces ramosus peroxidase (ARP) [10], pea cytosolic AP [11], peanut peroxidase (PNP) [12] and horseradish peroxidase C (HRPC) [13]. All these proteins share the same architecture, consisting of two all­ domains; two antiparallel helices from two domains form a crevice in which the haem group is inserted [14]. One helix, contributed by the C­terminal domain, contains the fifth (proximal) haem iron ligand (His­175 in CCP). The imidazole ring of the proximal His lies approximately perpendicular to the porphyrin plane with N² bonded to haem iron and N¹ hydrogen bonded to the buried carboxylate group of an Asp residue (Asp­235 in CCP). A number of peroxidases (CCP, AP, LiP, MnP) also contain an aromatic residue (Trp or Phe) parallel to and in van der Waals contact with the imidazole ring of the proximal His [12, 14]. The other helix, on the distal side of the haem, contributes three conserved residues (Arg­48, Trp­51, and His­52 in CCP), which form a ligand pocket for H₂O₂ (see Figure 2CYP). The table below lists haem environment residues in known 3­D structures.

Enzyme	Distal H2O2 binding pocket			Proximal haem iron ligand pocket			PDB code	Ref.
CCP	Arg­48	Trp­51	His­52	His­175	Trp­191	Asp­235	2cyp	[7]
LiP	Arg­43	Phe­46	His­47	His­176	Phe­193	Asp­238	1lga	[8]
MnP	Arg­42	Phe­45	His­46	His­173	Phe­190	Asp­242	1mnp	[9]
ARP	Arg­52	Phe­55	His­56	His­184	Leu­201	Asp­246	1arp	[10]
AP	Arg­38	Trp­41	His­42	His­163	Trp­179	Asp­208	1apx	[11]
PNP	Arg­38	Phe­41	His­42	His­169	Phe­213	Asp­239	1sch	[12]
HRPC	Arg­38	Phe­41	His­42	His­170	Phe­221	Asp­247	1atj	[13]

Animal haem peroxidases in enzyme databases

Note: Peroxidase (EC 1.11.1.7) includes both animal and fungal, plant and bacterial haem peroxidases.

Fungal, plant and bacterial haem peroxidases in motif databases

PRINTS ID	PRINTS AC	PROSITE/BLOCKS ID	PROSITE AC	BLOCKS AC
ASPEROXIDASE	PR00459	PEROXIDASE_1 PEROXIDASE_2	PS00435 PS00436	BL00435
BPEROXIDASE	PR00460
LIGNINASE	PR00462
PEROXIDASE	PR00458
PLPEROXIDASE	PR00461

Fungal, plant and bacterial haem peroxidases in alignment databases

Protein Superfamily	Pfam	LPFC 3­D alignment
00167; cytochrome c peroxidase 00169; peroxidase/catalase 00170; peroxidase 00174; lignin peroxidase	PF00141; peroxidase	peroxidase

PDB	scop	BSM	RELI Base	Header	¹
1a2f	-	1a2f	-	Cytochrome c peroxidase (M172K mutant); Saccharomyces cerevisiae	-
1a2g	-	1a2g	-	Cytochrome c peroxidase (M231H mutant); Saccharomyces cerevisiae	-
1aa4	1aa4	1aa4	1aa4	Cytochrome c peroxidase (T1M, T2K, P3T, W191G mutant); Saccharomyces cerevisiae	-
1ac4	1ac4	1ac4	1ac4	Cytochrome c peroxidase (W191G mutant) (complex with 2,3,4­trimethyl­1,3­thiazole); Saccharomyces cerevisiae	-
1ac8	1ac8	1ac8	1ac8	Cytochrome c peroxidase (W191G mutant) (complex with 3,4,5­trimethylthiazole); Saccharomyces cerevisiae	-
1aeb	1aeb	1aeb	1aeb	Cytochrome c peroxidase (W191G mutant) (complex with 3­methylthiazole); Saccharomyces cerevisiae	-
1aed	1aed	1aed	1aed	Cytochrome c peroxidase (W191G mutant) (complex with 3,4­dimethylthiazole); Saccharomyces cerevisiae	-
1aee	1aee	1aee	1aee	Cytochrome c peroxidase (W191G mutant) (complex with aniline); Saccharomyces cerevisiae	-
1aef	1aef	1aef	1aef	Cytochrome c peroxidase (W191G mutant) (complex with 3­aminopyridine); Saccharomyces cerevisiae	-
1aeg	1aeg	1aeg	1aeg	Cytochrome c peroxidase (W191G mutant) (complex with 4­aminopyridine); Saccharomyces cerevisiae	-
1aeh	1aeh	1aeh	1aeh	Cytochrome c peroxidase (W191G mutant) (complex with 2­amino­4­methylthiazole); Saccharomyces cerevisiae	-
1aej	1aej	1aej	1aej	Cytochrome c peroxidase (W191G mutant) (complex with 1­vinylimidazole); Saccharomyces cerevisiae	-
1aek	1aek	1aek	1aek	Cytochrome c peroxidase (W191G mutant) (complex with indoline); Saccharomyces cerevisiae	-
1aem	1aem	1aem	1aem	Cytochrome c peroxidase (W191G mutant) (complex with imidazo[1,2­a]pyridine); Saccharomyces cerevisiae	-
1aen	1aen	1aen	1aen	Cytochrome c peroxidase (W191G mutant) (complex with 2­amino­5­methylthiazole); Saccharomyces cerevisiae	-
1aeo	1aeo	1aeo	1aeo	Cytochrome c peroxidase (W191G mutant) (complex with 2­aminopyridine); Saccharomyces cerevisiae	-
1aeq	1aeq	1aeq	1aeq	Cytochrome c peroxidase (W191G mutant) (complex with 2­ethylimidazole); Saccharomyces cerevisiae	-
1aes	1aes	1aes	1aes	Cytochrome c peroxidase (W191G mutant) (complex with imidazole); Saccharomyces cerevisiae	-
1aet	1aet	1aet	1aet	Cytochrome c peroxidase (W191G mutant) (complex with 1­methylimidazole); Saccharomyces cerevisiae	-
1aeu	1aeu	1aeu	1aeu	Cytochrome c peroxidase (W191G mutant) (complex with 2­methylimidazole); Saccharomyces cerevisiae	-
1aev	1aev	1aev	1aev	Cytochrome c peroxidase (W191G mutant) (Tyr­236 modified with 2­aminothiazole); Saccharomyces cerevisiae	-
1apx	1apx	1apx	1apx	Ascorbate peroxidase (complex with K+); pea (Pisum sativum)	MS6PH1
1arp	1arp	1arp	1arp	Peroxidase (complex with Ca2+) (modified with N­acetyl­D­glucosamine); Arthromyces ramosus	MS5SK2
1aru	1aru	1aru	1aru	Peroxidase (complex with CN¯ and Ca2+) (modified with N­acetyl­D­glucosamine) (pH 7.5); Arthromyces ramosus	-
1arv	1arv	1arv	1arv	Peroxidase (complex with CN¯ and Ca2+) (modified with N­acetyl­D­glucosamine) (pH 5.0); Arthromyces ramosus	-
1arw	1arw	1arw	1arw	Peroxidase (complex with CN¯ and Ca2+) (modified with N­acetyl­D­glucosamine) (pH 4.0); Arthromyces ramosus	-
1arx	1arx	1arx	1arx	Peroxidase (complex with I¯, K+ and Ca2+) (modified with N­acetyl­D­glucosamine) (pH 6.5); Arthromyces ramosus	-
1ary	1ary	1ary	1ary	Peroxidase (complex with I¯, K+ and Ca2+) (modified with N­acetyl­D­glucosamine) (pH 5.0); Arthromyces ramosus	-
1atj	-	1atj	1atj	Peroxidase C1A (complex with Ca2+); horseradish	-
1bgp	-	1bgp	1bgp	Peroxidase 1 (complex with Ca2+ and Na+); Hordeum vulgare (barley) grain	-
1bva	-	1bva	-	Cytochrome c peroxidase [(manganese binding) D37E, P44D, V45D mutant] (complex with Mn2+); Saccharomyces cerevisiae	-
1cca	1cca	1cca	1cca	Cytochrome c peroxidase [insertion (M1, K2, T3) mutant]; Saccharomyces cerevisiae	-
1ccb	1ccb	1ccb	1ccb	Cytochrome c peroxidase [insertion (M1, K2, T3), D235E mutant]; Saccharomyces cerevisiae	-
1ccc	1ccc	1ccc	1ccc	Cytochrome c peroxidase [insertion (M1, K2, T3), D235A mutant]; Saccharomyces cerevisiae	-
1cce	1cce	1cce	1cce	Cytochrome c peroxidase [insertion (M1, K2, T3), H175G mutant]; Saccharomyces cerevisiae	-
1ccg	1ccg	1ccg	1ccg	Cytochrome c peroxidase [insertion (M1, K2, T3), H175G mutant] (complex with imidazole); Saccharomyces cerevisiae	-
1cci	1cci	1cci	1cci	Cytochrome c peroxidase [insertion (M1, K2, T3), T53I, D152G, F202 mutant] (complex with 2,3­dimethylimidazolium ion); Saccharomyces cerevisiae	-
1ccj	1ccj	1ccj	1ccj	Cytochrome c peroxidase (T1M, T2K, P3T, F202G mutant); Saccharomyces cerevisiae	-
1ccp	1ccp	1ccp	1ccp	Cytochrome c peroxidase [insertion (M1, I2)]; Saccharomyces cerevisiae	MMS91033
1cmp	1cmp	1cmp	1cmp	Cytochrome c peroxidase [insertion (M1, K2, T3), W191G mutant] (complex with 1,2­dimethylimidazole); Saccharomyces cerevisiae	-
1cmq	1cmq	1cmq	1cmq	Cytochrome c peroxidase [insertion (M1, K2, T3), W191G mutant]; Saccharomyces cerevisiae	-
1cmt	1cmt	1cmt	1cmt	Cytochrome c peroxidase [insertion (M1, K2, T3), W191G mutant]; Saccharomyces cerevisiae	-
1cmu	1cmu	1cmu	1cmu	Cytochrome c peroxidase [insertion (M1, K2, T3), W191G, D235N mutant]; Saccharomyces cerevisiae	-
1cpd	1cpd	1cpd	1cpd	Cytochrome c peroxidase [insertion (M1, I2), W191G mutant] (complex with NH4+); Saccharomyces cerevisiae	-
1cpe	1cpe	1cpe	1cpe	Cytochrome c peroxidase [insertion (M1, I2), W191G mutant] (complex with K+); Saccharomyces cerevisiae	-
1cpf	1cpf	1cpf	1cpf	Cytochrome c peroxidase [insertion (M1, I2), W191G mutant] (complex with tris+ ion); Saccharomyces cerevisiae	-
1cpg	1cpg	1cpg	1cpg	Cytochrome c peroxidase [insertion (M1, I2), W191Q mutant] (complex with K+); Saccharomyces cerevisiae	-
1cyf	1cyf	1cyf	1cyf	Cytochrome c peroxidase [insertion (M1, I2), C128A, A193C mutant]; Saccharomyces cerevisiae	-
1dcc	1dcc	1dcc	1dcc	Cytochrome c peroxidase [insertion (M1, I2), W191F mutant] (complex with O2); Saccharomyces cerevisiae	-
1gza	1gza	1gza	1gza	Peroxidase (complex with Ca2+ and I¯) (modified with N­acetyl­D­glucosamine) (pH 5.5); Arthromyces ramosus	-
1gzb	1gzb	1gzb	1gzb	Peroxidase (complex with Ca2+) (modified with N­acetyl­D­glucosamine) (pH 4.5); Arthromyces ramosus	-
1lga	1lga	1lga	1lga	Lignin peroxidase (ferric) (complex with Ca2+) (modified with N­acetyl­D­glucosamine); Phanerochaete chrysosporium	MMS94161
1llp	1llp	1llp	1llp	Lignin peroxidase (isozyme H2) (complex with Ca2+ and HO¯) (modified with N­acetyl­D­glucosamine, N­acetyl­D­galactosamine and ­D­mannose); Phanerochaete chrysosporium	MMS94160
1mn1	1mn1	1mn1	1mn1	Manganese peroxidase (D179N mutant) (complex with Ca2+) (modified with N­acetyl­D­glucosamine); Phanerochaete chrysosporium	-
1mn2	1mn2	1mn2	1mn2	Manganese peroxidase (E35Q, D179N mutant) (complex with Ca2+) (modified with N­acetyl­D­glucosamine); Phanerochaete chrysosporium	-
1mnp	1mnp	1mnp	1mnp	Manganese peroxidase (isozyme 1) (complex with Mn2+ and Ca2+) (modified with N­acetyl­D­glucosamine); Phanerochaete chrysosporium	MS5CD1
1qpa	1qpa	1qpa	1qpa	Lignin peroxidase (isozyme LIP4.65) (complex with Ca2+) (modified with N­acetyl­D­glucosamine, ­D­mannose and fucose; contains modified residue ß­hydroxytryptophan­171); Phanerochaete chrysosporium	-
1ryc	1ryc	1ryc	1ryc	Cytochrome c peroxidase (W191G mutant) (complex with benzimidazole); Saccharomyces cerevisiae	-
1sch	1sch	1sch	1sch	Peroxidase (complex with Ca2+) (modified with N­acetyl­D­glucosamine; contains pyroglutamic acid at N­terminus); peanut (Arachis hypogaea)	-
2ccp	2ccp	2ccp	2ccp	Cytochrome c peroxidase [insertion (M1, I2), D235N mutant]; Saccharomyces cerevisiae	MMS91033
2cep	2cep	2cep	2cep	Cytochrome c peroxidase [insertion (M1, I2), M230I mutant]; Saccharomyces cerevisiae	-
2cyp	2cyp	2cyp	2cyp	Cytochrome c peroxidase; Saccharomyces cerevisiae	-
2pcb	2pcb	2pcb	2pcb	Yeast cytochrome c peroxidase (CCP) complex with horse heart cytochrome c	MMS93043
2pcc	2pcc	2pcc	2pcc	Yeast cytochrome c peroxidase (CCP) complex with yeast iso­1­cytochrome c; Saccharomyces cerevisiae	MMS93044
3ccp	3ccp	3ccp	3ccp	Cytochrome c peroxidase [insertion (M1, I2), W191F mutant]; Saccharomyces cerevisiae	MMS91033
3ccx	3ccx	3ccx	3ccx	Cytochrome c peroxidase [insertion (M1, K2, T3), T52I, A147Y, D152G mutant]; Saccharomyces cerevisiae	-
4ccp	4ccp	4ccp	4ccp	Cytochrome c peroxidase [insertion (M1, I2), W51F mutant]; Saccharomyces cerevisiae	MMS91033
4ccx	4ccx	4ccx	4ccx	Cytochrome c peroxidase [insertion (M1, K2, T3), T53I, A147M, D152G mutant]; Saccharomyces cerevisiae	-
5ccp	5ccp	5ccp	5ccp	Cytochrome c peroxidase [insertion (M1, I2), H52L mutant]; Saccharomyces cerevisiae	-
6ccp	6ccp	6ccp	6ccp	Cytochrome c peroxidase [insertion (M1, I2), R48K mutant]; Saccharomyces cerevisiae	-
7ccp	7ccp	7ccp	7ccp	Cytochrome c peroxidase [insertion (M1, I2), R48L mutant]; Saccharomyces cerevisiae	-
-	-	-	-	Peroxidase (complex with Ca2+) (contains pyroglutamic acid at N­terminus); Coprinus cinereus	MS5LB11

¹ Macromolecular Structures abstract. Full text is available to BioMedNet Members

References

1. Li, H. and Poulos, T.L. (1994) Structural variation in heme enzymes: a comparative analysis of peroxidase and P450 crystal structures. Structure 2, 461-464.
2. Welinder, K.G. (1992) Superfamily of plant, fungal and bacterial peroxidases. Curr. Opin. Struct. Biol. 2, 388-393.
3. Dalton, D.A. (1991) Ascorbate peroxidase. In Everse, J., Everse, K.E. and Grisham, M.B., Eds. Peroxidases in Chemistry and Biology. CRC Press, Boca Raton, vol. II, pp. 139-153.
4. Welinder, K.G. (1991) Bacterial catalase­peroxidases are gene duplicated members of the plant peroxidase superfamily. Biochim. Biophys. Acta 1080, 215-220.
5. Reddy, C.A. and D'Souza, T.M. (1994) Physiology and molecular biology of the lignin peroxidases of Phanerochaete chrysosporium. FEMS Microbiol. Rev. 13, 137-152.
6. Campa, A. (1991) Biological roles of plant peroxidases: known and potential function. In Everse, J., Everse, K.E. and Grisham, M.B., Eds. Peroxidases in Chemistry and Biology. CRC Press, Boca Raton, vol. II, pp. 25-50.
7. Finzel, B.C., Poulos, T.L. and Kraut, J. (1984) Crystal structure of yeast cytochrome c peroxidase refined at 1.7­Å resolution. J. Biol. Chem. 259, 13027-13036.
8. Poulos, T.L., Edwards, S.L., Wariishi, H. and Gold, M.H. (1993) Crystallographic refinement of lignin peroxidase at 2 Å. J. Biol. Chem. 268, 4429-4440.
9. Sundaramoorthy, M., Kishi, K., Gold, M.H. and Poulos, T.L. (1994) The crystal structure of manganese peroxidase from Phanerochaete chrysosporium at 2.06­Å resolution. J. Biol. Chem. 269, 32759-32767.
10. Kunishima, N., Fukuyama, K., Matsubara, H., Hatanaka, H., Shibano, Y. and Amachi, T. (1994) Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9 Å resolution. Structural comparisons with the lignin and cytochrome c peroxidases. J. Mol. Biol. 235, 331-344.
11. Patterson, W.R. and Poulos, T.L. (1995) Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry 34, 4331-4341.
12. Schuller, D.J., Ban, N., van Huystee, R.B., McPherson, A. and Poulos, T.L. (1996) The crystal structure of peanut peroxidase. Structure 4, 311-321.
13. Gajhede, M., Schuller, D.J., Henriksen, A., Smith, A.T. and Poulos, T.L. (1997) Crystal structure of horseradish peroxidase C at 2.15 Å resolution. Nature Struct. Biol. 4, 1032-1038.
14. Bosshard, H.R., Anni, H. and Yonetani, T. (1991) Yeast cytochrome c peroxidase. In Everse, J., Everse, K.E. and Grisham, M.B., Eds. Peroxidases in Chemistry and Biology. CRC Press, Boca Raton, vol. II, pp. 51-84.

Bibliography on structural studies of fungal, plant and bacterial haem peroxidases

Reviews on fungal, plant and bacterial haem peroxidases

International Working Group on Plant Peroxidases (IWGPP)