| Literature References | 1. LI, H. AND POULOS, T.L.
Structural variation in heme enzymes: a comparative analysis of
peroxidase and P450 crystal structures.
STRUCTURE 2 461-464 (1994).
2. WELINDER, K.G.
Superfamily of plant, fungal and bacterial peroxidases.
CURR.OPIN.STRUCT.BIOL. 2 388-393 (1992).
3. DALTON, D.A.
Ascorbate peroxidase.
IN PEROXIDASES IN CHEMISTRY AND BIOLOGY, EVERSE, J., EVERSE, K.E. AND
GRISHAM, M.B., EDS. VOL.II PP.139-153 (1991). CRC PRESS, BOCA RATON.
4. WELINDER, K.G.
Bacterial catalase-peroxidases are gene duplicated members of the plant
peroxidase superfamily.
BIOCHIM.BIOPHYS.ACTA 1080 215-20 (1991).
5. REDDY, C.A. AND D'SOUZA, T.M.
Physiology and molecular biology of the lignin peroxidases of Phanerochaete
chrysosporium.
FEMS MICROBIOL.REV. 13 137-152 (1994).
6. CAMPA, A.
Biological roles of plant peroxidases: known and potential function.
IN PEROXIDASES IN CHEMISTRY AND BIOLOGY, EVERSE, J., EVERSE, K.E. AND
GRISHAM, M.B., EDS. VOL.II PP.25-50 (1991). CRC PRESS, BOCA RATON.
7. FINZEL, B.C., POULOS, T.L. AND KRAUT, J.
Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A
resolution.
J.BIOL.CHEM. 259 13027-13036 (1984).
8. POULOS, T.L., EDWARDS, S.L., WARIISHI, H. AND GOLD, M.H.
Crystallographic refinement of lignin peroxidase at 2 A.
J.BIOL.CHEM. 268 4429-4440 (1993).
9. SUNDARAMOORTHY, M., KISHI, K., GOLD, M.H. AND POULOS, T.L.
The crystal structure of manganese peroxidase from Phanerochaete
chrysosporium at 2.06-A resolution.
J.BIOL.CHEM. 269 32759-32767 (1994).
10. KUNISHIMA, N., FUKUYAMA, K., MATSUBARA, H., HATANAKA, H., SHIBANO, Y.
AND AMACHI, T.
Crystal structure of the fungal peroxidase from Arthromyces ramosus at 1.9A
resolution. Structural comparisons with the lignin and cytochrome c
peroxidases.
J.MOL.BIOL. 235 331-344 (1994).
11. PATTERSON, W.R. AND POULOS, T.L.
Crystal structure of recombinant pea cytosolic ascorbate peroxidase.
BIOCHEMISTRY 34 4331-4341 (1995).
12. SCHULLER, D.J., BAN, N., VAN HUYSTEE, R.B., MCPHERSON, A.
AND POULOS, T.L.
The crystal structure of peanut peroxidase.
STRUCTURE 4 311-321 (1996).
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| Documentation | Peroxidases are haem-containing enzymes that use hydrogen peroxide as
the electron acceptor to catalyse a number of oxidative reactions.
Most haem peroxidases follow the reaction scheme:
Fe(3+) + H2O2 --> [Fe(4+)=O]R' (Compound I) + H2O
[Fe(4+)=O]R' + substrate --> [Fe(4+)=O]R (Compound II) + oxidised substrate
[Fe(4+)=O]R + substrate --> Fe(3+) + H2O + oxidised substrate
In this mechanism, the enzyme reacts with one equivalent of H2O2 to give
[Fe(4+)=O]R' (compound I). This is a two-electron oxidation/reduction
reaction where H2O2 is reduced to water and the enzyme is oxidised. One
oxidising equivalent resides on iron, giving the oxyferryl [Fe(4+)=O]
intermediate, while in many peroxidases the porphyrin (R) is oxidised to
the porphyrin pi-cation radical (R'). Compound I then oxidises an organic
substrate to give a substrate radical [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 3 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 catalase-
peroxidases, exhibiting both peroxidase and catalase activities. It is
thought that catalase-peroxidase provides protection to cells under
oxidative stress [4].
Class II consists of secretory fungal peroxidases: ligninases, or lignin
peroxidases (LiPs), and manganese-dependent peroxidases (MnPs). These are
monomeric glycoproteins involved in the degradation of lignin. In MnP,
Mn(2+) serves as the reducing substrate [5]. Class II proteins contain 4
conserved disulphide bridges and 2 conserved calcium-binding sites.
Class III consists of the secretory plant peroxidases, which have multiple
tissue-specific functions: e.g., removal of hydrogen peroxide from
chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the
cell wall; defence responses towards wounding; indole-3-acetic acid (IAA)
catabolism; ethylene biosynthesis; and so on [6]. Class III proteins are
also monomeric glycoproteins, containing 4 conserved disulphide bridges
and 2 calcium ions, although the placement of the disulphides differs
from class II enzymes.
To date, 3D structures have been determined for yeast CCP [7], LiP [8] and
MnP [9] from Phanerochaete chrysosporium, a fungal peroxidase from
Arthromyces ramosus [10], pea cytosolic ascorbate peroxidase [11] and peanut
peroxidase [12]. All these proteins share the same architecture, consisting
of 2 all-alpha domains, between which the haem group is embedded.
PEROXIDASE is a 5-element fingerprint that provides a signature for fungal,
plant and bacterial peroxidases. The fingerprint was derived from an initial
alignment of 23 sequences: motif 1 contains invariant active site residues
(Arg and the "distal" His) and a conserved aromatic residue that together
form a ligand pocket for hydrogen peroxide (cf. PROSITE pattern PEROXIDASE_2
(PS00436)); motifs 2 and 3 are adjacent, motif 2 encoding helix D of CCP,
MnP and AP [7,9,11]; and motif 4 contains the invariant "proximal" His,
which serves the axial ligand of the haem iron, and spans the region encoded
by PROSITE pattern PEROXIDASE_1 (PS00435). Two iterations on OWL27.1 were
required to reach convergence, at which point a true set comprising 136
sequences was identified. Several partial matches were also found:
CATA_MYCTU fails to match motif 3; CATA_RHOCA and three fragments (PHU31095,
C32322, PS0012) lack motif 5; TOBPOXAN, POPHPOX14 and GMU41657 are fragments
lacking motif 1; MTU16727 is a fragment matching motifs 1, 2 and 4;
CATA_BACST matches motifs 1, 4 and 5; PS0010 and PS0011 are fragments
matching motifs 1-3; ATTS2079 is a fragment matching motifs 1 and 2;
PERX_WHEAT is a fragment matching motifs 2 and 3; and S29727 is a fragment
matching motifs 1 and 5.
An update on SPTR37_9f identified a true set of 228 sequences, and 18
partial matches.
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