Heme peroxidase signatures and profiles

Heme-binding peroxidases (EC 1.11.1.-) [1] carry out a variety of biosynthetic and degradative functions using hydrogen peroxide as the electron acceptor. The heme prosthetic group is protoporphyrin IX and the fifth ligand of the heme iron is a histidine (known as the proximal histidine). An other histidine residue (the distal histidine) serves as an acid-base catalyst in the reaction between hydrogen peroxide and the enzyme. The regions around these two active site residues are more or less conserved in a majority of peroxidases [2,3].

Heme peroxidases are widely distributed throughout bacteria, fungi, plants, and vertebrates. On the basis of structural properties they can be devided in two large superfamilies.

The plant peroxidase superfamily (can be grouped in three classes):

 Class I. Peroxidase of prokaryotic origin:
 - Plant  ascorbate  peroxidases.  They  play  a key role in hydrogen peroxide
   removal in the chloroplasts and cytosol of higher plants.
 - Yeast cytochrome c peroxidase (EC 1.11.1.5).
 - Prokaryotic catalase-peroxidases.  Some  bacterial  species produce enzymes
   that exhibit both catalase  and  broad-spectrum  peroxidase activities [4].
   Examples  of  such  enzymes are:  catalase HP I from Escherichia coli (gene
   katG) and perA from Bacillus stearothermophilus.

 Class II. Secreted fungal peroxidases:
 - Fungal ligninases. Ligninase catalyzes the first step in the degradation of
   lignin. It depolymerizes lignin by catalyzing the C(alpha)-C(beta) cleavage
   of the propyl side chains of lignin.

 Class III. Classical secretory plant peroxidases:
 - Plant peroxidases (EC 1.11.1.7).  Plants express a large number of isozymes
   of  peroxidases.   Some  of  them  play  a   role  in  cell-suberization by
   catalyzing the deposition of the  aromatic residues  of suberin on the cell
   wall, some are expressed as a defense response toward  wounding, others are
   involved in the metabolism of auxin and the biosynthesis of lignin.

The animal peroxidase superfamily:

• Myeloperoxidase (EC 1.11.1.7) (MPO). MPO is found in granulocytes and monocytes and plays a major role in the oxygen-dependent microbicidal system of neutrophils.
• Lactoperoxidase (EC 1.11.1.7) (LPO). LPO is a milk protein which acts as an antimicrobial agent.
• Eosinophil peroxidase (EC 1.11.1.7) (EPO). An enzyme found in the cytoplasmic granules of eosinophils.
• Thyroid peroxidase (EC 1.11.1.8) (TPO). TPO plays a central role in the biosynthesis of thyroid hormones. It catalyzes the iodination and coupling of the hormonogenic tyrosines in thyroglobulin to yield the thyroid hormones T3 and T4.

The two patterns we developed recognize both superfamilies. Our first pattern recognizes the proximal heme-binding site whereas the second pattern surrounded the distal active site. We also developed two profiles, one specific for the animal peroxidases superfamily and one directed against the plant peroxidase superfamily.