PROSITE documentation PDOC00394

Heme peroxidase signatures and profiles

Description

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.

Last update:

April 2006 / Pattern revised.

Technical section

PROSITE methods (with tools and information) covered by this documentation:

PEROXIDASE_3, PS50292; Animal heme peroxidase superfamily profile  (MATRIX)
Sequences known to belong to this class detected by the first profile: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Domain architecture view of Swiss-Prot proteins matching PS50292
PS50292
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50292
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50292
• Scan Swiss-Prot/TrEMBL entries against PS50292
• view ligand binding statistics
Matching PDB structures: 1CQE 1CVU 1CX2 1CXP ... [ALL]
PEROXIDASE_4, PS50873; Plant heme peroxidase family profile  (MATRIX)
Sequences known to belong to this class detected by the second profile: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Domain architecture view of Swiss-Prot proteins matching PS50873
PS50873
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50873
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50873
• Scan Swiss-Prot/TrEMBL entries against PS50873
• view ligand binding statistics
Matching PDB structures: 1A20 1A2F 1A2G 1AA4 ... [ALL]
PEROXIDASE_1, PS00435; Peroxidases proximal heme-ligand signature  (PATTERN)
Consensus pattern: [DET]-[LIVMTA]-{NSYL}-{RPFC}-[LIVM]-[LIVMSTAG]-[SAG]-[LIVMSTAG]-H-[STA]-[LIVMFY]
H is the proximal heme-binding ligand
Sequences known to belong to this class detected by the profile: ALL. for ligninase III from Phlebia radiata, and LPO
Other sequence(s) detected in Swiss-Prot: NONE.
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00435
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00435
• Scan Swiss-Prot/TrEMBL entries against PS00435
• view ligand binding statistics
Matching PDB structures: 1A20 1A2G 1AA4 1AC4 ... [ALL]
PEROXIDASE_2, PS00436; Peroxidases active site signature  (PATTERN)
Consensus pattern: [SGATV]-{D}-x(2)-[LIVMA]-R-[LIVMA]-x-[FW]-H-{V}-[SAC]
H is an active site residue
Sequences known to belong to this class detected by the profile: ALL. for vertebrate peroxidases (MPO, TPO, LPO, and EPO)
Other sequence(s) detected in Swiss-Prot: NONE.
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00436
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00436
• Scan Swiss-Prot/TrEMBL entries against PS00436
• view ligand binding statistics
Matching PDB structures: 1A20 1A2F 1A2G 1AA4 ... [ALL]

References

1 Authors Dawson J.H.
Title Probing structure-function relations in heme-containing oxygenases and peroxidases.
Source Science 240:433-439(1988).
PubMed ID 3358128
2 Authors Kimura S., Ikeda-Saito M.
Title Human myeloperoxidase and thyroid peroxidase, two enzymes with separate and distinct physiological functions, are evolutionarily related members of the same gene family.
Source Proteins 3:113-120(1988).
PubMed ID 2840655
3 Authors Henrissat B., Saloheimo M., Lavaitte S., Knowles J.K.C.
Title Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis.
Source Proteins 8:251-257(1990).
PubMed ID 2177893
4 Authors Welinder K.G.
Title Bacterial catalase-peroxidases are gene duplicated members of the plant peroxidase superfamily.
Source Biochim. Biophys. Acta 1080:215-220(1991).
PubMed ID 1954228

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