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PROSITE documentation PDOC51404

DyP-type peroxidase family





Description

Heme peroxidases were originally divided into two superfamilies, namely, the animal peroxidases and the plant peroxidases (class I, II and III), which include fungal (class II) and bacterial peroxidases. The DyP (for dye-decolorizing peroxidase) family constitutes a novel class of heme peroxidase. Because these enzymes were derived from fungal sources, the DyP family was thought to be structurally related to the class II secretory fungal peroxidases. However, the DyP family exhibits only low sequence similarity to classical fungal peroxidases, such as LiP and MnP, and does not contain the conserved proximal and distal histidines and an essential arginine found in other plant peroxidase superfamily members.

DyP proteins have several characteristics that distinguish them from all other peroxidases, including a particularly wide substrate specificity, a lack of homology to most other peroxidases, and the ability to function well under much lower pH conditions compared with the other plant peroxidases [1]. In terms of substrate specificity, DyP degrades the typical peroxidase substrates, but also degrades hydroxyl-free anthraquinone (many dyes are derived from anthraquinone compounds).

Crystal structures of DyP family members reveal two domains, each one adopting a ferredoxin-like fold (see <PDB: 2GVK>) [2]. The proteins consist of an N-terminal domain and a C-terminal domain likely to be related by a duplication of an ancestral gene, as inferred from the conserved topology of the domains. The heme iron is penta-coordinated, with the protein contributing a conserved histidine ligand to the iron center. A conserved Asp most likely acts as a proton donor/acceptor and takes the place of the catalytic histidine used by plant peroxidases. This Asp substitution helps explain why the DyP family is active at low pH [3].

The profile we developed covers the whole conserved region of DyP-type peroxidases.

Last update:

August 2008 / First entry.

Technical section

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

DYP_PEROXIDASE, PS51404; DyP-type peroxidase family  (MATRIX)


References

1AuthorsZubieta C. Krishna S.S. Kapoor M. Kozbial P. McMullan D. Axelrod H.L. Miller M.D. Abdubek P. Ambing E. Astakhova T. Carlton D. Chiu H.J. Clayton T. Deller M.C. Duan L. Elsliger M.A. Feuerhelm J. Grzechnik S.K. Hale J. Hampton E. Han G.W. Jaroszewski L. Jin K.K. Klock H.E. Knuth M.W. Kumar A. Marciano D. Morse A.T. Nigoghossian E. Okach L. Oommachen S. Reyes R. Rife C.L. Schimmel P. van den Bedem H. Weekes D. White A. Xu Q. Hodgson K.O. Wooley J. Deacon A.M. Godzik A. Lesley S.A. Wilson I.A.
TitleCrystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.
SourceProteins 69:223-233(2007).
PubMed ID17654545
DOI10.1002/prot.21550

2AuthorsZubieta C. Joseph R. Krishna S.S. McMullan D. Kapoor M. Axelrod H.L. Miller M.D. Abdubek P. Acosta C. Astakhova T. Carlton D. Chiu H.J. Clayton T. Deller M.C. Duan L. Elias Y. Elsliger M.A. Feuerhelm J. Grzechnik S.K. Hale J. Han G.W. Jaroszewski L. Jin K.K. Klock H.E. Knuth M.W. Kozbial P. Kumar A. Marciano D. Morse A.T. Murphy K.D. Nigoghossian E. Okach L. Oommachen S. Reyes R. Rife C.L. Schimmel P. Trout C.V. van den Bedem H. Weekes D. White A. Xu Q. Hodgson K.O. Wooley J. Deacon A.M. Godzik A. Lesley S.A. Wilson I.A.
TitleIdentification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA.
SourceProteins 69:234-243(2007).
PubMed ID17654547
DOI10.1002/prot.21673

3AuthorsSugano Y. Muramatsu R. Ichiyanagi A. Sato T. Shoda M.
TitleDyP, a unique dye-decolorizing peroxidase, represents a novel heme peroxidase family: ASP171 replaces the distal histidine of classical peroxidases.
SourceJ. Biol. Chem. 282:36652-36658(2007).
PubMed ID17928290
DOI10.1074/jbc.M706996200



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