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38  structures 1901  species 1  interaction 2768  sequences 7  architectures

Family: Dyp_perox (PF04261)

Summary: Dyp-type peroxidase family

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This is the Wikipedia entry entitled "DyP-type peroxidase family". More...

DyP-type peroxidase family Edit Wikipedia article

Dyp-type peroxidase family
PDB 2gvk EBI.jpg
crystal structure of a dye-decolorizing peroxidase (dyp) from bacteroides thetaiotaomicron vpi-5482 at 1.6 a resolution
Identifiers
Symbol Dyp_perox
Pfam PF04261
Pfam clan CL0032
InterPro IPR006314

In molecular biology, the DyP-type peroxidase family is a family of haem peroxidase enzymes. Haem peroxidases were originally divided into two superfamilies, namely, the animal peroxidases and the plant peroxidases (which are subdivided into class I, II and III), which include fungal (class II) and bacterial peroxidases. The DyP (for dye de-colourising peroxidase) family constitutes a novel class of haem 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.[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 haem iron is penta-coordinated, with the protein contributing a conserved histidine ligand to the iron centre. 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]

References[edit]

  1. ^ Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA (November 2007). "Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif". Proteins 69 (2): 223–33. doi:10.1002/prot.21550. PMID 17654545. 
  2. ^ Zubieta C, Joseph R, Krishna SS, McMullan D, Kapoor M, Axelrod HL, Miller MD, Abdubek P, Acosta C, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA (November 2007). "Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA". Proteins 69 (2): 234–43. doi:10.1002/prot.21673. PMID 17654547. 
  3. ^ Sugano Y, Muramatsu R, Ichiyanagi A, Sato T, Shoda M (December 2007). "DyP, a unique dye-decolorizing peroxidase, represents a novel heme peroxidase family: ASP171 replaces the distal histidine of classical peroxidases". J. Biol. Chem. 282 (50): 36652–8. doi:10.1074/jbc.M706996200. PMID 17928290. 

This article incorporates text from the public domain Pfam and InterPro IPR006314

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Dyp-type peroxidase family Provide feedback

This family of dye-decolourising peroxidases lack a typical heme-binding region.

Literature references

  1. Sugano Y, Nakano R, Sasaki K, Shoda M; , Appl Environ Microbiol 2000;66:1754-1758.: Efficient heterologous expression in Aspergillus oryzae of a unique dye-decolorizing peroxidase, DyP, of Geotrichum candidum Dec 1. PUBMED:10742277 EPMC:10742277


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006314

Haem 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 de-colourising peroxidase) family constitutes a novel class of haem 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 [PUBMED:17654545]. 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 [PUBMED:17654547]. 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 haem iron is penta-coordinated, with the protein contributing a conserved histidine ligand to the iron centre. 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 [PUBMED:17928290].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Dim_A_B_barrel (CL0032), which has the following description:

This superfamily of proteins possess a Ferredoxin-like fold. Pairs of these assemble into a beta barrel. The function of this barrel is quite varied and includes Muconolactone isomerase as well as monooxygenases.

The clan contains the following 18 members:

ABM AsnC_trans_reg Chlor_dismutase Dabb Dehydratase_hem DUF1330 DUF3291 DUF4188 DUF718 DUF881 Dyp_perox EthD MIase MmlI NapD NIPSNAP SOR YCII

Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(15)
Full
(2768)
Representative proteomes NCBI
(1917)
Meta
(88)
RP15
(143)
RP35
(307)
RP55
(438)
RP75
(529)
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  Seed
(15)
Full
(2768)
Representative proteomes NCBI
(1917)
Meta
(88)
RP15
(143)
RP35
(307)
RP55
(438)
RP75
(529)
Alignment:
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  Seed
(15)
Full
(2768)
Representative proteomes NCBI
(1917)
Meta
(88)
RP15
(143)
RP35
(307)
RP55
(438)
RP75
(529)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: TIGRFAMs (release 2.0);
Previous IDs: Dyp_perox_fam;
Type: Family
Author: TIGRFAMs, Finn RD
Number in seed: 15
Number in full: 2768
Average length of the domain: 307.60 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 85.21 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.2 20.3
Model length: 313
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Dyp_perox

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Dyp_perox domain has been found. There are 38 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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