Summary: Di-haem cytochrome c peroxidase

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Wikipedia: Di-haem cytochrome c peroxidase
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Di-haem cytochrome c peroxidase Edit Wikipedia article

Di-haem cytochrome c peroxidase

crystal structure of the di-haem cytochrome c peroxidase from pseudomonas aeruginosa

Identifiers

Symbol

CCP_MauG

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

In molecular biology, the di-haem cytochrome c peroxidase family is a group of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidizable substrate. However, since they possess two, instead of one, haem prosthetic groups, this family of bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site).^[1] The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised.^[2]

References

^ Fulop V, Ridout CJ, Greenwood C, Hajdu J (November 1995). "Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa". Structure. 3 (11): 1225–33. PMID 8591033. doi:10.1016/s0969-2126(01)00258-1.
^ Gak ER, Tsygankov YD, Chistoserdov AY (June 1997). "Organization of methylamine utilization genes (mau) in 'Methylobacillus flagellatum ' KT and analysis of mau mutants". Microbiology. 143 (6): 1827–35. PMID 9202457. doi:10.1099/00221287-143-6-1827.

This article incorporates text from the public domain Pfam and InterPro IPR004852

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

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Di-haem cytochrome c peroxidase Provide feedback

This is a family of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidisable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site) [1]. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised [2].

Literature references

Fulop V, Ridout CJ, Greenwood C, Hajdu J; , Structure 1995;3:1225-1233.: Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa. PUBMED:8591033 EPMC:8591033
Gak ER, Tsygankov YD, Chistoserdov AY; , Microbiology 1997;143:1827-1835.: Organization of methylamine utilization genes (mau) in 'Methylobacillus flagellatum' KT and analysis of mau mutants. PUBMED:9202457 EPMC:9202457

Internal database links

SCOOP:	Cytochrom_C
Similarity to PfamA using HHSearch:	DHOR

External database links

SCOP:

1eb7

This tab holds annotation information from the InterPro database.

InterPro entry IPR004852

This is a group of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidizable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site) [PUBMED:8591033]. The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognised [PUBMED:9202457].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function	oxidoreductase activity (GO:0016491)
Biological process	oxidation-reduction process (GO:0055114)

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 Cytochrome-c (CL0318), which has the following description:

This family includes proteins where a covalently-bound haem completes the core. The core is three helices in an open folded leaf formation. The members are monodomain cytochromes.

The clan contains the following 13 members:

CCP_MauG Cytochrom_C Cytochrom_C1 Cytochrom_C550 Cytochrome-c551 Cytochrome_CBB3 Dehyd-heme_bind DHC DHOR DUF1924 FixO Haem_bd PSCyt1

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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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.

	Seed (491)	Full (4407)	Representative proteomes				UniProt (20946)	NCBI (33011)	Meta (644)
	Seed (491)	Full (4407)	RP15 (596)	RP35 (1980)	RP55 (4486)	RP75 (7991)	UniProt (20946)	NCBI (33011)	Meta (644)
Jalview	View	View	View	View	View	View	View	View	View
HTML	View	View
PP/heatmap	₁	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (491)	Full (4407)	Representative proteomes				UniProt (20946)	NCBI (33011)	Meta (644)
	Seed (491)	Full (4407)	RP15 (596)	RP35 (1980)	RP55 (4486)	RP75 (7991)	UniProt (20946)	NCBI (33011)	Meta (644)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (491)	Full (4407)	Representative proteomes				UniProt (20946)	NCBI (33011)	Meta (644)
	Seed (491)	Full (4407)	RP15 (596)	RP35 (1980)	RP55 (4486)	RP75 (7991)	UniProt (20946)	NCBI (33011)	Meta (644)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	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.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

Note: You can also download the data file for the tree.

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

Seed source:

Pfam-B_3135 (release 6.5)

Previous IDs:

none

Type:

Family

Sequence Ontology:

SO:0100021

Author:

Mifsud W

Number in seed:

491

Number in full:

4407

Average length of the domain:

165.10 aa

Average identity of full alignment:

31 %

Average coverage of the sequence by the domain:

40.16 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	25.6	25.6
Trusted cut-off	25.6	25.7
Noise cut-off	25.5	25.5

Model length:

150

Family (HMM) version:

15

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Species distribution

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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Species trees

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Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

There are 4 interactions for this family. More...

CCP_MauG Me-amine-dh_L Cytochrom_C Cytochrom_C

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 CCP_MauG domain has been found. There are 88 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 sequence.

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Family: CCP_MauG (PF03150)

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Summary: Di-haem cytochrome c peroxidase

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Di-haem cytochrome c peroxidase Edit Wikipedia article

References

Di-haem cytochrome c peroxidase Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR004852

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures

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