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24  structures 890  species 1  interaction 1280  sequences 5  architectures

Family: Mn_catalase (PF05067)

Summary: Manganese containing catalase

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Manganese containing catalase Provide feedback

Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese [2].

Literature references

  1. Igarashi T, Kono Y, Tanaka K; , J Biol Chem 1996;271:29521-29524.: Molecular cloning of manganese catalase from Lactobacillus plantarum. PUBMED:8939876 EPMC:8939876

  2. Barynin VV, Whittaker MM, Antonyuk SV, Lamzin VS, Harrison PM, Artymiuk PJ, Whittaker JW; , Structure (Camb) 2001;9:725-738.: Crystal structure of manganese catalase from Lactobacillus plantarum. PUBMED:11587647 EPMC:11587647


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007760

Catalases (EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. There are three structurally independent classes of catalases: ubiquitous mono-functional haem-containing catalases (INTERPRO), bifunctional haem-containing catalase-peroxidases that are closely related to plant peroxidases (INTERPRO), and non-haem manganese-containing catalases [PUBMED:14745498].

This entry represents the non-haem Mn-catalases, which are found in several bacterial species [PUBMED:14871145]. The structure of the Mn catalase from Lactobacillus plantarum reveals a homo-hexamer, where each subunit contains a dimanganese active site that is accessed by a single substrate channel [PUBMED:11587647]. The dimanganese active site performs a two-electron catalytic cycle that alternately oxidises and reduces the dimanganese atoms in a manner that is similar to its haem-counterpart found in other catalases.

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 Ferritin (CL0044), which has the following description:

The members of this clan all share a distinctive four helical bundle. The four helices are arranged antiparallel with a left-handed twist. This helical bundle is distinguished from others by the long connection between the second and third helices. Some of the members contain a Fe or Mn dimer at the centre of the helical bundle. The ferritin fold was first described by Murzin AG and Chothia C, Cur Opin Struc Biol 1992, 2:895-903.

The clan contains the following 19 members:

Coat_F COQ7 DUF2202 DUF2383 DUF305 DUF4142 DUF4439 DUF892 FA_desaturase_2 Ferritin Ferritin-like Ferritin_2 MiaE MiaE_2 Mn_catalase PaaA_PaaC Phenol_Hydrox Ribonuc_red_sm Rubrerythrin

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(6)
Full
(1280)
Representative proteomes NCBI
(1030)
Meta
(18)
RP15
(112)
RP35
(214)
RP55
(248)
RP75
(300)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(6)
Full
(1280)
Representative proteomes NCBI
(1030)
Meta
(18)
RP15
(112)
RP35
(214)
RP55
(248)
RP75
(300)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(6)
Full
(1280)
Representative proteomes NCBI
(1030)
Meta
(18)
RP15
(112)
RP35
(214)
RP55
(248)
RP75
(300)
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.

Pfam alignments:

HMM logo

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 View help on the curation process

Seed source: COG3546
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 6
Number in full: 1280
Average length of the domain: 231.50 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 96.59 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.2 20.7
Model length: 284
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...

Mn_catalase

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 Mn_catalase domain has been found. There are 24 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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