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31  structures 318  species 4  interactions 7244  sequences 4  architectures

Family: MCR_alpha (PF02249)

Summary: Methyl-coenzyme M reductase alpha subunit, C-terminal domain

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Methyl-coenzyme M reductase alpha subunit, C-terminal domain Provide feedback

Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (PF02241), and 2 gamma (PF02240) subunits with two identical nickel porphinoid active sites [1]. The C-terminal domain is comprised of an all-alpha multi-helical bundle.

Literature references

  1. Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK; , Science 1997;278:1457-1462.: Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation PUBMED:9367957 EPMC:9367957


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009047

Methyl-coenzyme M reductase (MCR) catalyses the reduction of methyl-coenzyme M (CH3-SCoM) and coenzyme B (HS-CoB) to methane and the corresponding heterosulphide CoM-S-S-CoB (EC), the final step in methane biosynthesis. This reaction proceeds under anaerobic conditions by methanogenic Archaea [PUBMED:16260307], and requires a nickel-porphinoid prosthetic group, coenzyme F430, which is in the EPR-detectable Ni(I) oxidation state in the active enzyme. Studies on a catalytically inactive enzyme aerobically co-crystallized with coenzyme M displayed a fully occupied coenzyme M-binding site with no alternate conformations. The binding of coenzyme M appears to induce specific conformational changes that suggests a molecular mechanism by which the enzyme ensures that methyl-coenzyme M enters the substrate channel prior to coenzyme B, as required by the active-site geometry [PUBMED:11491299].

MCR is a hexamer composed of 2 alpha, 2 beta, and 2 gamma subunits with two identical nickel porphinoid active sites, which form two long active site channels with F430 embedded at the bottom [PUBMED:9367957, PUBMED:16234924].

This entry represents the C-terminal domain of the alpha subunit, which is comprised of an all-alpha multi-helical bundle.

Gene Ontology

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

Domain organisation

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

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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
(22)
Full
(7244)
Representative proteomes NCBI
(7541)
Meta
(13)
RP15
(10)
RP35
(32)
RP55
(41)
RP75
(49)
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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
(22)
Full
(7244)
Representative proteomes NCBI
(7541)
Meta
(13)
RP15
(10)
RP35
(32)
RP55
(41)
RP75
(49)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(22)
Full
(7244)
Representative proteomes NCBI
(7541)
Meta
(13)
RP15
(10)
RP35
(32)
RP55
(41)
RP75
(49)
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: Pfam-B_2706 (release 5.2)
Previous IDs: none
Type: Domain
Author: Mian N, Bateman A, Griffiths-Jones SR
Number in seed: 22
Number in full: 7244
Average length of the domain: 118.60 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 67.10 %

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 25.0 25.0
Trusted cut-off 32.7 26.7
Noise cut-off 21.8 21.4
Model length: 127
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

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

MCR_alpha_N MCR_gamma MCR_beta MCR_beta_N

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 MCR_alpha domain has been found. There are 31 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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