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153  structures 8520  species 0  interactions 12124  sequences 50  architectures

Family: S-AdoMet_synt_C (PF02773)

Summary: S-adenosylmethionine synthetase, C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "S-adenosylmethionine synthetase enzyme". More...

S-adenosylmethionine synthetase enzyme Edit Wikipedia article

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.

S-adenosylmethionine synthetase, C-terminal domain Provide feedback

The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.

Literature references

  1. Takusagawa F, Kamitori S, Markham GD; , Biochemistry 1996;35:2586-2596.: Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution. PUBMED:8611562 EPMC:8611562


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022630

S-adenosylmethionine synthetase (MAT, EC ) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP [ PUBMED:1696256 ]. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.

In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.

The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance [ PUBMED:1213535 ].

The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. This entry represents the C-terminal domain of S=adenosylmethionine synthetase and is found in association with and .

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(302)
Full
(12124)
Representative proteomes UniProt
(49038)
RP15
(1904)
RP35
(5991)
RP55
(11864)
RP75
(19080)
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PP/heatmap 1            

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

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

Format an alignment

  Seed
(302)
Full
(12124)
Representative proteomes UniProt
(49038)
RP15
(1904)
RP35
(5991)
RP55
(11864)
RP75
(19080)
Alignment:
Format:
Order:
Sequence:
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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
(302)
Full
(12124)
Representative proteomes UniProt
(49038)
RP15
(1904)
RP35
(5991)
RP55
(11864)
RP75
(19080)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Prosite
Previous IDs: S-AdoMet_syntD3;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 302
Number in full: 12124
Average length of the domain: 138.2 aa
Average identity of full alignment: 64 %
Average coverage of the sequence by the domain: 35.24 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.1 25.1
Noise cut-off 24.5 24.4
Model length: 138
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 S-AdoMet_synt_C domain has been found. There are 153 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044U0Q7 View 3D Structure Click here
A0A077YZ90 View 3D Structure Click here
A0A077ZAZ7 View 3D Structure Click here
A0A077ZGQ1 View 3D Structure Click here
A0A077ZM24 View 3D Structure Click here
A0A0D2ERJ8 View 3D Structure Click here
A0A0D2FHF6 View 3D Structure Click here
A0A0H3GXI4 View 3D Structure Click here
A0A0K0DSI9 View 3D Structure Click here
A0A0K0DZ08 View 3D Structure Click here
A0A0K0EMB3 View 3D Structure Click here
A0A0K0EMW7 View 3D Structure Click here
A0A0N4U4U3 View 3D Structure Click here
A0A0R0KXB0 View 3D Structure Click here
A0A175VQG1 View 3D Structure Click here
A0A1C1C986 View 3D Structure Click here
A0A1D6FHW2 View 3D Structure Click here
A0A1D6FUX8 View 3D Structure Click here
A0A1D8PF68 View 3D Structure Click here
A0A1P6BLP5 View 3D Structure Click here
A0A3P7DF53 View 3D Structure Click here
A0A3Q0KBJ2 View 3D Structure Click here
A0LCX5 View 3D Structure Click here
A0LF65 View 3D Structure Click here
A0Q2Y4 View 3D Structure Click here
A0QWT3 View 3D Structure Click here
A1A0T9 View 3D Structure Click here
A1B374 View 3D Structure Click here
A1BEZ3 View 3D Structure Click here
A1K301 View 3D Structure Click here
A1S9A6 View 3D Structure Click here
A1SJF9 View 3D Structure Click here
A1SZJ9 View 3D Structure Click here
A1T8H7 View 3D Structure Click here
A1TKT9 View 3D Structure Click here
A1UFL0 View 3D Structure Click here
A1VK01 View 3D Structure Click here
A1W3X4 View 3D Structure Click here
A1WSC8 View 3D Structure Click here
A2SKW6 View 3D Structure Click here