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161  structures 8981  species 0  interactions 134611  sequences 728  architectures

Family: Radical_SAM (PF04055)

Summary: Radical SAM superfamily

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 "Radical SAM". More...

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.

Radical SAM superfamily Provide feedback

Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.

Literature references

  1. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE; , Nucleic Acids Res 2001;29:1097-1106.: Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. PUBMED:11222759 EPMC:11222759

  2. Benjdia A, Leprince J, Guillot A, Vaudry H, Rabot S, Berteau O; , J Am Chem Soc. 2007;129:3462-3463.: Anaerobic sulfatase-maturating enzymes: radical SAM enzymes able to catalyze in vitro sulfatase post-translational modification. PUBMED:17335281 EPMC:17335281

  3. Berteau O, Guillot A, Benjdia A, Rabot S; , J Biol Chem. 2006;281:22464-22470.: A new type of bacterial sulfatase reveals a novel maturation pathway in prokaryotes. PUBMED:16766528 EPMC:16766528


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007197

Radical SAM proteins are found in all three domains of life and share an unusual Fe-S cluster associated with generation of a free radical by reductive cleavage of SAM and often provide an anaerobic or oxygen-independent mechanism that is found as an aerobic reaction in other proteins. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. These proteins function in DNA precursor, vitamin, cofactor, antibiotic and herbicide biosynthesis and in biodegradation pathways [ PUBMED:11222759 , PUBMED:15317939 ].

Radical SAM proteins share several common features, notably three strictly conserved cysteine residues generally included in the CxxxCxxC motif. These critical cysteines coordinate the unusual [4Fe-4S]2+/1+ cluster, while SAM serves as ligand for the fourth iron atom and acts as a cofactor or a cosubstrate [ PUBMED:11222759 ]. The radical SAM enzymes biochemically characterised to date have in common the cleavage of the [4Fe-4S]1+-SAM complex to [4Fe-4S]2+-Met and the 5'-deoxyadenosyl radical, which abstracts a hydrogen atom from the substrate to initiate a radical mechanism [ PUBMED:22761404 , PUBMED:18307109 ].

The Radical SAM domain is organised in a fold related to the beta-barrel or TIM barrel, in which beta-strands are arranged in a barrel-like array, with peripheral helices intervening between beta-strands. The [4Fe–4S] clusters and substrates are bound within the barrels, as is typical of TIM barrel enzymes [ PUBMED:28893989 , PUBMED:22579873 ].

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
(491)
Full
(134611)
Representative proteomes UniProt
(665595)
RP15
(21791)
RP35
(70349)
RP55
(137294)
RP75
(227877)
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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
(491)
Full
(134611)
Representative proteomes UniProt
(665595)
RP15
(21791)
RP35
(70349)
RP55
(137294)
RP75
(227877)
Alignment:
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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
(491)
Full
(134611)
Representative proteomes UniProt
(665595)
RP15
(21791)
RP35
(70349)
RP55
(137294)
RP75
(227877)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 491
Number in full: 134611
Average length of the domain: 169.50 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 41.73 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.5 29.5
Trusted cut-off 29.5 29.5
Noise cut-off 29.4 29.4
Model length: 167
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Radical_SAM domain has been found. There are 161 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
A0A0P0XTB0 View 3D Structure Click here
A0A0R0FIC1 View 3D Structure Click here
A0A0R0G6E6 View 3D Structure Click here
A0A0R0GA97 View 3D Structure Click here
A0A0R0GAG6 View 3D Structure Click here
A0A0R0HEM4 View 3D Structure Click here
A0A0R0I032 View 3D Structure Click here
A0A0R0IRV7 View 3D Structure Click here
A0A0R4J536 View 3D Structure Click here
A0A0R4J646 View 3D Structure Click here
A0A1D6F795 View 3D Structure Click here
A0A1D6G0E0 View 3D Structure Click here
A0A1D6G3V2 View 3D Structure Click here
A0A1D6GAM0 View 3D Structure Click here
A0A1D6HAY1 View 3D Structure Click here
A0A1D6JM25 View 3D Structure Click here
A0A1D6JS18 View 3D Structure Click here
A0A1D6KKP7 View 3D Structure Click here
A0A1D6L6E5 View 3D Structure Click here
A0A1D6MYU6 View 3D Structure Click here
A0A1D8PKD5 View 3D Structure Click here
A0A1D8PPU8 View 3D Structure Click here
A0A1D8PS33 View 3D Structure Click here
A0A2R8PX77 View 3D Structure Click here
A4HSJ7 View 3D Structure Click here
A4HWP3 View 3D Structure Click here
A4HWS3 View 3D Structure Click here
A4HY57 View 3D Structure Click here
A4I0J4 View 3D Structure Click here
A4IGH2 View 3D Structure Click here
B4FFP5 View 3D Structure Click here
B4FJY4 View 3D Structure Click here
B5DF48 View 3D Structure Click here
B6TM42 View 3D Structure Click here
B6TN12 View 3D Structure Click here
B8A031 View 3D Structure Click here
C0PGU3 View 3D Structure Click here
C0PN26 View 3D Structure Click here
C6KT59 View 3D Structure Click here
D3ZVG1 View 3D Structure Click here