Summary: Iron-sulfur cluster-binding domain
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Iron-sulfur cluster-binding domain Provide feedback
This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, PF04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.
Haft DH, Basu MK;, J Bacteriol. 2011;193:2745-2755.: Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. PUBMED:21478363 EPMC:21478363
Internal database links
|Similarity to PfamA using HHSearch:||DUF3463|
This tab holds annotation information from the InterPro database.
InterPro entry IPR023885
This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by INTERPRO. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulphatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins [PUBMED:21478363, PUBMED:21223593]. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. This domain has been named SPASM for Subtilosin, PQQ, Anaerobic Sulphatase, and Mycofactocin.
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We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||195|
|Number in full:||2872|
|Average length of the domain:||67.10 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||17.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||4|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 SPASM domain has been found. There are 10 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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