Summary: SAM domain (Sterile alpha motif)
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SAM domain (Sterile alpha motif) Provide feedback
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Stapleton D, Balan I, Pawson T, Sicheri F; , Nat Struct Biol 1999;6:44-49.: The crystal structure of an Eph receptor SAM domain reveals a mechanism for modular dimerization. PUBMED:9886291 EPMC:9886291
Internal database links
|Similarity to PfamA using HHSearch:||SAM_1 IGR|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011510
The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [PUBMED:9007998] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms [PUBMED:9886291]. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [PUBMED:9343432], nevertheless with a low affinity constant [PUBMED:9933164]. SAM domains also appear to possess the ability to bind RNA [PUBMED:14659692]. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding.
Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces [PUBMED:9343432]. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures [PUBMED:9933164].
This entry represents a second domain related to the SAM domain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||protein binding (GO:0005515)|
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SAM domains are found in a diverse set of proteins, which include scaffolding proteins, transcription regulators, translational regulators tyrosine kinases and serine/threonine kinases [1-3]. SAM domains are found in all eukaryotes and some bacteria  . Structures of SAM domains reveal a common five helical structure. The SAM domain is involved in a variety of functions. The most widespread function is in domain-domain interactions. The SAM domain performs domain-domain interactions using multifarious arrangements of the SAM domain. More recently, the SAM domain within the Smaug protein has been demonstrated to bind to the Nanos 3' UTR translation control element (Rfam:RF00161) . This clan currently only represents the diverse SAM domain family and does not contain the more divergent SAM/Pointed family (Pfam:PF02198).
The clan contains the following 5 members:KSR1-SAM SAM_1 SAM_2 SAM_PNT Ste50p-SAM
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||49|
|Number in full:||3625|
|Average length of the domain:||64.90 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||8.61 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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There are 2 interactions 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 SAM_2 domain has been found. There are 47 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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