Summary: SAM domain (Sterile alpha motif)
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Sterile alpha motif Edit Wikipedia article
| SAM domain (Sterile alpha motif) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||||
| Symbol | SAM_1 | ||||||||||
| Pfam | PF00536 | ||||||||||
| InterPro | IPR001660 | ||||||||||
| SMART | SAM | ||||||||||
| SCOPe | 1b0x / SUPFAM | ||||||||||
| CDD | cd09487 | ||||||||||
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| Ste50p-SAM | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 SAM domain from fungal protein Ste50p | |||||||||
| Identifiers | |||||||||
| Symbol | Ste50p-SAM | ||||||||
| Pfam | PF09235 | ||||||||
| Pfam clan | CL0003 | ||||||||
| InterPro | IPR015316 | ||||||||
| SCOPe | 1uqv / SUPFAM | ||||||||
| |||||||||
In molecular biology, the protein domain Sterile alpha motif (or SAM) is a putative protein interaction module present in a wide variety of proteins[1] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms.[2] 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,[3] nevertheless with a low affinity constant.[4]
SAM domains also appear to possess the ability to bind RNA.[5] 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.[3] 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.[4]
Contents
Fungal SAM
In molecular biology, the protein domain Ste50p mainly in fungi and some other types of eukaryotes. It plays a role in the mitogen-activated protein kinase cascades, a type of cell signalling that helps the cell respond to external stimuli, more specifically mating, cell growth, and osmo-tolerance [6] in fungi.
Function
The protein domain Ste50p has a role in detecting pheromones for mating. It is thought to be found bound to Ste11p in order to prolong the pheromone-induced signaling response. Furthermore, it is also involved in aiding the cell to respond to nitrogen starvation.[7]
Structure
The fungal Ste50p SAM consists of six helices, which form a compact, globular fold. It is a monomer in solution and often undergoes heterodimerisation (and in some cases oligomerisation) of the protein.[7]
Protein interaction
The SAM domain of Ste50p often interacts with the SAM domain of Ste11p. They form bonds through this association. It is important to note that the SAM domain of one protein will bind to the SAM of a different protein. SAM domains do not self-associate in vitro.[7] There is significant evidence for Ste50p oligomerization in vivo.[8]
Human proteins containing this domain
ANKS1A; ANKS1B; ANKS3; ANKS4B; ANKS6; BFAR; BICC1; CASKIN1; CASKIN2; CENTD1; CNKSR2; CNKSR3; DDHD2; EPHA1; EPHA10; EPHA2; EPHA5; EPHA6; EPHA7; EPHA8; EPHB1; EPHB2; EPHB3; EPHB4; FAM59A; HPH2; INPPL1; L3MBTL3; PHC1; PHC2; PHC3; PPFIA1; PPFIA2; PPFIA3; PPFIA4; PPFIBP1; PPFIBP2; SAMD1; SAMD13; SAMD14; SAMD3; SAMD4A; SAMD4B; SAMD5; SAMD7; SAMD8; SAMD9; SCMH1; SCML1; SCML2; SEC23IP; SGMS1; SHANK1; SHANK2; SHANK3; STARD13; UBP1; USH1G; ZCCHC14; p63; p73;
References
- ^ Bork P, Ponting CP, Hofmann K, Schultz J (1997). "SAM as a protein interaction domain involved in developmental regulation". Protein Sci. 6 (1): 249–253. doi:10.1002/pro.5560060128. PMC 2143507. PMID 9007998.
- ^ Pawson T, Stapleton D, Balan I, Sicheri F (1999). "The crystal structure of an Eph receptor SAM domain reveals a mechanism for modular dimerization". Nat. Struct. Biol. 6 (1): 44–49. doi:10.1038/4917. PMID 9886291.
- ^ a b Simon J, Peterson AJ, Kyba M, Bornemann D, Morgan K, Brock HW (1997). "A domain shared by the Polycomb group proteins Scm and ph mediates heterotypic and homotypic interactions". Mol. Cell. Biol. 17 (11): 6683–6692. doi:10.1128/MCB.17.11.6683. PMC 232522. PMID 9343432.
- ^ a b Goodwill KE, Thanos CD, Bowie JU (1999). "Oligomeric structure of the human EphB2 receptor SAM domain" (PDF). Science. 283 (5403): 833–836. doi:10.1126/science.283.5403.833. PMID 9933164.
- ^ Bowie JU, Kim CA (2003). "SAM domains: uniform structure, diversity of function". Trends Biochem. Sci. 28 (12): 625–628. doi:10.1016/j.tibs.2003.11.001. PMID 14659692.
- ^ Posas, F.; Witten, E. A.; Saito, H. (1998). "Requirement of STE50 for osmostress-induced activation of the STE11 mitogen-activated protein kinase kinase kinase in the high-osmolarity glycerol response pathway". Molecular and Cellular Biology. 18 (10): 5788–5796. doi:10.1128/mcb.18.10.5788. PMC 109165. PMID 9742096.
- ^ a b c Grimshaw SJ, Mott HR, Stott KM, Nielsen PR, Evetts KA, Hopkins LJ, Nietlispach D, Owen D (January 2004). "Structure of the sterile alpha motif (SAM) domain of the Saccharomyces cerevisiae mitogen-activated protein kinase pathway-modulating protein STE50 and analysis of its interaction with the STE11 SAM". J. Biol. Chem. 279 (3): 2192–201. doi:10.1074/jbc.M305605200. PMID 14573615.
- ^ Slaughter, BD; Huff JM; Wiegraebe W; Schwartz JW; Li R (2008). "SAM domain-based protein oligomerization observed by live-cell fluorescence fluctuation spectroscopy". PLOS ONE. 3 (4): e1931. doi:10.1371/journal.pone.0001931. PMC 2291563. PMID 18431466.
Structural evolution of p53, p63, and p73: Implication for heterotetramer formation
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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.
SAM domain (Sterile alpha motif) Provide feedback
It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.
Literature references
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Ponting CP; , Protein Sci 1995;4:1928-1930.: SAM: a novel motif in yeast sterile and Drosophila polyhomeotic proteins. PUBMED:8528090 EPMC:8528090
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Schultz J, Ponting CP, Hofmann K, Bork P; , Protein Sci 1997;6:249-253.: SAM as a protein interaction domain involved in developmental regulation. PUBMED:9007998 EPMC:9007998
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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
| SCOOP: | NCD1 SAM_2 SAM_3 SAM_4 SAM_PNT SAM_Ste50p |
| Similarity to PfamA using HHSearch: | SAM_2 IGR SAM_3 |
External database links
| HOMSTRAD: | SAM |
| SCOP: | 1b0x |
| SMART: | SAM |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001660
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 homologues. 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].
Gene Ontology
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) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan SAM (CL0003), which has the following description:
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 [3] . 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) [3]. 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 12 members:
IGR NCD1 SAM_1 SAM_2 SAM_3 SAM_4 SAM_DrpA SAM_Exu SAM_KSR1 SAM_LFY SAM_PNT SAM_Ste50pAlignments
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| RP15 (3308) |
RP35 (7944) |
RP55 (17595) |
RP75 (28008) |
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| PP/heatmap | 1 | ||||||||
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| Seed (56) |
Full (27252) |
Representative proteomes | UniProt (43814) |
NCBI (115808) |
Meta (94) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (3308) |
RP35 (7944) |
RP55 (17595) |
RP75 (28008) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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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.
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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
| Seed source: | [1],[2] |
| Previous IDs: | SAM_1; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Bateman A 
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| Number in seed: | 56 |
| Number in full: | 27252 |
| Average length of the domain: | 63.10 aa |
| Average identity of full alignment: | 23 % |
| Average coverage of the sequence by the domain: | 8.91 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 64 | ||||||||||||
| Family (HMM) version: | 31 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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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 SAM_1 domain has been found. There are 116 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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