Summary: Scd6-like Sm domain
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Scd6-like Sm domain Provide feedback
The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans . The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the the Rossmanoid YjeF-N domain [1,2]. In addition both EDC3 and Scd6p are found fused to the FDF domain [1,2].
Anantharaman V, Aravind L;, BMC Genomics. 2004;5:45.: Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability. PUBMED:15257761 EPMC:15257761
Tanaka KJ, Ogawa K, Takagi M, Imamoto N, Matsumoto K, Tsujimoto M;, J Biol Chem. 2006;281:40096-40106.: RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes. PUBMED:17074753 EPMC:17074753
Tritschler F, Eulalio A, Truffault V, Hartmann MD, Helms S, Schmidt S, Coles M, Izaurralde E, Weichenrieder O; , Mol Cell Biol. 2007;27:8600-8611.: A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting. PUBMED:17923697 EPMC:17923697
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR025609
The Lsm14 N-terminal domain is a type of LSM domain found in Lsm14 proteins (also known as Rap55) [PUBMED:17074753, PUBMED:18723115] and in the Saccharomyces cerevisiae homologue Scd6 [PUBMED:15225602]. The domain is also found in the human EDC3 protein (enhancer of mRNA-decapping protein 3) where it is fused to the the Rossmanoid YjeF-N domain [PUBMED:15257761]. In addition, both EDC3 and Scd6 are found fused to the FDF domain [PUBMED:15225602, PUBMED:15257761].
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Curation and family details
|Seed source:||Anantharaman V|
|Number in seed:||156|
|Number in full:||564|
|Average length of the domain:||94.00 aa|
|Average identity of full alignment:||40 %|
|Average coverage of the sequence by the domain:||21.39 %|
|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:||2|
|Download:||download the raw HMM for this family|
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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 LSM14 domain has been found. There are 5 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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