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46  structures 857  species 5  interactions 1017  sequences 24  architectures

Family: DSS1_SEM1 (PF05160)

Summary: DSS1/SEM1 family

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This is the Wikipedia entry entitled "DSS1/SEM1 protein family". More...

DSS1/SEM1 protein family Edit Wikipedia article

DSS1_SEM1
PDB 1miu EBI.jpg
structure of a brca2-dss1 complex
Identifiers
Symbol DSS1_SEM1
Pfam PF05160
InterPro IPR007834
SCOP 1iyj
SUPERFAMILY 1iyj

In molecular biology, the DSS1/SEM1 protein family is a family of short acidic proteins which includes the 26S proteasome complex subunits SEM1 from Saccharomyces cerevisiae and Drosophila and DSS1 (SHFM1) in mammals. In Saccharomyces cerevisiae, SEM1 is a regulator of both exocyst function and pseudohyphal differentiation.[1] Loss of DSS1 in Homo sapiens (human) has been associated with split hand/split foot malformations.[2] DSS1 is playing role as a modifier in a novel protein posttranslational modification,refer to as DSSylation, which is probably targeting oxidized proteins and guiding them to proteasomal degradation.[3]

References

  1. ^ Jantti J, Lahdenranta J, Olkkonen VM, Soderlund H, Keranen S (February 1999). "SEM1, a homologue of the split hand/split foot malformation candidate gene Dss1, regulates exocytosis and pseudohyphal differentiation in yeast". Proc. Natl. Acad. Sci. U.S.A. 96 (3): 909–14. doi:10.1073/pnas.96.3.909. PMC 15324Freely accessible. PMID 9927667. 
  2. ^ Ignatius J, Knuutila S, Scherer SW, Trask B, Kere J (June 1996). "Split hand/split foot malformation, deafness, and mental retardation with a complex cytogenetic rearrangement involving 7q21.3". J. Med. Genet. 33 (6): 507–10. doi:10.1136/jmg.33.6.507. PMC 1050639Freely accessible. PMID 8782053. 
  3. ^ Yinghao Zhang; Fang-Mei Chang; Jianjun Huang; Jacob J. Junco; Shivani K. Maffi; Hannah I. Pridgen; Gabriel Catano; Hong Dang; Xiang Ding; Fuquan Yang; Dae Joon Kim; Thomas J. Slaga; Rongqiao He; Sung-Jen Wei (February 2014). "DSSylation, a novel protein modification targets proteins induced by oxidative stress, and facilitates their degradation in cells". Protein Cell. 5 (2): 124–140. doi:10.1007/s13238-013-0018-8. PMC 3956975Freely accessible. PMID 24515614. 

This article incorporates text from the public domain Pfam and InterPro IPR007834

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.

DSS1/SEM1 family Provide feedback

This family contains the breast cancer tumour suppressor BRCA2-interacting protein DSS1 and its homologue SEM1, both of which are short acidic proteins. DSS1 has been shown to be a conserved component of the Rae1 mediated mRNA export pathway in Schizosaccharomyces pombe [1].

Literature references

  1. Thakurta AG, Gopal G, Yoon JH, Kozak L, Dhar R; , EMBO J 2005;24:2512-2523.: Homolog of BRCA2-interacting Dss1p and Uap56p link Mlo3p and Rae1p for mRNA export in fission yeast. PUBMED:15990877 EPMC:15990877

  2. Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y, Thoma NH, Zheng N, Chen PL, Lee WH, Pavletich NP; , Science 2002;297:1837-1848.: BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. PUBMED:12228710 EPMC:12228710

  3. Jantti J, Lahdenranta J, Olkkonen VM, Soderlund H, Keranen S; , Proc Natl Acad Sci U S A 1999;96:909-914.: SEM1, a homologue of the split hand/split foot malformation candidate gene Dss1, regulates exocytosis and pseudohyphal differentiation in yeast. PUBMED:9927667 EPMC:9927667


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007834

This family includes yeast Sem1 and its mammalian homologue, DSS1.

Sem1/DSS1 (also known as rpn15) is a component of lid subcomplex of 26S proteasome regulatory subunit [PUBMED:23643786, PUBMED:24412063, PUBMED:15117943]. Besides being a subunit of the 26S proteasome, Sem1/DSS1 associates with other protein complexes [PUBMED:26944332]. It is a component of the nuclear pore complex (NPC)-associated TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation [PUBMED:24896180, PUBMED:19289793, PUBMED:26456823].

Loss of DSS1 in humans has been associated with split hand/split foot malformations [PUBMED:8782053].

Gene Ontology

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Domain organisation

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Alignments

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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
(92)
Full
(1017)
Representative proteomes UniProt
(1401)
NCBI
(1248)
Meta
(3)
RP15
(270)
RP35
(562)
RP55
(810)
RP75
(1039)
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Format an alignment

  Seed
(92)
Full
(1017)
Representative proteomes UniProt
(1401)
NCBI
(1248)
Meta
(3)
RP15
(270)
RP35
(562)
RP55
(810)
RP75
(1039)
Alignment:
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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
(92)
Full
(1017)
Representative proteomes UniProt
(1401)
NCBI
(1248)
Meta
(3)
RP15
(270)
RP35
(562)
RP55
(810)
RP75
(1039)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   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

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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: Pfam-B_22209 (release 7.7)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Mistry J
Number in seed: 92
Number in full: 1017
Average length of the domain: 61.40 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 54.34 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.2 32.2
Trusted cut-off 32.8 32.5
Noise cut-off 30.7 32.1
Model length: 60
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 5 interactions for this family. More...

SAC3_GANP BRCA-2_helical DSS1_SEM1 PCI BRCA-2_OB1

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 DSS1_SEM1 domain has been found. There are 46 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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