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4  structures 214  species 0  interactions 621  sequences 31  architectures

Family: Med25 (PF11232)

Summary: Mediator complex subunit 25 PTOV activation and synapsin 2

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "MED25". More...

MED25 Edit Wikipedia article

MED25
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases MED25, ACID1, ARC92, CMT2B2, P78, PTOV2, BVSYS, TCBAP0758, mediator complex subunit 25
External IDs MGI: 1922863 HomoloGene: 12614 GeneCards: MED25
Gene location (Human)
Chromosome 19 (human)
Chr. Chromosome 19 (human)[1]
Chromosome 19 (human)
Genomic location for MED25
Genomic location for MED25
Band n/a Start 49,818,279 bp[1]
End 49,838,816 bp[1]
RNA expression pattern
PBB GE MED25 208110 x at fs.png

PBB GE MED25 215897 at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_030973

NM_029365
NM_001331206
NM_001331207
NM_001331208

RefSeq (protein)

NP_112235

NP_001318135
NP_001318136
NP_001318137
NP_083641

Location (UCSC) Chr 19: 49.82 – 49.84 Mb Chr 19: 44.88 – 44.89 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Mediator of RNA polymerase II transcription subunit 25 is an enzyme that in humans is encoded by the MED25 gene.[5][6][7]

Interactions

MED25 has been shown to interact with MED4.[8]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000104973 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000002968 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Yu W, Andersson B, Worley KC, Muzny DM, Ding Y, Liu W, Ricafrente JY, Wentland MA, Lennon G, Gibbs RA (Apr 1997). "Large-scale concatenation cDNA sequencing". Genome Research. 7 (4): 353–8. PMC 139146Freely accessible. PMID 9110174. doi:10.1101/gr.7.4.353. 
  6. ^ Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, Böcher M, Blöcker H, Bauersachs S, Blum H, Lauber J, Düsterhöft A, Beyer A, Köhrer K, Strack N, Mewes HW, Ottenwälder B, Obermaier B, Tampe J, Heubner D, Wambutt R, Korn B, Klein M, Poustka A (Mar 2001). "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs". Genome Research. 11 (3): 422–35. PMC 311072Freely accessible. PMID 11230166. doi:10.1101/gr.GR1547R. 
  7. ^ "Entrez Gene: MED25 mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)". 
  8. ^ Tomomori-Sato C, Sato S, Parmely TJ, Banks CA, Sorokina I, Florens L, Zybailov B, Washburn MP, Brower CS, Conaway RC, Conaway JW (Feb 2004). "A mammalian mediator subunit that shares properties with Saccharomyces cerevisiae mediator subunit Cse2". The Journal of Biological Chemistry. 279 (7): 5846–51. PMID 14638676. doi:10.1074/jbc.M312523200. 

Further reading

External links


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This is the Wikipedia entry entitled "Mediator (coactivator)". More...

Mediator (coactivator) Edit Wikipedia article

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.

Mediator complex subunit 25 PTOV activation and synapsin 2 Provide feedback

Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function [4]. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear [3].

Literature references

  1. Yang F, DeBeaumont R, Zhou S, Naar AM; , Proc Natl Acad Sci U S A. 2004;101:2339-2344.: The activator-recruited cofactor/Mediator coactivator subunit ARC92 is a functionally important target of the VP16 transcriptional activator. PUBMED:14983011 EPMC:14983011

  2. Backstrom S, Elfving N, Nilsson R, Wingsle G, Bjorklund S; , Mol Cell. 2007;26:717-729.: Purification of a plant mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. PUBMED:17560376 EPMC:17560376

  3. Lee HK, Park UH, Kim EJ, Um SJ; , EMBO J. 2007;26:3545-3557.: MED25 is distinct from TRAP220/MED1 in cooperating with CBP for retinoid receptor activation. PUBMED:17641689 EPMC:17641689

  4. Lariviere L, Seizl M, van Wageningen S, Rother S, van de Pasch L, Feldmann H, Strasser K, Hahn S, Holstege FC, Cramer P; , Genes Dev. 2008;22:872-877.: Structure-system correlation identifies a gene regulatory Mediator submodule. PUBMED:18381891 EPMC:18381891


This tab holds annotation information from the InterPro database.

InterPro entry IPR021394

Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [PUBMED:14983011, PUBMED:17560376]. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II, but it would appear that each of the four different sections has a slightly different function [PUBMED:18381891]. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. The PTOV domain is the domain through which Med25 co-operates with the histone acetyltransferase CBP [PUBMED:17641689].

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 SPOC (CL0616), which has the following description:

The crystal structure of the SPOC domain [3] showed it has similarity with the beta barrel domain of the Ku proteins. These domains share a 7 stranded beta barrel. In the Ku proteins this domain interacts DNA, whereas the SPOC domain mediates protein binding.

The clan contains the following 4 members:

Ku Med25 Sld7_N SPOC

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(19)
Full
(621)
Representative proteomes UniProt
(1140)
NCBI
(1783)
Meta
(0)
RP15
(98)
RP35
(171)
RP55
(331)
RP75
(577)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(19)
Full
(621)
Representative proteomes UniProt
(1140)
NCBI
(1783)
Meta
(0)
RP15
(98)
RP35
(171)
RP55
(331)
RP75
(577)
Alignment:
Format:
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Sequence:
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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
(19)
Full
(621)
Representative proteomes UniProt
(1140)
NCBI
(1783)
Meta
(0)
RP15
(98)
RP35
(171)
RP55
(331)
RP75
(577)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped 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

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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: manual
Previous IDs: Med25_PTOV1;Med25_PTOV-SD2;
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 19
Number in full: 621
Average length of the domain: 142.80 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 27.85 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.9 25.2
Noise cut-off 20.0 21.5
Model length: 154
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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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 Med25 domain has been found. There are 4 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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