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0  structures 687  species 0  interactions 938  sequences 7  architectures

Family: Med16 (PF11635)

Summary: Mediator complex subunit 16

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 "MED16". More...

MED16 Edit Wikipedia article

MED16
Identifiers
AliasesMED16, DRIP92, THRAP5, TRAP95, mediator complex subunit 16
External IDsOMIM: 604062 MGI: 2158394 HomoloGene: 64602 GeneCards: MED16
Gene location (Human)
Chromosome 19 (human)
Chr.Chromosome 19 (human)[1]
Chromosome 19 (human)
Genomic location for MED16
Genomic location for MED16
Band19p13.3Start867,630 bp[1]
End893,218 bp[1]
RNA expression pattern
PBB GE THRAP5 43544 at fs.png

PBB GE THRAP5 221544 s at fs.png

PBB GE THRAP5 221418 s at fs.png
More reference expression data
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_005481

NM_001163276
NM_198107
NM_001359629

RefSeq (protein)

NP_005472

XP_006513550.1
XP_006513551.1

Location (UCSC)Chr 19: 0.87 – 0.89 MbChr 10: 79.89 – 79.91 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Mediator of RNA polymerase II transcription subunit 16 is an enzyme that in humans is encoded by the MED16 gene.[5][6][7]


Interactions

MED16 has been shown to interact with Thyroid hormone receptor alpha,[6] Estrogen receptor alpha[8] and Cyclin-dependent kinase 8.[6][8]

References

  1. ^ a b c ENSG00000175221 GRCh38: Ensembl release 89: ENSG00000282092, ENSG00000175221 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000013833 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Naar AM, Erdjument-Bromage H, Tempst P, Freedman LP (Jun 1999). "Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex". Nature. 398 (6730): 824–8. Bibcode:1999Natur.398..824R. doi:10.1038/19783. PMID 10235266.
  6. ^ a b c Ito M, Yuan CX, Malik S, Gu W, Fondell JD, Yamamura S, Fu ZY, Zhang X, Qin J, Roeder RG (Apr 1999). "Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators". Mol Cell. 3 (3): 361–70. doi:10.1016/S1097-2765(00)80463-3. PMID 10198638.
  7. ^ "Entrez Gene: THRAP5 thyroid hormone receptor associated protein 5".
  8. ^ a b Kang, Yun Kyoung; Guermah Mohamed; Yuan Chao-Xing; Roeder Robert G (Mar 2002). "The TRAP/Mediator coactivator complex interacts directly with estrogen receptors alpha and beta through the TRAP220 subunit and directly enhances estrogen receptor function in vitro". Proc. Natl. Acad. Sci. U.S.A. United States. 99 (5): 2642–7. Bibcode:2002PNAS...99.2642K. doi:10.1073/pnas.261715899. ISSN 0027-8424. PMC 122401. PMID 11867769.

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 16 Provide feedback

Mediator is a large complex of up to 33 proteins that is conserved from plants through 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-activity 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. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression [4]. Several members including the human protein, Q9Y2X0 have one or more WD40 domains on them, PF00400.

Literature references

  1. Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, , Mol Cell. 2004;14:553-557.: A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. PUBMED:15175151 EPMC:15175151

  2. Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, Conaway JW, Conaway RC; , Mol Cell. 2004;14:685-691.: A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. PUBMED:15175163 EPMC:15175163

  3. 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

  4. Kim TW, Kwon YJ, Kim JM, Song YH, Kim SN, Kim YJ; , Proc Natl Acad Sci U S A. 2004;101:12153-12158.: MED16 and MED23 of Mediator are coactivators of lipopolysaccharide- and heat-shock-induced transcriptional activators. PUBMED:15297616 EPMC:15297616


This tab holds annotation information from the InterPro database.

InterPro entry IPR021665

Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [PUBMED:15175151,PUBMED:15175163]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity 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. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression [PUBMED:15297616]. Several members including the human protein, SWISSPROT, have one or more WD40 domains on them, .

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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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
(15)
Full
(938)
Representative proteomes UniProt
(1559)
NCBI
(1930)
Meta
(0)
RP15
(104)
RP35
(305)
RP55
(586)
RP75
(905)
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Key: ✓ available, x not generated, not available.

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  Seed
(15)
Full
(938)
Representative proteomes UniProt
(1559)
NCBI
(1930)
Meta
(0)
RP15
(104)
RP35
(305)
RP55
(586)
RP75
(905)
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
(15)
Full
(938)
Representative proteomes UniProt
(1559)
NCBI
(1930)
Meta
(0)
RP15
(104)
RP35
(305)
RP55
(586)
RP75
(905)
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: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 15
Number in full: 938
Average length of the domain: 601.40 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 80.95 %

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 25.0 25.0
Noise cut-off 24.8 24.8
Model length: 758
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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