Mediator of RNA polymerase II transcription subunit 13 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Preferred order of sections

Names and origin

Protein names

Recommended name:
Mediator of RNA polymerase II transcription subunit 13

Alternative name(s):
Mediator complex subunit 13
Protein SCA1
Suppressor of RNA polymerase B SSN2

Gene names

Name:	SSN2
Synonyms:	MED13, NUT8, RYE3, SCA1, SRB9, UME2
Ordered Locus Names:	YDR443C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	1420 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Component of the SRB8-11 complex. The SRB8-11 complex is a regulatory module of the Mediator complex which is itself involved in regulation of basal and activated RNA polymerase II-dependent transcription. The SRB8-11 complex may be involved in the transcriptional repression of a subset of genes regulated by Mediator. It may inhibit the association of the Mediator complex with RNA polymerase II to form the holoenzyme complex. The SRB8-11 complex phosphorylates the C-terminal domain (CTD) of the largest subunit of RNA polymerase II RPB1 at serines 2 and 5. Ref.5 Ref.6 Ref.8 Ref.9 Ref.10 Ref.11
Subunit structure	Component of the SRB8-11 complex which consists of SRB8, SSN2/SRB9, SSN3/SRB10 and SSN8/SRB11. The SRB8-11 complex associates with the Mediator complex. The SSN3/SRB10 and SSN8/SRB11 kinase-cyclin pair also associate with the RNA polymerase II holoenzyme.
Subcellular location	Nucleus Probable.
Post-translational modification	Phosphorylated. PKA-dependent phosphorylation at 'Ser-608' is enhanced by activation of the RAS signaling pathway. Ref.6 Ref.12 Ref.13 Ref.14
Sequence similarities	Belongs to the Mediator complex subunit 13 family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Activator Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD positive regulation of transcription from RNA polymerase II promoter by galactose Inferred from mutant phenotype Ref.10. Source: SGD
Cellular component	integral to membrane Inferred from electronic annotation. Source: InterPro mediator complex Inferred from direct assay Ref.5 Ref.7. Source: SGD
Molecular function	RNA polymerase II transcription coactivator activity Inferred from direct assay Ref.10. Source: SGD RNA polymerase II transcription factor recruiting transcription factor activity Inferred from mutant phenotype Ref.10. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1420

1420

Mediator of RNA polymerase II transcription subunit 13

PRO_0000072215

Regions

Compositional bias

526 – 529

4

Poly-Asn

Compositional bias

657 – 664

8

Poly-Glu

Compositional bias

813 – 816

4

Poly-Ser

Compositional bias

1005 – 1008

4

Poly-Leu

Compositional bias

1121 – 1136

16

Poly-Gln

Amino acid modifications

Modified residue

370

1

Phosphoserine Ref.12

Modified residue

375

1

Phosphoserine Ref.12 Ref.14

Modified residue

425

1

Phosphoserine Ref.13 Ref.14

Modified residue

444

1

Phosphoserine Ref.13

Modified residue

450

1

Phosphoserine Ref.13

Modified residue

453

1

Phosphothreonine Ref.13

Modified residue

587

1

Phosphoserine Ref.14

Modified residue

608

1

Phosphoserine; by PKA Ref.6

Modified residue

636

1

Phosphoserine Ref.14

Modified residue

703

1

Phosphoserine Ref.14

Modified residue

748

1

Phosphoserine Ref.14

Experimental info

Mutagenesis

608

1

S → A: Loss of function; when associated with A-1236. Ref.6

Mutagenesis

1236

1

S → A: Loss of function; when associated with A-608. Ref.6

Sequence conflict

38

1

D → E in AAA18614. Ref.2

Sequence conflict

812

1

E → V in AAA18614. Ref.2

Sequence conflict

859

1

T → S in AAA18614. Ref.2

Sequence conflict

877 – 878

2

VK → GE in AAA18614. Ref.2

Sequence conflict

887

1

T → P in AAA18614. Ref.2

Sequence conflict

1284

1

Y → S in AAA18614. Ref.2

Sequences

Sequence

Length

Mass (Da)

Tools

P38931 [UniParc].

Last modified February 1, 1996. Version 2.
Checksum: 7F6CF4BBE0FAC918
Show »

FASTA

1,420

160,001

        10         20         30         40         50         60 
MSSDASTYRL EDVLSSFYRV EKIKKINYHQ YISKAQNDQW SIQMEFMLRK QDPKTLVALL 

        70         80         90        100        110        120 
SRDLWCFSIN DDPVPTPPAI EHKPVSPDKI GTFTADYSKP NLPPHYALFL KALRRKIYIN 

       130        140        150        160        170        180 
LALGSHNKLI QFGNACISLS GVPNYLVQLE PHLFVNGDLT VSLCAKNMGL VPMKEENLEE 

       190        200        210        220        230        240 
SFLSKHALYL APSGIRMHLA PASKQGYLIT PPKHTELLLT TLSVSHGINL QNKKNLKWVA 

       250        260        270        280        290        300 
VVPDLGHLNG HTPTIASYLT PLLEAKKLVW PLHLIFAQPV ADIENSTSGD PSEFHCLQDA 

       310        320        330        340        350        360 
LDAIDDFIQL KQTAAYRTPG SSGVLSSNIA GTNPLSSDGA YTEQFQHYKN NSISSQPASY 

       370        380        390        400        410        420 
HSVQETNKIS PKDFSPNFTG IDKLMLSPSD QFAPAFLNTP NNNINENELF NDRKQTTVSN 

       430        440        450        460        470        480 
DLENSPLKTE LEANGRSLEK VNNSVSKTGS VDTLHNKEGT LEQREQNENL PSDKSDSMVD 

       490        500        510        520        530        540 
KELFGEDEDE DLFGDSNKSN STNESNKSIS DEITEDMFEM SDEEENNNNK SINKNNKEMH 

       550        560        570        580        590        600 
TDLGKDIPFF PSSEKPNIRT MSGTTKRLNG KRKYLDIPID EMTLPTSPLY MDPGAPLPVE 

       610        620        630        640        650        660 
TPRDRRKSVF APLNFNPIIE NNVDNKYKSG GKFSFSPLQK EEALNFDISM ADLSSSEEEE 

       670        680        690        700        710        720 
DEEENGSSDE DLKSLNVRDD MKPSDNISTN TNIHEPQYIN YSSIPSLQDS IIKQENFNSV 

       730        740        750        760        770        780 
NDANITSNKE GFNSIWKIPQ NDIPQTESPL KTVDSSIQPI ESNIKMTLED NNVTSNPSEF 

       790        800        810        820        830        840 
TPNMVNSEIS NLPKDKSGIP EFTPADPNLS FESSSSLPFL LRHMPLASIP DIFITPTPVV 

       850        860        870        880        890        900 
TISEKEQDIL DLIAEQVVTD YNILGNLGIP KIAYRGVKDC QEGLITTTML QLFSTFDRLN 

       910        920        930        940        950        960 
GNDTISKFYN MKQPYVFVKK HHELIKVKHD SQPFIKFLNF RPPNGIKNFK SLLLSSSFKE 

       970        980        990       1000       1010       1020 
DCLSFAPTLS QTYINQELGF CELLKLTNED PPGLMYLKAF DKNKLLLLAA QIVSYCSNNK 

      1030       1040       1050       1060       1070       1080 
NSIKNVPPIL IILPLDNATL TELVDKANIF QVIKNEVCAK MPNIELYLKV IPMDFIRNVL 

      1090       1100       1110       1120       1130       1140 
VTVDQYVNVA ISIYNMLPPK SVKFTHIAHT LPEKVNFRTM QQQQMQQQQQ QQQQQQNNST 

      1150       1160       1170       1180       1190       1200 
GSSSIIYYDS YIHLAYSRSV DKEWVFAALS DSYGQGSMTK TWYVGNSRGK FDDACNQIWN 

      1210       1220       1230       1240       1250       1260 
IALNLASKKF GKICLILTRL NGILPDDELM NWRRLSGRNI HLAVVCVDDN SKISFIDEDK 

      1270       1280       1290       1300       1310       1320 
LYPSFKPIYK DTRFGGRMDM TRLYDYEIRD IDQDIHGIVF QHPFPLAHSQ HRCAIRSGAL 

      1330       1340       1350       1360       1370       1380 
IKFKKCDGDT VWDKFAVNLL NCPHSDSTQL LETILEEFRN LAALNVWYGL SDGEDGHIPW 

      1390       1400       1410       1420 
HILAVKKMMN TLVHTRVKIA NTSAATVHTA TSSSIILSDK

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Association of an activator with an RNA polymerase II holoenzyme." Hengartner C.J., Thompson C.M., Zhang J., Chao D.M., Liao S.-M., Koleske A.J., Okamura S., Young R.A. Genes Dev. 9:897-910(1995) [PubMed: 7774808] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"Suppression analysis reveals a functional difference between the serines in positions two and five in the consensus sequence of the C-terminal domain of yeast RNA polymerase II." Yuryev A., Corden J.L. Genetics 143:661-671(1996) [PubMed: 8725217] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast." Borggrefe T., Davis R., Erdjument-Bromage H., Tempst P., Kornberg R.D. J. Biol. Chem. 277:44202-44207(2002) [PubMed: 12200444] [Abstract] Cited for: IDENTIFICATION IN THE SRB8-11 COMPLEX, FUNCTION OF THE SRB8-11 COMPLEX.
[6]	"The Ras/PKA signaling pathway directly targets the Srb9 protein, a component of the general RNA polymerase II transcription apparatus." Chang Y.-W., Howard S.C., Herman P.K. Mol. Cell 15:107-116(2004) [PubMed: 15225552] [Abstract] Cited for: FUNCTION, PHOSPHORYLATION AT SER-608 BY PKA, MUTAGENESIS OF SER-608 AND SER-1236.
[7]	"A high resolution protein interaction map of the yeast Mediator complex." Guglielmi B., van Berkum N.L., Klapholz B., Bijma T., Boube M., Boschiero C., Bourbon H.-M., Holstege F.C.P., Werner M. Nucleic Acids Res. 32:5379-5391(2004) [PubMed: 15477388] [Abstract] Cited for: TOPOLOGY OF THE MEDIATOR COMPLEX.
[8]	"Mediator and TFIIH govern carboxyl-terminal domain-dependent transcription in yeast extracts." Nair D., Kim Y., Myers L.C. J. Biol. Chem. 280:33739-33748(2005) [PubMed: 16076843] [Abstract] Cited for: FUNCTION OF THE MEDIATOR COMPLEX.
[9]	"Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets." van de Peppel J., Kettelarij N., van Bakel H., Kockelkorn T.T.J.P., van Leenen D., Holstege F.C.P. Mol. Cell 19:511-522(2005) [PubMed: 16109375] [Abstract] Cited for: FUNCTION.
[10]	"The Saccharomyces cerevisiae Srb8-Srb11 complex functions with the SAGA complex during Gal4-activated transcription." Larschan E., Winston F. Mol. Cell. Biol. 25:114-123(2005) [PubMed: 15601835] [Abstract] Cited for: FUNCTION OF THE SRB8-11 COMPLEX.
[11]	"Genome-wide location of the coactivator mediator: binding without activation and transient Cdk8 interaction on DNA." Andrau J.-C., van de Pasch L., Lijnzaad P., Bijma T., Koerkamp M.G., van de Peppel J., Werner M., Holstege F.C.P. Mol. Cell 22:179-192(2006) [PubMed: 16630888] [Abstract] Cited for: FUNCTION.
[12]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-370 AND SER-375, MASS SPECTROMETRY. Strain: ADR376.
[13]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-425; SER-444; SER-450 AND THR-453, MASS SPECTROMETRY.
[14]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-375; SER-425; SER-587; SER-636; SER-703 AND SER-748, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U23812 Genomic DNA. Translation: AAA91316.1. U09176 Unassigned DNA. Translation: AAA18614.1. U33007 Genomic DNA. Translation: AAB64875.1. BK006938 Genomic DNA. Translation: DAA12279.1.
PIR	B57062.
RefSeq	NP_010731.1. NM_001180751.1.
3D structure databases
ProteinModelPortal	P38931.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5947N.
IntAct	P38931. 15 interactions.
MINT	MINT-658715.
STRING	P38931.
Proteomic databases
PeptideAtlas	P38931.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDR443C; YDR443C; YDR443C.
GeneID	852053.
KEGG	sce:YDR443C.
NMPDR	fig\|4932.3.peg.1504.
Organism-specific databases
CYGD	YDR443c.
SGD	S000002851. SSN2.
Phylogenomic databases
eggNOG	fuNOG04918.
HOGENOM	HBG203301.
OMA	WCFSIND.
OrthoDB	EOG43R6VR.
Gene expression databases
ArrayExpress	P38931.
Genevestigator	P38931.
GermOnline	YDR443C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR009401. Mediator_Med13. IPR018174. Mediator_Med13_fun. IPR004316. RAG1-activating-rel. [Graphical view]
KO	K15165.
PANTHER	PTHR10791:SF3. Mediator-of-RNAPII_su13. 1 hit. PTHR10791. MtN3_slv_TM. 1 hit.
Pfam	PF06333. Med13_C. 2 hits. [Graphical view]
ProtoNet	Search...
Other
NextBio	970317.

Entry information

Entry name

SSN2_YEAST

Accession

Primary (citable) accession number: P38931
Secondary accession number(s): D6VT69

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1996
Last modified:	December 14, 2011
This is version 94 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents