<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Detailed information on MDP31729

Description Mediator of RNA polymerase II transcription subunit 4
SequenceMSVQDTKAVEFSMGHIRSSSVSLVAEATSNTNSEDKLSKVQLYEDLCRYEDTLSKLVESVDRFKPNLDIAKDLIRTDEALFENVKLLAEYDNIYRNLQKIDKDSEELDSKTRKILEILNECHDELKALPMLEQVEFEKNTILQQRSKINSTELLDYATKLSKFTKIPPTFDKGAVGPNNFIWPAEDALRRGMLAMASLHSKELTRIPGEEVEETEVPTVPPSQSEEQKGQMAKKEGTPKTDSFIFDGTAKEVGDEADNTKDKEKEENNDDALDLDLDLFDPDDF
Length284
PositionMiddle
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
KingdomFungi
LineageEukaryota> Fungi> Dikarya> Ascomycota> Saccharomycotina> Saccharomycetes> Saccharomycetales> Saccharomycetaceae> Saccharomyces.
Aromaticity0.06
Grand average of hydropathy-0.732
Instability index43.90
Isoelectric point4.54
Molecular weight32204.56
Publications
PubMed=8972579
PubMed=9169874
PubMed=24374639
PubMed=9420330
PubMed=11555651
PubMed=14562095
PubMed=14562106
PubMed=15126497
PubMed=15175151
PubMed=14749387
PubMed=15477388
PubMed=15710619
PubMed=16002404
PubMed=16076843
PubMed=16263706
PubMed=17192271
PubMed=17330950
PubMed=17287358
PubMed=18407956
PubMed=19779198
PubMed=22814378
PubMed=12191485

Function

Annotated function Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene- specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. The Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. 
ECO:0000269	PubMed:11555651
ECO:0000269	PubMed:16076843
ECO:0000269	PubMed:16263706
GO - Cellular Component
core mediator complex	GO:0070847	IDA:SGD
mediator complex	GO:0016592	IEA:InterPro
GO - Biological Function
RNA polymerase II core promoter sequence-specific DNA binding	GO:0000979	IDA:SGD
transcription coregulator activity	GO:0003712	IBA:GO_Central
GO - Biological Process
regulation of transcription by RNA polymerase II	GO:0006357	IBA:GO_Central
transcription by RNA polymerase II	GO:0006366	IDA:SGD

Interaction

Binary Interactions
[Q12343<-->Q08278: MED7]	NbExp=4	EBI-31503,EBI-10674
[Q12343<-->P47822: SRB7]	NbExp=4	EBI-31503,EBI-18046

Repeat regions

Repeats

>MDP31729
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      75.43|      25|     163|      75|     108|       1
---------------------------------------------------------------------------
   48-   72 (42.68/25.89)	RYEDTL...SKLVESVDRFKPNLD.IAKD
   75-  103 (32.75/45.74)	RTDEALfenVKLLAEYDNIYRNLQkIDKD
---------------------------------------------------------------------------
---------------------------------------------------------------------------
No. of Repeats|Total Score|Length  |Diagonal| BW-From|   BW-To|   Level
             2|      41.17|      12|      15|     140|     151|       2
---------------------------------------------------------------------------
  140-  151 (19.92/10.54)	TILQQRSKINST
  158-  169 (21.25/11.58)	TKLSKFTKIPPT
---------------------------------------------------------------------------


Explaination for Stockholm format The "Stockholm" format is a system for marking up features in a multiple alignment. These mark-up annotations are preceded by a 'magic' label, of which there are four types. The Stockholm format is used by HMMER, Pfam, and Belvu. Mark-up lines include any characters except whitespace. Underscore ("_") is used instead of space.

#=GR (seqname) PP (Generic per-Sequence AND per-Column markup, exactly 1 char per column) where PP is Posterior Probability [0-9*], (0=0.00-0.05; 1=0.05-0.15; *=0.95-1.00)

#=GC PP_cons line is Stockholm-format consensus posterior probability annotation for the entire column. It’s calculated simply as the arithmetic mean of the per-residue posterior probabilities in that column. This should prove useful in phylogenetic inference applications, for example, where it’s common to mask away non confidently aligned columns of a multiple alignment. The PP_cons line provides an objective measure of the confidence assigned to each column.

#=GC RF line is Stockholm-format reference coordinate annotation, with an x marking each column that the profile considered to be consensus.

Alignment of MDP31729 with Med4 domain of Kingdom Fungi



     
       
      
        
        
        


      
      
   
   

      

      














Intrinsically Disordered Regions








IDR SequenceStartStop




1) HSKELTRIPGEEVEETEVPTVPPSQSEEQKGQMAKKEGTPKTDSFIFDGTAKEVGDEADNTKDKEKEENNDDALDLDLDLF
199
279










Molecular Recognition Features






MoRF SequenceStartStop




1) QMAKK
2) TPKTDSFIFDGTAKEVGDEADNTKDKEKEENNDDALDLDLDLFDPDDF
230
237
234
284