Gene

KWMTBOMO06731  Validated by peptides from experiments

Pre Gene Modal

BGIBMGA011747

Annotation

PREDICTED:_histone_deacetylase_Rpd3_[Papilio_polytes]

Location

Bomo_Chr11(-):13226301-13233292      View in EpiBrowser

Full name

Histone deacetylase       + More
Histone deacetylase Rpd3      

Location in the cell

Nuclear   Reliability : 4.489

CDS

ATGTCTATGCAACCGCACAGTAAGAAAAGAGTGTGTTACTATTATGACAGCGATATTGGAAACTACTATTACGGACAAGGGCATCCAATGAAACCTCACCGCATACGTATGACCCACAATTTACTCCTCAACTATGGACTCTATCGAAAAATGGAGATTTATAGGCCTCACAAAGCCACAGCTGATGAAATGACAAAATTCCATTCAGATGATTACATTAGATTCCTGCGTTCTATTCGACCTGACAATGTTTCTGAGTACAACAAACAAATGCAGAGATTTAATGTAGGTGAAGATTGTCCTGTTTTTGATGGCCTGTATGAATTTTGTCAGTTGTCTGCTGGGGGTTCAGTTGCAGCAGCTGTAAAACTGAATAAGCAGGCCTCAGAAATATGCATAAACTGGGGTGGTGGCCTCCATCATGCAAAGAAGTCTGAAGCGTCAGGTTTCTGTTATGTTAATGACATTGTTCTTGGCATATTGGAGTTGCTGAAATACCATCAAAGAGTACTATATATTGACATAGATGTGCATCATGGTGATGGTGTTGAAGAAGCTTTCTACACCACGGACAGAGTAATGACCGTTTCCTTTCATAAATATGGAGAATATTTTCCTGGAACAGGTGATTTGCGGGACATTGGTGCTGGTAAAGGCAAATACTATGCTGTAAATATACCCCTTCGTGATGGAATGGATGATGAGTCATATGAGTCTATCTTTGTTCCCATTATATCTAAAGTTATGGAGACATTCCAACCAAGTGCTGTAGTACTACAGTGTGGTGCTGATTCTCTGACAGGTGACAGATTGGGTTGTTTCAACTTGACTGTTCGAGGTCATGGACGCTGTGTAGAACTTGTCAAGAGGTTTGGACTTCCATTCTTACTAGTCGGCGGAGGCGGATATACCATACGTAATGTATCTCGCTGTTGGACTTACGAGACATCTGTTGCACTTGGTGTGGAAATAGCCAATGAACTACCATATAATGACTACTTTGAGTACTTTGGGCCCGATTTCAAACTACACATATCACCAAGTAACATGTCCAATCAAAACACACCCGAATATCTGGAAAAGATAAAAAATAGACTGTTCGAGAATCTCAGAATGCTCCCACATGCGCCAGGAGTACAAGTGCAAGCCATACCTGAAGATGCTGTCAATGATGAGTCAGATGATGAAGATAAAATAGACAAAGATGAGAGATTACCACAGAGTGATAAGGACAAGCGCATCGCTAACGACGGCGAGCTGTCGGACTCCGAGGACGAGGGCGACGGGCGACGCGACAACCGAGCCTACCGCGCGCCGCAGCGCAAGCGTCCGCGACTCGACAAGGAACCCTTGCAGATCAAGGACGATCTTAAACCTGATGACATGAAGGATGACGTTAAAAACGTTAGCAACGCGGAAGAATCAAAGAAGGACATGCCACCGAATCCCTGA

Protein

MSMQPHSKKRVCYYYDSDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATADEMTKFHSDDYIRFLRSIRPDNVSEYNKQMQRFNVGEDCPVFDGLYEFCQLSAGGSVAAAVKLNKQASEICINWGGGLHHAKKSEASGFCYVNDIVLGILELLKYHQRVLYIDIDVHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNIPLRDGMDDESYESIFVPIISKVMETFQPSAVVLQCGADSLTGDRLGCFNLTVRGHGRCVELVKRFGLPFLLVGGGGYTIRNVSRCWTYETSVALGVEIANELPYNDYFEYFGPDFKLHISPSNMSNQNTPEYLEKIKNRLFENLRMLPHAPGVQVQAIPEDAVNDESDDEDKIDKDERLPQSDKDKRIANDGELSDSEDEGDGRRDNRAYRAPQRKRPRLDKEPLQIKDDLKPDDMKDDVKNVSNAEESKKDMPPNP

Description

Catalyzes the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4) (PubMed:11571273, PubMed:28245922, PubMed:12408863). Histone deacetylation may constitute a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events (PubMed:11571273, PubMed:8955276, PubMed:15545624, PubMed:15306652). For instance, deacetylation of histone H3 may be a prerequisite for the subsequent recruitment of the histone methyltransferase Su(var)3-9 to histones (PubMed:11571273). Involved in position-effect variegation (PEV) (PubMed:11571273). In the larval brain, part of a regulatory network including the transcriptional repressors klu, dpn and E(spl)mgamma-HLH which is required for type II neuroblast self-renewal and for maintaining erm in an inactive state in intermediate neural progenitors (INP) (PubMed:28245922).

Catalytic Activity

Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

Subunit

Interacts with Su(var)3-9. Component of a form of the Esc/E(z) complex present specifically during early embryogenesis which is composed of Caf1, esc, E(z), Su(z)12, Pcl and Rpd3. The Esc/E(z) complex may also associate with Pcl and Rpd3 during early embryogenesis. This complex is distinct from the PRC1 complex, which contains many other PcG proteins like Pc, Ph, Psc, Su(z)2. The 2 complexes however cooperate and interact together during the first 3 hours of development to establish PcG silencing. Interacts with the histone methyltransferase Su(var)3-9. Component of a complex that contains at least Rpd3, CoRest and Su(var)3-3/Hdm. Component of the DREAM complex at least composed of Myb, Caf1, mip40, mip120, mip130, E2f2, Dp, Rbf, Rbf2, lin-52, Rpd3 and l(3)mbt. Interacts with neuronal repressor Ttk88.

Similarity

Belongs to the histone deacetylase family. HD Type 1 subfamily.
Belongs to the histone deacetylase family. HD type 1 subfamily.

Keywords

Chromatin regulator   Complete proteome   Developmental protein   Hydrolase   Nucleus   Phosphoprotein   Reference proteome   Repressor   Transcription   Transcription regulation  

Feature

chain  Histone deacetylase Rpd3

Uniprot

A0A2A4K903   A0A194PF89   A0A212F5S3   A0A0N1IGB9   A0A1Q3EXC7   B0WJ91   + More
Q17CF0   A0A1Q3EXB1   A0A182GNN5   A0A023EUU4   B4MFY7   Q17CE9   A0A1Q3EXC6   U5EW58   B4IZ79   E3W281   E3W278   E3VX32   E3VX22   A0A0M4E8U0   B4MMY6   W8C8N5   A0A0J9RPK2   B4HU89   B3NC63   Q94517   B4QR08   A0A2M4AQV8   A0A1W4VAJ1   B4PIA1   A0A347ZJC4   A0A182FGH3   W5JF61   B3M9I7   A0A034WDK2   A0A0J7L4B5   A0A0A1WN83   B4KX99   A0A0K8VJ62   Q29EB4   A0A084WMI3   A0A182WBY2   A0A1Y1NG16   E3W282   S4NV65   A0A1I8M0Y6   A0A3B0JW31   A0A3B0J6G3   E2AL67   A0A182IKH6   A0A2J7QBD0   A0A336MS89   A0A182Y7V6   A0A1B0FJF6   A0A1A9Y199   A0A1A9UXP8   A0A1B0AZ17   A0A1A9ZWK4   A0A182V3V5   D6WG88   A0A182K1D6   A0A1L7N254   A0A182LKN9   A0A182TYI1   A0A182I495   A0A182X957   A0A182MWC0   A0A182RR67   A0A088AP92   E2B313   A0A195FTX4   A0A026WND6   A0A151I2N9   A0A158NKZ2   I1V501   A0A1I8PP67   Q7Q5D2   A0A151IM03   A0A151X3P9   J3JWV8   A0A151JAD5   F4WWT9   N6T0I9   A0A1L8DX14   A0A1A9W4R5   A0A1B6LWH4   B4HCY7   A0A1B6FBN9   A0A182QB58   A0A182NIY3   A0A232FI77   A0A3B0K2G2   A0A0R3P6D5   A0A1B6D3Z1   A0A0R3P695   K7J9J6   A0A182T387   A0A182NZT1   A0A2A3ESP9   A0A0A9YBV7  

EC Number

3.5.1.98

Pubmed

26354079    22118469    17510324    26483478    24945155    17994087    + More
24495485    22936249    8955276    10655219    10731132    12537572    12537569    11571273    12533794    12408863    12697833    15545624    15306652    18327897    28245922    17550304    20920257    23761445    25348373    25830018    15632085    24438588    28004739    23622113    25315136    20798317    25244985    18362917    19820115    27956627    20966253    24508170    30249741    21347285    12364791    22516182    23537049    21719571    28648823    20075255    25401762    26823975   

EMBL

NWSH01000021    PCG80701.1    KQ459606    KPI91688.1    AGBW02010142    OWR49087.1    + More
KQ460499    KPJ14288.1    GFDL01015083    JAV19962.1    DS231957    EDS29016.1    CH477309    EAT44001.1    GFDL01015100    JAV19945.1    JXUM01014757    JXUM01014758    JXUM01014759    JXUM01014760    KQ560412    KXJ82549.1    GAPW01001354    JAC12244.1    CH940669    EDW58248.1    EAT44002.1    GFDL01015081    JAV19964.1    GANO01003103    JAB56768.1    CH916366    EDV95601.1    HQ379193    ADO79638.1    HQ379190    ADO79635.1    HQ326584    ADO79632.1    HQ323752    HQ379189    HQ379191    HQ379192    ADO79633.1    ADO79634.1    ADO79636.1    ADO79637.1    CP012525    ALC43366.1    CH963847    EDW73542.1    GAMC01007366    GAMC01007365    JAB99189.1    CM002912    KMY97652.1    CH480817    EDW50510.1    CH954178    EDV50951.1    Y09258    AF086715    AF026949    AE014296    AY058487    CM000363    EDX09245.1    GGFK01009838    MBW43159.1    CM000159    EDW93443.1    FX985692    BBA84430.1    ADMH02001685    ETN61439.1    CH902618    EDV38993.1    GAKP01006198    JAC52754.1    LBMM01000796    KMQ97471.1    GBXI01014146    JAD00146.1    CH933809    EDW17557.1    GDHF01013412    JAI38902.1    CH379070    EAL30147.2    ATLV01024463    KE525352    KFB51427.1    GEZM01007639    JAV95026.1    HQ379194    ADO79639.1    GAIX01011651    JAA80909.1    OUUW01000002    SPP77576.1    SPP77577.1    GL440492    EFN65822.1    NEVH01016301    PNF25885.1    UFQT01001840    UFQT01003493    SSX31969.1    SSX35065.1    CCAG010004434    JXJN01006110    KQ971328    EEZ99767.1    LC096257    BAW19561.1    APCN01002287    AXCM01012496    GL445250    EFN89982.1    KQ981281    KYN43339.1    KK107152    QOIP01000007    EZA57151.1    RLU20012.1    KQ976546    KYM80955.1    ADTU01019057    JQ663527    AFI26262.1    AAAB01008960    EAA11382.2    KQ977085    KYN05918.1    KQ982557    KYQ55022.1    APGK01049592    APGK01049593    APGK01049594    BT127726    KB741156    KB632169    AEE62688.1    ENN73570.1    ERL89485.1    KQ979308    KYN21971.1    GL888413    EGI61327.1    ENN73569.1    GFDF01003084    JAV11000.1    GEBQ01011935    JAT28042.1    CH479537    EDW33672.1    GECZ01029352    GECZ01022436    GECZ01015271    JAS40417.1    JAS47333.1    JAS54498.1    AXCN02000463    NNAY01000158    OXU30451.1    SPP77578.1    KRT08680.1    GEDC01016932    GEDC01014994    JAS20366.1    JAS22304.1    KRT08681.1    AAZX01002696    KZ288193    PBC34071.1    GBHO01013975    GBRD01013839    GDHC01019818    JAG29629.1    JAG51987.1    JAP98810.1   

Proteomes

UP000218220    UP000053268    UP000007151    UP000053240    UP000002320    UP000008820    + More
UP000069940    UP000249989    UP000008792    UP000001070    UP000092553    UP000007798    UP000001292    UP000008711    UP000000803    UP000000304    UP000192221    UP000002282    UP000069272    UP000000673    UP000007801    UP000036403    UP000009192    UP000001819    UP000030765    UP000075920    UP000095301    UP000268350    UP000000311    UP000075880    UP000235965    UP000076408    UP000092444    UP000092443    UP000078200    UP000092460    UP000092445    UP000075903    UP000007266    UP000075881    UP000075882    UP000075902    UP000075840    UP000076407    UP000075883    UP000075900    UP000005203    UP000008237    UP000078541    UP000053097    UP000279307    UP000078540    UP000005205    UP000095300    UP000007062    UP000078542    UP000075809    UP000019118    UP000030742    UP000078492    UP000007755    UP000091820    UP000008744    UP000075886    UP000075884    UP000215335    UP000002358    UP000075901    UP000075885    UP000242457   

PRIDE

Q94517    I1V501   

Pfam

PF00850   Hist_deacetyl

Interpro

IPR000286   His_deacetylse        + More
IPR023696   Ureohydrolase_dom_sf       
IPR037138   His_deacetylse_dom_sf       
IPR023801   His_deacetylse_dom       
IPR003084   His_deacetylse_1       

SUPFAM

SSF52768   SSF52768       

Gene 3D

3.40.800.20    

ProteinModelPortal

A0A2A4K903   A0A194PF89   A0A212F5S3   A0A0N1IGB9   A0A1Q3EXC7   B0WJ91   + More
Q17CF0   A0A1Q3EXB1   A0A182GNN5   A0A023EUU4   B4MFY7   Q17CE9   A0A1Q3EXC6   U5EW58   B4IZ79   E3W281   E3W278   E3VX32   E3VX22   A0A0M4E8U0   B4MMY6   W8C8N5   A0A0J9RPK2   B4HU89   B3NC63   Q94517   B4QR08   A0A2M4AQV8   A0A1W4VAJ1   B4PIA1   A0A347ZJC4   A0A182FGH3   W5JF61   B3M9I7   A0A034WDK2   A0A0J7L4B5   A0A0A1WN83   B4KX99   A0A0K8VJ62   Q29EB4   A0A084WMI3   A0A182WBY2   A0A1Y1NG16   E3W282   S4NV65   A0A1I8M0Y6   A0A3B0JW31   A0A3B0J6G3   E2AL67   A0A182IKH6   A0A2J7QBD0   A0A336MS89   A0A182Y7V6   A0A1B0FJF6   A0A1A9Y199   A0A1A9UXP8   A0A1B0AZ17   A0A1A9ZWK4   A0A182V3V5   D6WG88   A0A182K1D6   A0A1L7N254   A0A182LKN9   A0A182TYI1   A0A182I495   A0A182X957   A0A182MWC0   A0A182RR67   A0A088AP92   E2B313   A0A195FTX4   A0A026WND6   A0A151I2N9   A0A158NKZ2   I1V501   A0A1I8PP67   Q7Q5D2   A0A151IM03   A0A151X3P9   J3JWV8   A0A151JAD5   F4WWT9   N6T0I9   A0A1L8DX14   A0A1A9W4R5   A0A1B6LWH4   B4HCY7   A0A1B6FBN9   A0A182QB58   A0A182NIY3   A0A232FI77   A0A3B0K2G2   A0A0R3P6D5   A0A1B6D3Z1   A0A0R3P695   K7J9J6   A0A182T387   A0A182NZT1   A0A2A3ESP9   A0A0A9YBV7  

PDB

4BKX     E-value=0,     Score=1764

KEGG

101744526    K06067 histone deacetylase 1/2 [EC:3.5.1.98] | (RefSeq) histone deacetylase Rpd3

PATHWAY

04213    Longevity regulating pathway - multiple species - Bombyx mori (domestic silkworm)
04330    Notch signaling pathway - Bombyx mori (domestic silkworm)

GO

GO:0032041   GO:0005634   GO:0046872   GO:0004407   GO:1902692   GO:0000122   GO:0070983   GO:0070822   GO:0030261   GO:0035065   GO:0050771   GO:0008340   GO:0031523   GO:0007350   GO:0003714   GO:0005705   GO:0006342   GO:2001229   GO:0016581   GO:0035098   GO:0061086   GO:0045879   GO:0005700   GO:0048477   GO:0016580   GO:0010629   GO:0016575   GO:0008134   GO:0000118   GO:0006325   GO:0017053   GO:0006355   GO:0000785   GO:0016458   GO:0045664   GO:0045892   GO:0031061   GO:0005654   GO:0005737   GO:0070932   GO:0045944   GO:0070933   GO:0005840   GO:0006412   GO:0016705   GO:0020037   GO:0006811   GO:0016020   GO:0006260  

Subcellular location

Nucleus  

Length:

483

Number of predicted TMHs:

0

Exp number of AAs in TMHs:

0.03981

Exp number, first 60 AAs:

0.0019

Total prob of N-in:

0.01053

outside

1  -  483

 

 

Pi

192.435527

Theta

167.205133

Tajima's D

0.103474

CLR

1.240932

CSRT

0.39638018099095

Interpretation

Uncertain