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Protein

Histone deacetylase clr3

Gene

clr3

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Required for proper positioning of nucleosomes at heterochromatic loci and for transcriptional gene silencing (TGS) function of the Snf2/Hdac-containing repressor complex (SHREC).1 Publication

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei195 – 1951By similarity

GO - Molecular functioni

GO - Biological processi

  • chromatin silencing at centromere Source: PomBase
  • chromatin silencing at rDNA Source: PomBase
  • chromatin silencing at silent mating-type cassette Source: PomBase
  • chromatin silencing at telomere Source: PomBase
  • histone deacetylation Source: PomBase
  • histone H3 deacetylation Source: GOC
  • maintenance of chromatin silencing at silent mating-type cassette Source: PomBase
  • negative regulation of transcription from RNA polymerase II promoter Source: PomBase
  • nucleosome positioning Source: PomBase
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase clr3 (EC:3.5.1.98)
Alternative name(s):
Cryptic loci regulator 3
Gene namesi
Name:clr3
ORF Names:SPBC800.03
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
ProteomesiUP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC800.03.
PomBaseiSPBC800.03. clr3.

Subcellular locationi

GO - Cellular componenti

  • chromosome, telomeric region Source: UniProtKB-SubCell
  • mating-type region heterochromatin Source: PomBase
  • nuclear chromatin Source: PomBase
  • nuclear pericentric heterochromatin Source: PomBase
  • nuclear subtelomeric heterochromatin Source: PomBase
  • nucleolar chromatin Source: PomBase
  • nucleus Source: PomBase
  • rDNA heterochromatin Source: PomBase
  • SHREC complex Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus, Telomere

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi232 – 2321D → N: No activity; weak silencing defect. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 687687Histone deacetylase clr3PRO_0000114739Add
BLAST

Proteomic databases

MaxQBiP56523.

Interactioni

Subunit structurei

Interacts with ccq1, clr1, clr2 and mit1.1 Publication

Protein-protein interaction databases

BioGridi277339. 138 interactions.
DIPiDIP-59446N.
MINTiMINT-4691084.
STRINGi4896.SPBC800.03.1.

Structurei

3D structure databases

ProteinModelPortaliP56523.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni55 – 385331Histone deacetylaseAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0123.
HOGENOMiHOG000161343.
InParanoidiP56523.
KOiK11407.
OMAiCYDDRMK.
OrthoDBiEOG75B8GB.
PhylomeDBiP56523.

Family and domain databases

Gene3Di3.40.800.20. 1 hit.
InterProiIPR019154. Arb2_domain.
IPR000286. His_deacetylse.
IPR023801. His_deacetylse_dom.
IPR017321. Hist_deAcase_II_yeast.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF09757. Arb2. 1 hit.
PF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFiPIRSF037919. HDAC_II_yeast. 1 hit.
PRINTSiPR01270. HDASUPER.

Sequencei

Sequence statusi: Complete.

P56523-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLASNSDGAS TSVKPSDDAV NTVTPWSILL TNNKPMSGSE NTLNNESHEM
60 70 80 90 100
SQILKKSGLC YDPRMRFHAT LSEVDDHPED PRRVLRVFEA IKKAGYVSNV
110 120 130 140 150
PSPSDVFLRI PAREATLEEL LQVHSQEMYD RVTNTEKMSH EDLANLEKIS
160 170 180 190 200
DSLYYNNESA FCARLACGSA IETCTAVVTG QVKNAFAVVR PPGHHAEPHK
210 220 230 240 250
PGGFCLFNNV SVTARSMLQR FPDKIKRVLI VDWDIHHGNG TQMAFYDDPN
260 270 280 290 300
VLYVSLHRYE NGRFYPGTNY GCAENCGEGP GLGRTVNIPW SCAGMGDGDY
310 320 330 340 350
IYAFQRVVMP VAYEFDPDLV IVSCGFDAAA GDHIGQFLLT PAAYAHMTQM
360 370 380 390 400
LMGLADGKVF ISLEGGYNLD SISTSALAVA QSLLGIPPGR LHTTYACPQA
410 420 430 440 450
VATINHVTKI QSQYWRCMRP KHFDANPKDA HVDRLHDVIR TYQAKKLFED
460 470 480 490 500
WKITNMPILR DSVSNVFNNQ VLCSSNFFQK DNLLVIVHES PRVLGNGTSE
510 520 530 540 550
TNVLNLNDSL LVDPVSLYVE WAMQQDWGLI DINIPEVVTD GENAPVDILS
560 570 580 590 600
EVKELCLYVW DNYVELSISK NIFFIGGGKA VHGLVNLASS RNVSDRVKCM
610 620 630 640 650
VNFLGTEPLV GLKTASEEDL PTWYYRHSLV FVSSSNECWK KAKRAKRRYG
660 670 680
RLMQSEHTET SDMMEQHYRA VTQYLLHLLQ KARPTSQ
Length:687
Mass (Da):76,792
Last modified:July 15, 1998 - v1
Checksum:i6B0E4184A056D899
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF064207 Genomic DNA. Translation: AAD05212.1.
CU329671 Genomic DNA. Translation: CAC01518.1.
PIRiT43797.
RefSeqiNP_595104.1. NM_001021011.2.

Genome annotation databases

EnsemblFungiiSPBC800.03.1; SPBC800.03.1:pep; SPBC800.03.
GeneIDi2540821.
KEGGispo:SPBC800.03.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF064207 Genomic DNA. Translation: AAD05212.1.
CU329671 Genomic DNA. Translation: CAC01518.1.
PIRiT43797.
RefSeqiNP_595104.1. NM_001021011.2.

3D structure databases

ProteinModelPortaliP56523.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277339. 138 interactions.
DIPiDIP-59446N.
MINTiMINT-4691084.
STRINGi4896.SPBC800.03.1.

Proteomic databases

MaxQBiP56523.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC800.03.1; SPBC800.03.1:pep; SPBC800.03.
GeneIDi2540821.
KEGGispo:SPBC800.03.

Organism-specific databases

EuPathDBiFungiDB:SPBC800.03.
PomBaseiSPBC800.03. clr3.

Phylogenomic databases

eggNOGiCOG0123.
HOGENOMiHOG000161343.
InParanoidiP56523.
KOiK11407.
OMAiCYDDRMK.
OrthoDBiEOG75B8GB.
PhylomeDBiP56523.

Miscellaneous databases

NextBioi20801938.
PROiP56523.

Family and domain databases

Gene3Di3.40.800.20. 1 hit.
InterProiIPR019154. Arb2_domain.
IPR000286. His_deacetylse.
IPR023801. His_deacetylse_dom.
IPR017321. Hist_deAcase_II_yeast.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF09757. Arb2. 1 hit.
PF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFiPIRSF037919. HDAC_II_yeast. 1 hit.
PRINTSiPR01270. HDASUPER.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast."
    Grewal S.I.S., Bonaduce M.J., Klar A.J.S.
    Genetics 150:563-576(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  3. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  4. "SHREC, an effector complex for heterochromatic transcriptional silencing."
    Sugiyama T., Cam H.P., Sugiyama R., Noma K., Zofall M., Kobayashi R., Grewal S.I.S.
    Cell 128:491-504(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH CCQ1; CLR1; CLR2 AND MIT1, SUBCELLULAR LOCATION, MUTAGENESIS OF ASP-232.

Entry informationi

Entry nameiCLR3_SCHPO
AccessioniPrimary (citable) accession number: P56523
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: July 15, 1998
Last modified: June 24, 2015
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.