CLR3_SCHPO
ID CLR3_SCHPO Reviewed; 687 AA.
AC P56523;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Histone deacetylase clr3;
DE EC=3.5.1.98 {ECO:0000269|PubMed:17289569};
DE AltName: Full=Cryptic loci regulator 3;
GN Name=clr3; ORFNames=SPBC800.03;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=9755190; DOI=10.1093/genetics/150.2.563;
RA Grewal S.I.S., Bonaduce M.J., Klar A.J.S.;
RT "Histone deacetylase homologs regulate epigenetic inheritance of
RT transcriptional silencing and chromosome segregation in fission yeast.";
RL Genetics 150:563-576(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [3]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=16823372; DOI=10.1038/nbt1222;
RA Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
RA Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
RA Yoshida M.;
RT "ORFeome cloning and global analysis of protein localization in the fission
RT yeast Schizosaccharomyces pombe.";
RL Nat. Biotechnol. 24:841-847(2006).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH CCQ1; CLR1; CLR2 AND MIT1,
RP SUBCELLULAR LOCATION, AND MUTAGENESIS OF ASP-232.
RX PubMed=17289569; DOI=10.1016/j.cell.2006.12.035;
RA Sugiyama T., Cam H.P., Sugiyama R., Noma K., Zofall M., Kobayashi R.,
RA Grewal S.I.S.;
RT "SHREC, an effector complex for heterochromatic transcriptional
RT silencing.";
RL Cell 128:491-504(2007).
CC -!- FUNCTION: Responsible for the deacetylation of lysine residues on the
CC N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone
CC deacetylation gives a tag for epigenetic repression and plays an
CC important role in transcriptional regulation, cell cycle progression
CC and developmental events. Histone deacetylases act via the formation of
CC large multiprotein complexes. Required for proper positioning of
CC nucleosomes at heterochromatic loci and for transcriptional gene
CC silencing (TGS) function of the Snf2/Hdac-containing repressor complex
CC (SHREC). {ECO:0000269|PubMed:17289569}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-
CC [histone]; Xref=Rhea:RHEA:58196, Rhea:RHEA-COMP:9845, Rhea:RHEA-
CC COMP:11338, ChEBI:CHEBI:15377, ChEBI:CHEBI:29969, ChEBI:CHEBI:30089,
CC ChEBI:CHEBI:61930; EC=3.5.1.98;
CC Evidence={ECO:0000269|PubMed:17289569};
CC -!- SUBUNIT: Interacts with ccq1, clr1, clr2 and mit1.
CC {ECO:0000269|PubMed:17289569}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17289569}.
CC Chromosome, centromere {ECO:0000269|PubMed:17289569}. Chromosome,
CC telomere {ECO:0000269|PubMed:17289569}. Note=Associates with major
CC heterochromatin, centromeres, sub-telomeres, rDNA and the mat locus.
CC {ECO:0000269|PubMed:17289569}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC subfamily. {ECO:0000305}.
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DR EMBL; AF064207; AAD05212.1; -; Genomic_DNA.
DR EMBL; CU329671; CAC01518.1; -; Genomic_DNA.
DR PIR; T43797; T43797.
DR RefSeq; NP_595104.1; NM_001021011.2.
DR PDB; 5IKK; X-ray; 2.40 A; A=31-687.
DR PDBsum; 5IKK; -.
DR AlphaFoldDB; P56523; -.
DR SMR; P56523; -.
DR BioGRID; 277339; 157.
DR DIP; DIP-59446N; -.
DR IntAct; P56523; 1.
DR STRING; 4896.SPBC800.03.1; -.
DR ESTHER; schpo-clr3; Arb2_domain.
DR MaxQB; P56523; -.
DR PaxDb; P56523; -.
DR EnsemblFungi; SPBC800.03.1; SPBC800.03.1:pep; SPBC800.03.
DR GeneID; 2540821; -.
DR KEGG; spo:SPBC800.03; -.
DR PomBase; SPBC800.03; clr3.
DR VEuPathDB; FungiDB:SPBC800.03; -.
DR eggNOG; KOG1343; Eukaryota.
DR HOGENOM; CLU_007727_4_0_1; -.
DR InParanoid; P56523; -.
DR OMA; FVSPACY; -.
DR PhylomeDB; P56523; -.
DR Reactome; R-SPO-3214815; HDACs deacetylate histones.
DR Reactome; R-SPO-3371511; HSF1 activation.
DR Reactome; R-SPO-4551638; SUMOylation of chromatin organization proteins.
DR Reactome; R-SPO-5617833; Cilium Assembly.
DR Reactome; R-SPO-9646399; Aggrephagy.
DR PRO; PR:P56523; -.
DR Proteomes; UP000002485; Chromosome II.
DR GO; GO:0000785; C:chromatin; IDA:PomBase.
DR GO; GO:0099115; C:chromosome, subtelomeric region; IDA:PomBase.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:1990342; C:heterochromatin island; IDA:PomBase.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
DR GO; GO:0031934; C:mating-type region heterochromatin; IDA:PomBase.
DR GO; GO:0005730; C:nucleolus; IDA:PomBase.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0005721; C:pericentric heterochromatin; IDA:PomBase.
DR GO; GO:0033553; C:rDNA heterochromatin; IDA:PomBase.
DR GO; GO:0070824; C:SHREC complex; IDA:PomBase.
DR GO; GO:0110129; C:SHREC2 complex; IDA:PomBase.
DR GO; GO:0140720; C:subtelomeric heterochromatin; EXP:PomBase.
DR GO; GO:0004407; F:histone deacetylase activity; IDA:PomBase.
DR GO; GO:0031078; F:histone deacetylase activity (H3-K14 specific); IMP:PomBase.
DR GO; GO:0006325; P:chromatin organization; IMP:PomBase.
DR GO; GO:0031507; P:heterochromatin assembly; IMP:PomBase.
DR GO; GO:0016575; P:histone deacetylation; IBA:GO_Central.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0090053; P:positive regulation of pericentric heterochromatin assembly; IMP:CACAO.
DR GO; GO:0000183; P:rDNA heterochromatin assembly; IMP:PomBase.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:PomBase.
DR GO; GO:0030466; P:silent mating-type cassette heterochromatin assembly; IMP:PomBase.
DR Gene3D; 3.40.800.20; -; 1.
DR InterPro; IPR019154; Arb2_domain.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR023801; His_deacetylse_dom.
DR InterPro; IPR037138; His_deacetylse_dom_sf.
DR InterPro; IPR017321; Hist_deAcase_II_yeast.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR Pfam; PF09757; Arb2; 1.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PIRSF; PIRSF037919; HDAC_II_yeast; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Centromere; Chromatin regulator; Chromosome; Hydrolase;
KW Nucleus; Reference proteome; Repressor; Telomere; Transcription;
KW Transcription regulation.
FT CHAIN 1..687
FT /note="Histone deacetylase clr3"
FT /id="PRO_0000114739"
FT REGION 55..385
FT /note="Histone deacetylase"
FT ACT_SITE 195
FT /evidence="ECO:0000250"
FT MUTAGEN 232
FT /note="D->N: No histone deacetylase activity; weak
FT silencing defect."
FT /evidence="ECO:0000269|PubMed:17289569"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 65..68
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 82..93
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 117..129
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 146..151
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 160..178
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 181..188
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 209..220
FT /evidence="ECO:0007829|PDB:5IKK"
FT TURN 222..224
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 228..232
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 239..245
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 249..258
FT /evidence="ECO:0007829|PDB:5IKK"
FT TURN 260..263
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 279..281
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 285..293
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 297..306
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 308..315
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 318..324
FT /evidence="ECO:0007829|PDB:5IKK"
FT TURN 333..335
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 341..351
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 355..357
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 369..383
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 398..411
FT /evidence="ECO:0007829|PDB:5IKK"
FT TURN 412..414
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 435..451
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 470..473
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 477..479
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 481..488
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 492..494
FT /evidence="ECO:0007829|PDB:5IKK"
FT TURN 506..508
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 510..512
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 515..524
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 528..533
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 548..562
FT /evidence="ECO:0007829|PDB:5IKK"
FT TURN 563..566
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 570..577
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 580..590
FT /evidence="ECO:0007829|PDB:5IKK"
FT TURN 594..596
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 597..603
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 619..626
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 628..632
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 637..639
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 647..649
FT /evidence="ECO:0007829|PDB:5IKK"
FT STRAND 652..654
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 660..666
FT /evidence="ECO:0007829|PDB:5IKK"
FT HELIX 668..678
FT /evidence="ECO:0007829|PDB:5IKK"
SQ SEQUENCE 687 AA; 76792 MW; 6B0E4184A056D899 CRC64;
MLASNSDGAS TSVKPSDDAV NTVTPWSILL TNNKPMSGSE NTLNNESHEM SQILKKSGLC
YDPRMRFHAT LSEVDDHPED PRRVLRVFEA IKKAGYVSNV PSPSDVFLRI PAREATLEEL
LQVHSQEMYD RVTNTEKMSH EDLANLEKIS DSLYYNNESA FCARLACGSA IETCTAVVTG
QVKNAFAVVR PPGHHAEPHK PGGFCLFNNV SVTARSMLQR FPDKIKRVLI VDWDIHHGNG
TQMAFYDDPN VLYVSLHRYE NGRFYPGTNY GCAENCGEGP GLGRTVNIPW SCAGMGDGDY
IYAFQRVVMP VAYEFDPDLV IVSCGFDAAA GDHIGQFLLT PAAYAHMTQM LMGLADGKVF
ISLEGGYNLD SISTSALAVA QSLLGIPPGR LHTTYACPQA VATINHVTKI QSQYWRCMRP
KHFDANPKDA HVDRLHDVIR TYQAKKLFED WKITNMPILR DSVSNVFNNQ VLCSSNFFQK
DNLLVIVHES PRVLGNGTSE TNVLNLNDSL LVDPVSLYVE WAMQQDWGLI DINIPEVVTD
GENAPVDILS EVKELCLYVW DNYVELSISK NIFFIGGGKA VHGLVNLASS RNVSDRVKCM
VNFLGTEPLV GLKTASEEDL PTWYYRHSLV FVSSSNECWK KAKRAKRRYG RLMQSEHTET
SDMMEQHYRA VTQYLLHLLQ KARPTSQ
