P56523 (CLR3_SCHPO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone deacetylase clr3
EC=3.5.1.98

Alternative name(s):
Cryptic loci regulator 3

Gene names

Name:	clr3
ORF Names:	SPBC800.03

Organism

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) [Reference proteome]

Taxonomic identifier

284812 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › Taphrinomycotina › Schizosaccharomycetes › Schizosaccharomycetales › Schizosaccharomycetaceae › Schizosaccharomyces › Schizosaccharomyces pombe

Protein attributes

Sequence length	687 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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). Ref.4
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Subunit structure	Interacts with ccq1, clr1, clr2 and mit1. Ref.4
Subcellular location	Nucleus. Chromosome › centromere. Chromosome › telomere. Note: Associates with major heterochromatin, centromeres, sub-telomeres, rDNA and the mat locus. Ref.3 Ref.4
Sequence similarities	Belongs to the histone deacetylase family. HD type 2 subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Centromere Chromosome Nucleus Telomere
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cellular response to cadmium ion Inferred from mutant phenotype PubMed 18684775. Source: PomBase chromatin silencing at centromere Inferred from mutant phenotype Ref.1. Source: PomBase chromatin silencing at rDNA Inferred from mutant phenotype PubMed 11884604. Source: PomBase chromatin silencing at telomere Inferred from mutant phenotype Ref.1. Source: PomBase detoxification of cadmium ion Inferred from mutant phenotype PubMed 18684775. Source: PomBase histone H4 deacetylation Inferred from electronic annotation. Source: GOC maintenance of chromatin silencing at silent mating-type cassette Non-traceable author statement. Source: PomBase negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.4. Source: PomBase nucleosome positioning Inferred from mutant phenotype Ref.4. Source: PomBase regulation of histone methylation Inferred from mutant phenotype PubMed 11283354. Source: PomBase transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	SHREC complex Inferred from direct assay Ref.4. Source: PomBase centromeric heterochromatin Inferred from direct assay Ref.4. Source: PomBase mating-type region heterochromatin Inferred from direct assay Ref.4. Source: PomBase nucleolar chromatin Inferred from direct assay PubMed 11884604. Source: PomBase rDNA heterochromatin Inferred from direct assay Ref.4. Source: PomBase telomeric heterochromatin Inferred from direct assay Ref.4. Source: PomBase
Molecular_function	NAD-dependent histone deacetylase activity (H3-K14 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K18 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H3-K9 specific) Inferred from electronic annotation. Source: EC NAD-dependent histone deacetylase activity (H4-K16 specific) Inferred from electronic annotation. Source: EC histone deacetylase activity (H3-K14 specific) Inferred from mutant phenotype PubMed 11884604. Source: PomBase
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 687	687	Histone deacetylase clr3		PRO_0000114739
Regions
	Region	55 – 385	331	Histone deacetylase
Sites
	Active site	195	1	By similarity
Experimental info
	Mutagenesis	232	1	D → N: No activity; weak silencing defect. Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P56523 [UniParc]. Last modified July 15, 1998. Version 1. Checksum: 6B0E4184A056D899	FASTA	687	76,792
	10 20 30 40 50 60 MLASNSDGAS TSVKPSDDAV NTVTPWSILL TNNKPMSGSE NTLNNESHEM SQILKKSGLC 70 80 90 100 110 120 YDPRMRFHAT LSEVDDHPED PRRVLRVFEA IKKAGYVSNV PSPSDVFLRI PAREATLEEL 130 140 150 160 170 180 LQVHSQEMYD RVTNTEKMSH EDLANLEKIS DSLYYNNESA FCARLACGSA IETCTAVVTG 190 200 210 220 230 240 QVKNAFAVVR PPGHHAEPHK PGGFCLFNNV SVTARSMLQR FPDKIKRVLI VDWDIHHGNG 250 260 270 280 290 300 TQMAFYDDPN VLYVSLHRYE NGRFYPGTNY GCAENCGEGP GLGRTVNIPW SCAGMGDGDY 310 320 330 340 350 360 IYAFQRVVMP VAYEFDPDLV IVSCGFDAAA GDHIGQFLLT PAAYAHMTQM LMGLADGKVF 370 380 390 400 410 420 ISLEGGYNLD SISTSALAVA QSLLGIPPGR LHTTYACPQA VATINHVTKI QSQYWRCMRP 430 440 450 460 470 480 KHFDANPKDA HVDRLHDVIR TYQAKKLFED WKITNMPILR DSVSNVFNNQ VLCSSNFFQK 490 500 510 520 530 540 DNLLVIVHES PRVLGNGTSE TNVLNLNDSL LVDPVSLYVE WAMQQDWGLI DINIPEVVTD 550 560 570 580 590 600 GENAPVDILS EVKELCLYVW DNYVELSISK NIFFIGGGKA VHGLVNLASS RNVSDRVKCM 610 620 630 640 650 660 VNFLGTEPLV GLKTASEEDL PTWYYRHSLV FVSSSNECWK KAKRAKRRYG RLMQSEHTET 670 680 SDMMEQHYRA VTQYLLHLLQ KARPTSQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF064207 Genomic DNA. Translation: AAD05212.1. CU329671 Genomic DNA. Translation: CAC01518.1.
PIR	T43797.
RefSeq	NP_595104.1. NM_001021011.2.
3D structure databases
ProteinModelPortal	P56523.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-59446N.
STRING	4896.SPBC800.03-1.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	SPBC800.03.1; SPBC800.03.1:pep; SPBC800.03.
GeneID	2540821.
KEGG	spo:SPBC800.03.
Organism-specific databases
PomBase	SPBC800.03.
Phylogenomic databases
eggNOG	COG0123.
HOGENOM	HOG000161343.
KO	K11407.
OMA	IDPHPED.
OrthoDB	EOG498Z80.
Family and domain databases
Gene3D	3.40.800.20. 1 hit.
InterPro	IPR019154. Arb2_domain. IPR000286. His_deacetylse. IPR023801. His_deacetylse_dom. IPR017321. Hist_deAcase_II_yeast. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 1 hit.
Pfam	PF09757. Arb2. 1 hit. PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PIRSF	PIRSF037919. HDAC_II_yeast. 1 hit.
PRINTS	PR01270. HDASUPER.
ProtoNet	Search...
Other
NextBio	20801938.

Entry information

Entry name

CLR3_SCHPO

Accession

Primary (citable) accession number: P56523

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	July 15, 1998
Last modified:	May 1, 2013
This is version 93 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program