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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)DescriptionActionsGraphical viewLength
Active sitei195By similarity1

GO - Molecular functioni

  • histone deacetylase activity Source: PomBase
  • histone deacetylase activity (H3-K14 specific) Source: PomBase
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC

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
  • 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

Enzyme and pathway databases

ReactomeiR-SPO-3371511. HSF1 activation.

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
Proteomesi
  • UP000002485 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)DescriptionActionsGraphical viewLength
Mutagenesisi232D → N: No activity; weak silencing defect. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001147391 – 687Histone deacetylase clr3Add BLAST687

Proteomic databases

MaxQBiP56523.
PRIDEiP56523.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi277339. 145 interactors.
DIPiDIP-59446N.
MINTiMINT-4691084.

Structurei

Secondary structure

1687
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi57 – 61Combined sources5
Helixi65 – 68Combined sources4
Helixi82 – 93Combined sources12
Beta strandi106 – 110Combined sources5
Helixi117 – 129Combined sources13
Helixi140 – 142Combined sources3
Helixi146 – 151Combined sources6
Helixi160 – 178Combined sources19
Beta strandi181 – 188Combined sources8
Helixi209 – 220Combined sources12
Turni222 – 224Combined sources3
Beta strandi228 – 232Combined sources5
Beta strandi234 – 236Combined sources3
Helixi239 – 245Combined sources7
Beta strandi249 – 258Combined sources10
Turni260 – 263Combined sources4
Helixi269 – 271Combined sources3
Helixi279 – 281Combined sources3
Beta strandi285 – 293Combined sources9
Helixi297 – 306Combined sources10
Helixi308 – 315Combined sources8
Beta strandi318 – 324Combined sources7
Turni333 – 335Combined sources3
Helixi341 – 351Combined sources11
Helixi355 – 357Combined sources3
Beta strandi359 – 363Combined sources5
Helixi369 – 383Combined sources15
Helixi398 – 411Combined sources14
Turni412 – 414Combined sources3
Helixi435 – 451Combined sources17
Beta strandi470 – 473Combined sources4
Helixi477 – 479Combined sources3
Beta strandi481 – 488Combined sources8
Beta strandi492 – 494Combined sources3
Turni506 – 508Combined sources3
Beta strandi510 – 512Combined sources3
Helixi515 – 524Combined sources10
Beta strandi528 – 533Combined sources6
Helixi548 – 562Combined sources15
Turni563 – 566Combined sources4
Beta strandi570 – 577Combined sources8
Helixi580 – 590Combined sources11
Turni594 – 596Combined sources3
Beta strandi597 – 603Combined sources7
Helixi619 – 626Combined sources8
Beta strandi628 – 632Combined sources5
Helixi637 – 639Combined sources3
Helixi647 – 649Combined sources3
Beta strandi652 – 654Combined sources3
Helixi660 – 666Combined sources7
Helixi668 – 678Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IKKX-ray2.40A31-687[»]
ProteinModelPortaliP56523.
SMRiP56523.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni55 – 385Histone deacetylaseAdd BLAST331

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000161343.
InParanoidiP56523.
KOiK11407.
OMAiCYDDRMK.
OrthoDBiEOG092C3GJU.
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IKKX-ray2.40A31-687[»]
ProteinModelPortaliP56523.
SMRiP56523.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277339. 145 interactors.
DIPiDIP-59446N.
MINTiMINT-4691084.

Proteomic databases

MaxQBiP56523.
PRIDEiP56523.

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

HOGENOMiHOG000161343.
InParanoidiP56523.
KOiK11407.
OMAiCYDDRMK.
OrthoDBiEOG092C3GJU.
PhylomeDBiP56523.

Enzyme and pathway databases

ReactomeiR-SPO-3371511. HSF1 activation.

Miscellaneous databases

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...

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: November 2, 2016
This is version 116 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.