P53973 (HDA1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone deacetylase HDA1
EC=3.5.1.98

Gene names

Name:	HDA1
Ordered Locus Names:	YNL021W
ORF Names:	N2819

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	706 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.
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Subcellular location	Nucleus.
Miscellaneous	Present with 3050 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the histone deacetylase family. HD type 2 subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	gene silencing by RNA Inferred from mutant phenotype PubMed 18022365. Source: SGD gene silencing involved in chronological cell aging Inferred from mutant phenotype PubMed 18022365. Source: SGD histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC negative regulation of chromatin silencing involved in replicative cell aging Inferred from mutant phenotype PubMed 10512855. Source: SGD negative regulation of transcription by transcription factor localization Inferred from genetic interaction PubMed 17974563. Source: SGD negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 11172717PubMed 17121596. Source: SGD positive regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 17706600. Source: SGD regulation of chromatin silencing at telomere Inferred from mutant phenotype Ref.3. Source: SGD regulation of transcription by chromatin organization Inferred from mutant phenotype PubMed 11867538. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	HDA1 complex Inferred from direct assay PubMed 11287668PubMed 8663039Ref.3. Source: SGD
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 chromatin binding Inferred from direct assay PubMed 16415367. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		5	EBI-8206,EBI-8206
HDA2	Q06629	7	EBI-8206,EBI-32800
HDA3	Q06623	7	EBI-8206,EBI-38663

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 706	706	Histone deacetylase HDA1		PRO_0000114738
Regions
	Region	67 – 396	330	Histone deacetylase
Sites
	Active site	206	1	By similarity

Sequences

	Sequence		Length	Mass (Da)
	P53973 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: 4E7069E66D03264D	FASTA	706	80,070
	10 20 30 40 50 60 MDSVMVKKEV LENPDHDLKR KLEENKEEEN SLSTTSKSKR QVIVPVCMPK IHYSPLKTGL 70 80 90 100 110 120 CYDVRMRYHA KIFTSYFEYI DPHPEDPRRI YRIYKILAEN GLINDPTLSG VDDLGDLMLK 130 140 150 160 170 180 IPVRAATSEE ILEVHTKEHL EFIESTEKMS REELLKETEK GDSVYFNNDS YASARLPCGG 190 200 210 220 230 240 AIEACKAVVE GRVKNSLAVV RPPGHHAEPQ AAGGFCLFSN VAVAAKNILK NYPESVRRIM 250 260 270 280 290 300 ILDWDIHHGN GTQKSFYQDD QVLYVSLHRF EMGKYYPGTI QGQYDQTGEG KGEGFNCNIT 310 320 330 340 350 360 WPVGGVGDAE YMWAFEQVVM PMGREFKPDL VIISSGFDAA DGDTIGQCHV TPSCYGHMTH 370 380 390 400 410 420 MLKSLARGNL CVVLEGGYNL DAIARSALSV AKVLIGEPPD ELPDPLSDPK PEVIEMIDKV 430 440 450 460 470 480 IRLQSKYWNC FRRRHANSGC NFNEPINDSI ISKNFPLQKA IRQQQQHYLS DEFNFVTLPL 490 500 510 520 530 540 VSMDLPDNTV LCTPNISESN TIIIVVHDTS DIWAKRNVIS GTIDLSSSVI IDNSLDFIKW 550 560 570 580 590 600 GLDRKYGIID VNIPLTLFEP DNYSGMITSQ EVLIYLWDNY IKYFPSVAKI AFIGIGDSYS 610 620 630 640 650 660 GIVHLLGHRD TRAVTKTVIN FLGDKQLKPL VPLVDETLSE WYFKNSLIFS NNSHQCWKEN 670 680 690 700 ESRKPRKKFG RVLRCDTDGL NNIIEERFEE ATDFILDSFE EWSDEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription." Rundlett S.E., Carmen A.A., Kobayashi R., Bavykin S., Turner B.M., Grunstein M. Proc. Natl. Acad. Sci. U.S.A. 93:14503-14508(1996) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[4]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z71297 Genomic DNA. Translation: CAA95883.1. BK006947 Genomic DNA. Translation: DAA10524.1.
PIR	S62933.
RefSeq	NP_014377.1. NM_001182860.1.
3D structure databases
ProteinModelPortal	P53973.
SMR	P53973. Positions 55-439.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1360N.
IntAct	P53973. 17 interactions.
MINT	MINT-387448.
STRING	4932.YNL021W.
Proteomic databases
PaxDb	P53973.
PeptideAtlas	P53973.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YNL021W; YNL021W; YNL021W.
GeneID	855710.
KEGG	sce:YNL021W.
Organism-specific databases
CYGD	YNL021w.
SGD	S000004966. HDA1.
Phylogenomic databases
eggNOG	COG0123.
GeneTree	ENSGT00530000062809.
HOGENOM	HOG000161343.
KO	K11407.
OMA	IDPHPED.
OrthoDB	EOG498Z80.
Gene expression databases
Genevestigator	P53973.
GermOnline	YNL021W. Saccharomyces cerevisiae.
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	980058.

Entry information

Entry name

HDA1_YEAST

Accession

Primary (citable) accession number: P53973
Secondary accession number(s): D6W1F8

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	May 1, 2013
This is version 108 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program