Q06623 (HDA3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
HDA1 complex subunit 3

Alternative name(s):
Histone deacetylase complex 1 subunit 3

Gene names

Name:	HDA3
Synonyms:	PLO1
Ordered Locus Names:	YPR179C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	655 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for activity of HDA1 histone deacetylase complex. The HDA1 histone deacetylase complex is 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. Ref.3 Ref.4
Subunit structure	Heterodimer with HDA2. Component of the HDA1 histone deacetylase complex composed of at least one HDA1 homodimer and one HDA2/HDA3 heterodimer. Interacts with HDA1 and HDA3. Ref.4
Subcellular location	Nucleus Ref.5.
Miscellaneous	Present with 1100 molecules/cell in log phase SD medium. Ref.6
Sequence similarities	Belongs to the HDA2/3 family. HDA3 subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Coiled coil
Molecular function	Chromatin regulator Repressor
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	chromosome segregation Inferred from mutant phenotype. Source: SGD gene silencing by RNA Inferred from mutant phenotype. Source: SGD gene silencing involved in chronological cell aging Inferred from mutant phenotype. Source: SGD histone deacetylation Inferred from direct assay Ref.4Ref.3. Source: SGD negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.4. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	HDA1 complex Inferred from direct assay Ref.4Ref.3. Source: SGD
Molecular function	DNA binding Inferred from direct assay. Source: SGD chromatin binding Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
HDA1	P53973	7	EBI-38663,EBI-8206
HDA2	Q06629	5	EBI-38663,EBI-32800

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 655

655

HDA1 complex subunit 3

PRO_0000083932

Regions

Coiled coil

482 – 632

151

Potential

Secondary structure

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655

Helix Strand Turn

Details...

Beta strand

31 – 35

5

Helix

39 – 51

13

Helix

53 – 61

9

Turn

62 – 65

4

Helix

68 – 79

12

Helix

83 – 86

4

Helix

88 – 90

3

Helix

105 – 111

7

Helix

116 – 126

11

Beta strand

131 – 137

7

Helix

142 – 150

9

Beta strand

156 – 159

4

Beta strand

175 – 182

8

Turn

188 – 190

3

Beta strand

200 – 204

5

Helix

214 – 220

7

Beta strand

235 – 240

6

Helix

244 – 250

7

Helix

260 – 272

13

Helix

273 – 275

3

Turn

282 – 284

3

Helix

285 – 289

5

Turn

290 – 292

3

Helix

293 – 295

3

Helix

296 – 300

5

Helix

319 – 328

10

Sequences

	Sequence		Length	Mass (Da)
	Q06623 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: CC8F8F73D6B78E45	FASTA	655	75,463
	10 20 30 40 50 60 MDLLRILDTK PIPTIVDATT LGISGNTSGD YWLPTTMSLY QKELTDQIVS LHYSDILRYF 70 80 90 100 110 120 ETSHYKEDVI LESMKTMCLN GSLVATHPYL LIDHYMPKSL ITRDVPAHLA ENSGKFSVLR 130 140 150 160 170 180 DLINLVQEYE TETAIVCRPG RTMDLLEALL LGNKVHIKRY DGHSIKSKQK ANDFSCTVHL 190 200 210 220 230 240 FSSEGINFTK YPIKSKARFD MLICLDTTVD TSQKDIQYLL QYKRERKGLE RYAPIVRLVA 250 260 270 280 290 300 INSIDHCRLF FGKKFDKNSR EYLENVTAAM VILRDRLGTL PPDLRPIYSQ KLHYLVEWLE 310 320 330 340 350 360 NPTVPWPLPD IYPLKQYTSM DVERSLLTEV HFKKSDDQLE DAFSNCSKKR GRHGANKAAS 370 380 390 400 410 420 STVAGIEDNI TPSFYSTKRL KNDYYTNPLK QDMTQLTGIT TADNSSNVNY HLSSGIITHK 430 440 450 460 470 480 LIQSMGEVYM DICVQKQELD DYSCLDDLQN DHLKFFSNED EKIIKEYETV LRTNNENLNR 490 500 510 520 530 540 SHELEVENNL KFSQIETLEK DIETLKGSLM AQGETLSKLK DAFVKTDNVQ DEIEKEERVS 550 560 570 580 590 600 VSRDTEKKYM EQEIKRAVDA IRENEEETHK LNEKQNGLES ELKLKFEKSE ISTKELNEKI 610 620 630 640 650 GFLKKELKLE NDLNEELVGQ LSKTMDNLEN LTIPRVRTQN GNTKKKSRAK KPGNV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed: 9169875] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"HDA1 and HDA3 are components of a yeast histone deacetylase (HDA) complex." Carmen A.A., Rundlett S.E., Grunstein M. J. Biol. Chem. 271:15837-15844(1996) [PubMed: 8663039] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE HDA1 HISTONE DEACETYLASE COMPLEX.
[4]	"HDA2 and HDA3 are related proteins that interact with and are essential for the activity of the yeast histone deacetylase HDA1." Wu J., Carmen A.A., Kobayashi R., Suka N., Grunstein M. Proc. Natl. Acad. Sci. U.S.A. 98:4391-4396(2001) [PubMed: 11287668] [Abstract] Cited for: FUNCTION, INTERACTION WITH HDA1 AND HDA3.
[5]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[6]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U25842 Genomic DNA. Translation: AAB68112.1.
BK006949 Genomic DNA. Translation: DAA11595.1.

PIR

S59836.

RefSeq

NP_015505.1. NM_001184276.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3HGQ	X-ray	3.00	A/B/C/D	6-333	[»]
3HGT	X-ray	2.20	A/B	6-333	[»]

ProteinModelPortal

Q06623.

SMR

Q06623. Positions 27-331.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4636N.

IntAct

Q06623. 7 interactions.

MINT

MINT-563224.

STRING

Q06623.

Proteomic databases

PeptideAtlas

Q06623.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YPR179C; YPR179C; YPR179C.

GeneID

856309.

KEGG

sce:YPR179C.

NMPDR

fig|4932.3.peg.6654.

Organism-specific databases

CYGD

YPR179c.

SGD

S000006383. HDA3.

Phylogenomic databases

eggNOG

fuNOG04208.

GeneTree

EFGT00050000001913.

HOGENOM

HBG204014.

OMA

YQKELTD.

OrthoDB

EOG418FX1.

Gene expression databases

ArrayExpress

Q06623.

Genevestigator

Q06623.

GermOnline

YPR179C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR021006. HDA_complex_subunit-2/3.
[Graphical view]

Pfam

PF11496. HDA2-3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

981679.

Entry information

Entry name

HDA3_YEAST

Accession

Primary (citable) accession number: Q06623
Secondary accession number(s): D6W4H9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 25, 2005
Last sequence update:	November 1, 1996
Last modified:	December 14, 2011
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program