O17323 (HDA4_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Histone deacetylase 4
EC=3.5.1.98

Alternative name(s):
CeHDA-7
Histone deacetylase 7

Gene names

Name:	hda-4
Synonyms:	hda-7
ORF Names:	C10E2.3

Organism

Caenorhabditis elegans [Reference proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Protostomia › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	869 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 By similarity. May be involved in muscle development.
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Subunit structure	Isoform b interacts with mef-2. Ref.1
Subcellular location	Nucleus Probable.
Tissue specificity	Expressed in body-wall muscle cells, hypodermal seam cells and neuronal cells including sensory amphid neuronal processes, the nerve ring, ventral nerve cords and motor neuronal commissures. Ref.1
Sequence similarities	Belongs to the histone deacetylase family. HD type 2 subfamily.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	apoptotic process Inferred from sequence or structural similarity Ref.1. Source: WormBase growth Inferred from mutant phenotype PubMed 14551910. Source: WormBase histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC intracellular protein kinase cascade Inferred from sequence or structural similarity Ref.1. Source: WormBase locomotion Inferred from mutant phenotype PubMed 14551910. Source: WormBase negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 17170704. Source: WormBase post-embryonic body morphogenesis Inferred from mutant phenotype PubMed 14551910. Source: WormBase regulation of neuron differentiation Inferred from mutant phenotype PubMed 17170704. Source: WormBase response to DNA damage stimulus Inferred from sequence or structural similarity Ref.1. Source: WormBase transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from sequence or structural similarity Ref.1. Source: WormBase histone deacetylase complex Inferred from sequence or structural similarity Ref.1. Source: WormBase
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 calmodulin binding Inferred from sequence or structural similarity Ref.1. Source: WormBase histone deacetylase activity Inferred from sequence or structural similarity Ref.1. Source: WormBase transcription corepressor activity Inferred from sequence or structural similarity Ref.1. Source: WormBase
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform a (identifier: O17323-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: No experimental confirmation available.

Isoform b (identifier: O17323-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-53: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 869	869	Histone deacetylase 4		PRO_0000114742
Regions
	Region	460 – 802	343	Histone deacetylase
	Compositional bias	80 – 86	7	Poly-Gln
	Compositional bias	857 – 868	12	Gln-rich
Sites
	Active site	608	1	By similarity
Natural variations
	Alternative sequence	1 – 53	53	Missing in isoform b.		VSP_044209

Sequences

	Sequence		Length	Mass (Da)
	Isoform a [UniParc]. Last modified October 3, 2012. Version 3. Checksum: 0F186275170F82C3	FASTA	869	94,411
	10 20 30 40 50 60 MEEASSSTGS AGGAGPSVPN LPSTSEAAIG QTNLEPESIA LLQSQLQEYR QKQMDLIGHF 70 80 90 100 110 120 QRAQQELSVQ HMHNLYAALQ QQQQLQNLQT ERSAVNPLLI SQQHSTEDQN SGPAAPLSLA 130 140 150 160 170 180 NSLTNLLSSS NGNLSVPQTP TKEHHPTAPT SNRKCDLPRS NSTTISQLTK DRLKNMIANR 190 200 210 220 230 240 SKGESNSQSN LMSNSVTANG NGHDNGRKLK NSNSQVNVSS PHFEPYRLPT SLANAHNLQQ 250 260 270 280 290 300 ASEFQLRKVN SEPNLKMRIR AKLLSKGSSP VQHVQQNNSQ FNFTHPQLKR SDSETSQNVP 310 320 330 340 350 360 LDFMQSSSQT NLPHLMLPSP SLPNLAAAGA FHGLNLPVGQ DLNAFMAVAN LSPFLSLPSL 370 380 390 400 410 420 LNKKLELGGL TDEGDRNGLI GSSSTSSLAS NVSMGSHQYQ SLLKQQIRDL VLRRKSLVRE 430 440 450 460 470 480 DPEGEGLAEL YNGLLPQAKL QQLQALAAES GFLAKQEPTC TTGLGYDQAM VRHECCCGNN 490 500 510 520 530 540 ASHVENGGRI QSIWSKLIEH GHVQKCEKVT AKKASLEQLQ LVHSQTYTTF FAVSPTACLK 550 560 570 580 590 600 IDANSLPLKR FLQLPCGGIG VDSDTYFNDA STQTAARLAA GTLIELSSQV AEGRLKNGFA 610 620 630 640 650 660 CIRPPGHHAE HEQAMGFCFF NNVAVAVKVL QTKYPAQCAK IAIIDWDVHH GNGTQLSFEN 670 680 690 700 710 720 DPNVLYMSLH RHDKGNFFPG TGSVTEVGKN DAKGLTVNVP FSGDVMRDPE YLAAWRTVIE 730 740 750 760 770 780 PVMASFCPDF IIVSAGFDAC HGHPNALGGY EVTPEMFGYM TKSLLNYASG KVVLALEGGY 790 800 810 820 830 840 DLKSISEAAQ QCVQALIGES DDAGRLSSVA LESLPNPSAV ETLQKVIAIH KSYWPALHGQ 850 860 EAAINTTEMQ WRNLKLQVQM QQQQQQQQT
	Isoform b [UniParc]. Checksum: DB4E641C91546161	FASTA	816	88,982
	10 20 30 40 50 60 MDLIGHFQRA QQELSVQHMH NLYAALQQQQ QLQNLQTERS AVNPLLISQQ HSTEDQNSGP 70 80 90 100 110 120 AAPLSLANSL TNLLSSSNGN LSVPQTPTKE HHPTAPTSNR KCDLPRSNST TISQLTKDRL 130 140 150 160 170 180 KNMIANRSKG ESNSQSNLMS NSVTANGNGH DNGRKLKNSN SQVNVSSPHF EPYRLPTSLA 190 200 210 220 230 240 NAHNLQQASE FQLRKVNSEP NLKMRIRAKL LSKGSSPVQH VQQNNSQFNF THPQLKRSDS 250 260 270 280 290 300 ETSQNVPLDF MQSSSQTNLP HLMLPSPSLP NLAAAGAFHG LNLPVGQDLN AFMAVANLSP 310 320 330 340 350 360 FLSLPSLLNK KLELGGLTDE GDRNGLIGSS STSSLASNVS MGSHQYQSLL KQQIRDLVLR 370 380 390 400 410 420 RKSLVREDPE GEGLAELYNG LLPQAKLQQL QALAAESGFL AKQEPTCTTG LGYDQAMVRH 430 440 450 460 470 480 ECCCGNNASH VENGGRIQSI WSKLIEHGHV QKCEKVTAKK ASLEQLQLVH SQTYTTFFAV 490 500 510 520 530 540 SPTACLKIDA NSLPLKRFLQ LPCGGIGVDS DTYFNDASTQ TAARLAAGTL IELSSQVAEG 550 560 570 580 590 600 RLKNGFACIR PPGHHAEHEQ AMGFCFFNNV AVAVKVLQTK YPAQCAKIAI IDWDVHHGNG 610 620 630 640 650 660 TQLSFENDPN VLYMSLHRHD KGNFFPGTGS VTEVGKNDAK GLTVNVPFSG DVMRDPEYLA 670 680 690 700 710 720 AWRTVIEPVM ASFCPDFIIV SAGFDACHGH PNALGGYEVT PEMFGYMTKS LLNYASGKVV 730 740 750 760 770 780 LALEGGYDLK SISEAAQQCV QALIGESDDA GRLSSVALES LPNPSAVETL QKVIAIHKSY 790 800 810 WPALHGQEAA INTTEMQWRN LKLQVQMQQQ QQQQQT

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of CeHDA-7, a class II histone deacetylase interacting with MEF-2 in Caenorhabditis elegans." Choi K.Y., Ji Y.J., Jee C., Kim do H., Ahnn J. Biochem. Biophys. Res. Commun. 293:1295-1300(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM B), TISSUE SPECIFICITY, INTERACTION WITH MEF-2. Strain: Bristol N2.
[2]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING. Strain: Bristol N2.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	FO080490, FO080492 Genomic DNA. Translation: CCD64116.1. FO080490, FO080492 Genomic DNA. Translation: CCF23337.1.
PIR	T32425.
RefSeq	NP_001257278.1. NM_001270349.1. NP_001257279.1. NM_001270350.1.
3D structure databases
ProteinModelPortal	O17323.
SMR	O17323. Positions 461-834.
ModBase	Search...
Protein-protein interaction databases
MINT	MINT-4299370.
STRING	6239.C10E2.3.
Proteomic databases
PaxDb	O17323.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	C10E2.3b; C10E2.3b; C10E2.3.
GeneID	181723.
KEGG	cel:CELE_C10E2.3.
UCSC	C10E2.3. c. elegans.
Organism-specific databases
CTD	181723.
WormBase	C10E2.3a; CE42060; WBGene00001837; hda-4. C10E2.3b; CE37192; WBGene00001837; hda-4.
Phylogenomic databases
eggNOG	COG0123.
GeneTree	ENSGT00530000062809.
HOGENOM	HOG000112870.
KO	K11406.
OMA	NGFACIR.
Gene expression databases
ArrayExpress	O17323.
Family and domain databases
Gene3D	3.40.800.20. 1 hit.
InterPro	IPR000286. His_deacetylse. IPR023801. His_deacetylse_dom. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 1 hit.
Pfam	PF00850. Hist_deacetyl. 1 hit. [Graphical view]
PRINTS	PR01270. HDASUPER.
ProtoNet	Search...
Other
NextBio	915090.

Entry information

Entry name

HDA4_CAEEL

Accession

Primary (citable) accession number: O17323
Secondary accession number(s): H1ZUW2, Q400M0

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2003
Last sequence update:	October 3, 2012
Last modified:	May 1, 2013
This is version 87 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project