Histone deacetylase 6 - Caenorhabditis elegans

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Q20296 (HDA6_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 91. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Histone deacetylase 6
EC=3.5.1.98

Gene names

Name:	hda-6
ORF Names:	F41H10.6

Organism

Caenorhabditis elegans [Reference proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	955 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Probable histone deacetylase. Histone deacetylases are 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.
Catalytic activity	Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.
Cofactor	Binds 3 zinc ions per subunit By similarity.
Subcellular location	Nucleus Probable.
Sequence similarities	Belongs to the histone deacetylase family. HD type 2 subfamily. Contains 1 UBP-type zinc finger.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Chromatin regulator Hydrolase Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone H3 deacetylation Inferred from electronic annotation. Source: GOC histone H4 deacetylation Inferred from electronic annotation. Source: GOC regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
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 protein deacetylase activity Inferred from sequence or structural similarity PubMed 16525063. Source: WormBase zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

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

Isoform b (identifier: Q20296-1) 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: Derived from EST data. No experimental confirmation available.

Isoform a (identifier: Q20296-2) The sequence of this isoform differs from the canonical sequence as follows: 797-863: VTPSNYGLDI...TCPHLKEVKP → IIIGSVLNSK...VMEKLENMKL 864-955: Missing.
Note: Derived from EST data. No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 955

955

Histone deacetylase 6

PRO_0000114743

Regions

Zinc finger

873 – 934

UBP-type

Region

15 – 337

323

Histone deacetylase 1

Region

425 – 749

325

Histone deacetylase 2

Region

896 – 898

Ubiquitin binding By similarity

Region

924 – 931

Ubiquitin binding By similarity

Sites

Active site

146

1 By similarity

Active site

561

2 By similarity

Metal binding

855

Zinc 1 By similarity

Metal binding

857

Zinc 1 By similarity

Metal binding

875

Zinc 3 By similarity

Metal binding

878

Zinc 3 By similarity

Metal binding

887

Zinc 2 By similarity

Metal binding

890

Zinc 2 By similarity

Metal binding

895

Zinc 3 By similarity

Metal binding

902

Zinc 3 By similarity

Metal binding

906

Zinc 2 By similarity

Metal binding

912

Zinc 2 By similarity

Metal binding

925

Zinc 1 By similarity

Metal binding

928

Zinc 1 By similarity

Natural variations

Alternative sequence

797 – 863

VTPSN…KEVKP → IIIGSVLNSKLINKNGKSSA ATLKVKGKAATDPVKQADDS RRYNTRRRRSANDEVEDVME KLENMKL in isoform a.

VSP_007436

Alternative sequence

864 – 955

Missing in isoform a.

VSP_007437

Sequences

Sequence		Length	Mass (Da)
Isoform b [UniParc]. Last modified May 16, 2003. Version 2. Checksum: 315C314B5ACC9E0E Show »	FASTA	955	106,749
10 20 30 40 50 60 MLFEDRQKNR STGPTLIGFN QTQNEHENTV CPTHPESSDR ILKIKEALTK TKILEKCTVL 70 80 90 100 110 120 TNFLEIDDAD LEVTHDKSMV KDLMESEKKT QEDINSQCEK YDSVFMTENS MKVAKDGVAC 130 140 150 160 170 180 VRDLTNRIMA NEASNGFAVV RPPGHHADSV SPCGFCLFNN VAQAAEEAFF SGAERILIVD 190 200 210 220 230 240 LDVHHGHGTQ RIFYDDKRVL YFSIHRHEHG LFWPHLPESD FDHIGSGKGL GYNANLALNE 250 260 270 280 290 300 TGCTDSDYLS IIFHVLLPLA TQFDPHFVII SAGFDALLGD PLGGMCLTPD GYSHILYHLK 310 320 330 340 350 360 SLAQGRMLVV LEGGYNHQIS AVAVQRCVRV LLGYAPFSIE LNEAPKESTV DSCVSLVSVL 370 380 390 400 410 420 RHHWNCFDYF PSRTSLRLAQ WPIVNTKVIY NYDPTTRRAD TGEIIQDELA STEFTASDVI 430 440 450 460 470 480 PTENMETLIY FNEGDDAHFD LEEDNHPEKP ARTRRILKTL RESGVLEKCV DRNCERIATN 490 500 510 520 530 540 EEIRLVHTKK MLEHLRTTET MKDEELMEEA EKEFNSIYLT RDTLKVARKA VGAVLQSVDE 550 560 570 580 590 600 IFEKDAGQRN ALVIVRPPGH HASASKSSGF CIFNNVAVAA KYAQRRHKAK RVLILDWDVH 610 620 630 640 650 660 HGNGTQEIFY EDSNVMYMSI HRHDKGNFYP IGEPKDYSDV GEGAGEGMSV NVPFSGVQMG 670 680 690 700 710 720 DNEYQMAFQR VIMPIAYQFN PDLVLISAGF DAAVDDPLGE YKVTPETFAL MTYQLSSLAG 730 740 750 760 770 780 GRIITVLEGG YNLTSISNSA QAVCEVLQNR SMLRRLREEK EQFATKPQKI ESSCIKTIRE 790 800 810 820 830 840 VCAVQQKYWS ILKGFQVTPS NYGLDIDDEA YDDDSIDMAD QSSSSGSSSS STRPSHNLEI 850 860 870 880 890 900 MDSGPAHAVV PLATCPHLKE VKPLPPAKIN ARTACSECQI GAEVWTCLTC YKYNCGRFVN 910 920 930 940 950 EHAMMHHLSS SHPMALSMAD LSVWCYPCDS YVHNPALIGA KSAAHESKFG ETMPS « Hide
Isoform a [UniParc]. Checksum: F36CAF4F3DC93AB7 Show »	FASTA	863	97,087
10 20 30 40 50 60 MLFEDRQKNR STGPTLIGFN QTQNEHENTV CPTHPESSDR ILKIKEALTK TKILEKCTVL 70 80 90 100 110 120 TNFLEIDDAD LEVTHDKSMV KDLMESEKKT QEDINSQCEK YDSVFMTENS MKVAKDGVAC 130 140 150 160 170 180 VRDLTNRIMA NEASNGFAVV RPPGHHADSV SPCGFCLFNN VAQAAEEAFF SGAERILIVD 190 200 210 220 230 240 LDVHHGHGTQ RIFYDDKRVL YFSIHRHEHG LFWPHLPESD FDHIGSGKGL GYNANLALNE 250 260 270 280 290 300 TGCTDSDYLS IIFHVLLPLA TQFDPHFVII SAGFDALLGD PLGGMCLTPD GYSHILYHLK 310 320 330 340 350 360 SLAQGRMLVV LEGGYNHQIS AVAVQRCVRV LLGYAPFSIE LNEAPKESTV DSCVSLVSVL 370 380 390 400 410 420 RHHWNCFDYF PSRTSLRLAQ WPIVNTKVIY NYDPTTRRAD TGEIIQDELA STEFTASDVI 430 440 450 460 470 480 PTENMETLIY FNEGDDAHFD LEEDNHPEKP ARTRRILKTL RESGVLEKCV DRNCERIATN 490 500 510 520 530 540 EEIRLVHTKK MLEHLRTTET MKDEELMEEA EKEFNSIYLT RDTLKVARKA VGAVLQSVDE 550 560 570 580 590 600 IFEKDAGQRN ALVIVRPPGH HASASKSSGF CIFNNVAVAA KYAQRRHKAK RVLILDWDVH 610 620 630 640 650 660 HGNGTQEIFY EDSNVMYMSI HRHDKGNFYP IGEPKDYSDV GEGAGEGMSV NVPFSGVQMG 670 680 690 700 710 720 DNEYQMAFQR VIMPIAYQFN PDLVLISAGF DAAVDDPLGE YKVTPETFAL MTYQLSSLAG 730 740 750 760 770 780 GRIITVLEGG YNLTSISNSA QAVCEVLQNR SMLRRLREEK EQFATKPQKI ESSCIKTIRE 790 800 810 820 830 840 VCAVQQKYWS ILKGFQIIIG SVLNSKLINK NGKSSAATLK VKGKAATDPV KQADDSRRYN 850 860 TRRRRSANDE VEDVMEKLEN MKL « Hide

References

[1]	"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]. Strain: Bristol N2.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	FO081367 Genomic DNA. Translation: CCD71098.1. FO081367 Genomic DNA. Translation: CCD71099.1.
RefSeq	NP_500787.1. NM_068386.3. NP_500788.1. NM_068387.3.
UniGene	Cel.12964.
3D structure databases
ProteinModelPortal	Q20296.
SMR	Q20296. Positions 34-367, 442-793, 851-954.
ModBase	Search...
Proteomic databases
PaxDb	Q20296.
PRIDE	Q20296.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	F41H10.6b; F41H10.6b; F41H10.6.
GeneID	177316.
KEGG	cel:CELE_F41H10.6.
UCSC	Y51H1A.5.1. c. elegans.
Organism-specific databases
CTD	177316.
WormBase	F41H10.6a; CE20772; WBGene00018319; hdac-6. F41H10.6b; CE25887; WBGene00018319; hdac-6.
Phylogenomic databases
eggNOG	COG0123.
GeneTree	ENSGT00530000062809.
HOGENOM	HOG000004769.
KO	K11407.
Gene expression databases
ArrayExpress	Q20296.
Family and domain databases
Gene3D	3.30.40.10. 1 hit. 3.40.800.20. 2 hits.
InterPro	IPR000286. His_deacetylse. IPR023801. His_deacetylse_dom. IPR013083. Znf_RING/FYVE/PHD. IPR001607. Znf_UBP. [Graphical view]
PANTHER	PTHR10625. PTHR10625. 1 hit.
Pfam	PF00850. Hist_deacetyl. 2 hits. PF02148. zf-UBP. 1 hit. [Graphical view]
PRINTS	PR01270. HDASUPER.
PROSITE	PS50271. ZF_UBP. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	896234.

Entry information

Entry name

HDA6_CAEEL

Accession

Primary (citable) accession number: Q20296
Secondary accession number(s): Q9BI90, Q9BI91

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	May 16, 2003
Last modified:	May 1, 2013
This is version 91 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project

Relevant documents

Caenorhabditis elegans

Caenorhabditis elegans: entries, gene names and cross-references to WormBase

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Molecule processing

Regions

Sites

Natural variations

Sequences

References

Cross-references

Sequence databases

3D structure databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents