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Protein

Elongator complex protein 3

Gene

elp3

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Catalytic histone acetyltransferase subunit of the RNA polymerase II elongator complex, which is a component of the RNA polymerase II (Pol II) holoenzyme and is involved in transcriptional elongation. Elongator may play a role in chromatin remodeling. Involved in acetylation of alpha-tubulin (By similarity). May also have a methyltransferase activity (By similarity). Involved in neurogenesis (PubMed:18996918).1 PublicationBy similarity

Catalytic activityi

Acetyl-CoA + [histone] = CoA + acetyl-[histone].

Cofactori

[4Fe-4S] clusterBy similarityNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi100 – 1001Iron-sulfur (4Fe-4S-S-AdoMet)By similarity
Metal bindingi110 – 1101Iron-sulfur (4Fe-4S-S-AdoMet)By similarity
Metal bindingi113 – 1131Iron-sulfur (4Fe-4S-S-AdoMet)By similarity

GO - Molecular functioni

  1. histone acetyltransferase activity Source: GO_Central
  2. iron-sulfur cluster binding Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW
  4. phosphorylase kinase regulator activity Source: UniProtKB

GO - Biological processi

  1. axonogenesis Source: ZFIN
  2. histone acetylation Source: GO_Central
  3. regulation of protein kinase activity Source: GOC
  4. regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  5. transcription elongation from RNA polymerase II promoter Source: GO_Central
  6. tRNA wobble uridine modification Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Neurogenesis, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

ReactomeiREACT_310649. HATs acetylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Elongator complex protein 3 (EC:2.3.1.48)
Gene namesi
Name:elp3
ORF Names:si:ch211-63o20.8, zgc:113140
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
ProteomesiUP000000437 Componenti: Chromosome 20

Organism-specific databases

ZFINiZDB-GENE-050327-35. elp3.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. Elongator holoenzyme complex Source: GO_Central
  3. histone acetyltransferase complex Source: GO_Central
  4. transcription elongation factor complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

ELP3 morpholino knockdown in embryos at 27 hpf results in abnormal motor neuron axonal branching and length.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 548548Elongator complex protein 3PRO_0000283989Add
BLAST

Expressioni

Gene expression databases

BgeeiQ5RIC0.

Interactioni

Subunit structurei

Component of the RNA polymerase II elongator complex (Elongator). Elongator associates with the C-terminal domain (CTD) of Pol II largest subunit (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliQ5RIC0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini397 – 548152N-acetyltransferasePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ELP3 family.Curated
Contains 1 N-acetyltransferase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG1243.
GeneTreeiENSGT00390000013141.
HOGENOMiHOG000227514.
HOVERGENiHBG107845.
InParanoidiQ5RIC0.
KOiK07739.
OMAiGYKVVSH.
OrthoDBiEOG7V765W.
PhylomeDBiQ5RIC0.
TreeFamiTF105752.

Family and domain databases

Gene3Di3.40.630.30. 1 hit.
3.80.30.20. 1 hit.
InterProiIPR016181. Acyl_CoA_acyltransferase.
IPR006638. Elp3/MiaB/NifB.
IPR000182. GNAT_dom.
IPR005910. Hist_AcTrfase_ELP3.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
[Graphical view]
PfamiPF00583. Acetyltransf_1. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF005669. Hist_AcTrfase_ELP3. 1 hit.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
SUPFAMiSSF55729. SSF55729. 2 hits.
TIGRFAMsiTIGR01211. ELP3. 1 hit.
PROSITEiPS51186. GNAT. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q5RIC0-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MGKPKKKSDL SRAELMMMTI ADVIKQLVEA HEEGKDINLN KVKTKTSAKY
60 70 80 90 100
GLSAQPRLVD IIAAVPPHYR RALVPKLKAK PIRTASGIAV VAVMCKPHRC
110 120 130 140 150
PHISFTGNIC VYCPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPYLQTR
160 170 180 190 200
HRVEQLKQLG HSVDKVEFIV MGGTFMALPE EYRDYFIRNL HDALSGHTSN
210 220 230 240 250
NVTEAVRYSE RSNTKCVGIT IETRPDYCLK RHLSDMLGYG CTRLEIGVQS
260 270 280 290 300
VYEDVARDTN RGHTVRAVCE SFHLAKDAGF KVVAHMMPDL PNVGMERDVE
310 320 330 340 350
QFIEFFENPA FRPDGLKLYP TLVIRGTGLY ELWKTGRYKS YSPSALVDLV
360 370 380 390 400
ARILALVPPW TRVYRVQRDI PMPLVSSGVE HGNLRELALA RMKDMGTECR
410 420 430 440 450
DVRTREVGIQ EIHHKVRPYQ VELIRRDYVA NGGWETFLSY EDPEQDILIG
460 470 480 490 500
LLRLRRCSPQ SFRPELKGGV SIVRELHVYG SVVPVSSRDP SKFQHQGFGM
510 520 530 540
MLMEEAERIA RDEHGSSKLA VISGVGTRNY YRKMGYELEG PYMVKNLY

Note: No experimental confirmation available.

Length:548
Mass (Da):62,259
Last modified:June 12, 2007 - v3
Checksum:i8761FBFC0FE684DE
GO
Isoform 2 (identifier: Q5RIC0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-15: Missing.

Note: No experimental confirmation available.

Show »
Length:533
Mass (Da):60,589
Checksum:i70C0C16D4E4E0129
GO
Isoform 3 (identifier: Q5RIC0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-93: Missing.

Note: No experimental confirmation available.

Show »
Length:455
Mass (Da):52,132
Checksum:i1A1227439D70C4E7
GO

Sequence cautioni

The sequence CAI12039.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti263 – 2631H → Y in AAH91787 (Ref. 2) Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 9393Missing in isoform 3. 1 PublicationVSP_026085Add
BLAST
Alternative sequencei1 – 1515Missing in isoform 2. CuratedVSP_026084Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX279523 Genomic DNA. Translation: CAI12039.1. Sequence problems.
BC091787 mRNA. Translation: AAH91787.1.
BC096810 mRNA. Translation: AAH96810.1.
RefSeqiNP_001014344.2. NM_001014322.2. [Q5RIC0-1]
UniGeneiDr.84313.

Genome annotation databases

EnsembliENSDART00000138226; ENSDARP00000113240; ENSDARG00000042005. [Q5RIC0-2]
ENSDART00000152836; ENSDARP00000127220; ENSDARG00000042005. [Q5RIC0-3]
GeneIDi541509.
KEGGidre:541509.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX279523 Genomic DNA. Translation: CAI12039.1. Sequence problems.
BC091787 mRNA. Translation: AAH91787.1.
BC096810 mRNA. Translation: AAH96810.1.
RefSeqiNP_001014344.2. NM_001014322.2. [Q5RIC0-1]
UniGeneiDr.84313.

3D structure databases

ProteinModelPortaliQ5RIC0.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000138226; ENSDARP00000113240; ENSDARG00000042005. [Q5RIC0-2]
ENSDART00000152836; ENSDARP00000127220; ENSDARG00000042005. [Q5RIC0-3]
GeneIDi541509.
KEGGidre:541509.

Organism-specific databases

CTDi55140.
ZFINiZDB-GENE-050327-35. elp3.

Phylogenomic databases

eggNOGiCOG1243.
GeneTreeiENSGT00390000013141.
HOGENOMiHOG000227514.
HOVERGENiHBG107845.
InParanoidiQ5RIC0.
KOiK07739.
OMAiGYKVVSH.
OrthoDBiEOG7V765W.
PhylomeDBiQ5RIC0.
TreeFamiTF105752.

Enzyme and pathway databases

ReactomeiREACT_310649. HATs acetylate histones.

Miscellaneous databases

NextBioi20879291.
PROiQ5RIC0.

Gene expression databases

BgeeiQ5RIC0.

Family and domain databases

Gene3Di3.40.630.30. 1 hit.
3.80.30.20. 1 hit.
InterProiIPR016181. Acyl_CoA_acyltransferase.
IPR006638. Elp3/MiaB/NifB.
IPR000182. GNAT_dom.
IPR005910. Hist_AcTrfase_ELP3.
IPR007197. rSAM.
IPR023404. rSAM_horseshoe.
[Graphical view]
PfamiPF00583. Acetyltransf_1. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF005669. Hist_AcTrfase_ELP3. 1 hit.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
SUPFAMiSSF55729. SSF55729. 2 hits.
TIGRFAMsiTIGR01211. ELP3. 1 hit.
PROSITEiPS51186. GNAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (MAY-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
    Tissue: Embryo.
  3. Cited for: FUNCTION, DISRUPTION PHENOTYPE.

Entry informationi

Entry nameiELP3_DANRE
AccessioniPrimary (citable) accession number: Q5RIC0
Secondary accession number(s): Q4V9M7, Q58ER7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 17, 2007
Last sequence update: June 12, 2007
Last modified: April 1, 2015
This is version 80 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.