Elongator complex protein 3 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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Q02908 (ELP3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 102. History...

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

Documents (3) |

Third-party data

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

Names and origin

Protein names

Recommended name:
Elongator complex protein 3
EC=2.3.1.48

Alternative name(s):
Gamma-toxin target 3

Gene names

Name:	ELP3
Synonyms:	HPA1, TOT3
Ordered Locus Names:	YPL086C

Organism

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

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	557 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as catalytic subunit of the RNA polymerase II elongator complex, which is a major histone acetyltransferase component of the RNA polymerase II (Pol II) holoenzyme and is involved in transcriptional elongation. Association with elongating RNAPII requires a hyperphosphorylated state of the RNAPII C-terminal domain (CTD). Elongator binds to both naked and nucleosomal DNA, can acetylate both core and nucleosomal histones, and is involved in chromatin remodeling. It acetylates histones H3, preferentially at 'Lys-14', and H4, preferentially at 'Lys-8'. It functions as a gamma-toxin target (TOT); disruption of the complex confers resistance to Kluyveromyces lactis toxin zymocin (pGKL1 killer toxin). May also be involved in sensitiviy to Pichia inositovora toxin. May be involved in tRNA modification. ELP3 is required for the complex integrity and for the association of the complex with nascent RNA transcript. Independently, ELP3 may be involved in polarized exocytosis. Is required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA. Ref.3 Ref.4 Ref.5 Ref.7 Ref.8 Ref.9 Ref.13 Ref.15 Ref.16
Catalytic activity	Acetyl-CoA + [histone] = CoA + acetyl-[histone].
Cofactor	Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine By similarity.
Subunit structure	Component of the RNA polymerase II elongator complex, which consists of IKI3, ELP2, ELP3, ELP4, IKI1 and ELP6. IKI3, ELP2, and ELP3 form the Elongator core complex. ELP3 interacts with KTI12. Ref.5 Ref.6 Ref.7 Ref.14
Subcellular location	Cytoplasm. Nucleus Ref.3 Ref.11 Ref.15.
Miscellaneous	Present with 4760 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the ELP3 family. Contains 1 N-acetyltransferase domain.

Ontologies

Keywords
Biological process	Protein transport Transcription Transcription regulation Transport
Cellular component	Cytoplasm Nucleus
Domain	Repeat
Ligand	Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine
Molecular function	Acyltransferase Chromatin regulator Transferase
PTM	Isopeptide bond Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	protein transport Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.7. Source: SGD tRNA wobble uridine modification Inferred from mutant phenotype PubMed 18755837. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	Elongator holoenzyme complex Inferred from direct assay Ref.7. Source: SGD cytoplasm Inferred from direct assay PubMed 12139626. Source: SGD nucleus Inferred from direct assay PubMed 12139626. Source: SGD
Molecular_function	histone acetyltransferase activity Inferred from direct assay Ref.5. Source: SGD iron-sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
IKI1	P38874	6	EBI-33957,EBI-9061

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 557

557

Elongator complex protein 3

PRO_0000235811

Regions

Domain

405 – 557

153

N-acetyltransferase

Sites

Metal binding

108

Iron-sulfur (4Fe-4S-S-AdoMet) Probable

Metal binding

118

Iron-sulfur (4Fe-4S-S-AdoMet) Probable

Metal binding

121

Iron-sulfur (4Fe-4S-S-AdoMet) Probable

Amino acid modifications

Cross-link

453

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10

Experimental info

Mutagenesis

108

C → S: Eliminates iron contents; when associated with S-118 and S-121. Ref.17

Mutagenesis

118

C → S: Eliminates iron contents; when associated with S-108 and S-121. Ref.17

Mutagenesis

121

C → S: Eliminates iron contents; when associated with S-108 and S-118. Ref.17

Sequences

Sequence

Length

Mass (Da)

Tools

Q02908 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 64EF8B42D3C3102E
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FASTA

557

63,657

        10         20         30         40         50         60 
MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL 

        70         80         90        100        110        120 
KQQPRLTDII NSIPDQYKKY LLPKLKAKPV RTASGIAVVA VMCKPHRCPH IAYTGNICVY 

       130        140        150        160        170        180 
CPGGPDSDFE YSTQSYTGYE PTSMRAIRAR YDPYEQARGR VEQLKQLGHS IDKVEYVLMG 

       190        200        210        220        230        240 
GTFMSLPKEY REDFIVKLHN ALSGFNGNDI DEAILYSQQS LTKCVGITIE TRPDYCTQTH 

       250        260        270        280        290        300 
LDDMLKYGCT RLEIGVQSLY EDVARDTNRG HTVRSVCETF AVSKDAGYKV VSHMMPDLPN 

       310        320        330        340        350        360 
VGMERDIEQF KEYFENPDFR TDGLKIYPTL VIRGTGLYEL WKTGRYKSYS ANALVDLVAR 

       370        380        390        400        410        420 
ILALVPPWTR IYRVQRDIPM PLVTSGVDNG NLRELALARM KDLGTTCRDV RTREVGIQEV 

       430        440        450        460        470        480 
HHKVQPDQVE LIRRDYYANG GWETFLSYED PKKDILIGLL RLRKASKKYT YRKEFTSQRT 

       490        500        510        520        530        540 
SIVRELHVYG SVVPLHSRDP RKFQHQGFGT LLMEEAERIA KEEHGSEKIS VISGVGVRNY 

       550 
YGKLGYELDG PYMSKRI

« Hide

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. Hani J. Nature 387:103-105(1997) [PubMed] [Europe PMC] [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]	"Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation." Otero G., Fellows J., Li Y., de Bizemont T., Dirac A.M., Gustafsson C.M., Erdjument-Bromage H., Tempst P., Svejstrup J.Q. Mol. Cell 3:109-118(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE RNA POLYMERASE II ELONGATOR COMPLEX IN TRANSCRIPTIONAL REGULATION, SUBCELLULAR LOCATION.
[4]	"Saccharomyces cerevisiae Elongator mutations confer resistance to the Kluyveromyces lactis zymocin." Frohloff F., Fichtner L., Jablonowski D., Breunig K.D., Schaffrath R. EMBO J. 20:1993-2003(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE RNA POLYMERASE II ELONGATOR COMPLEX IN ZYMOCIN SENSITIVITY.
[5]	"A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme." Wittschieben B.O., Otero G., de Bizemont T., Fellows J., Erdjument-Bromage H., Ohba R., Li Y., Allis C.D., Tempst P., Svejstrup J.Q. Mol. Cell 4:123-128(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE RNA POLYMERASE II ELONGATOR COMPLEX.
[6]	"RNA polymerase II elongator holoenzyme is composed of two discrete subcomplexes." Winkler G.S., Petrakis T.G., Ethelberg S., Tokunaga M., Erdjument-Bromage H., Tempst P., Svejstrup J.Q. J. Biol. Chem. 276:32743-32749(2001) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE RNA POLYMERASE II ELONGATOR COMPLEX.
[7]	"Characterization of a six-subunit holo-elongator complex required for the regulated expression of a group of genes in Saccharomyces cerevisiae." Krogan N.J., Greenblatt J.F. Mol. Cell. Biol. 21:8203-8212(2001) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION IN THE RNA POLYMERASE II ELONGATOR COMPLEX, FUNCTION OF THE RNA POLYMERASE II ELONGATOR COMPLEX IN TRANSCRIPTIONAL REGULATION.
[8]	"Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo." Winkler G.S., Kristjuhan A., Erdjument-Bromage H., Tempst P., Svejstrup J.Q. Proc. Natl. Acad. Sci. U.S.A. 99:3517-3522(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE RNA POLYMERASE II ELONGATOR COMPLEX IN HISTONE ACETYLATION.
[9]	"Structural and functional analysis of the killer element pPin1-3 from Pichia inositovora." Klassen R., Meinhardt F. Mol. Genet. Genomics 270:190-199(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE RNA POLYMERASE II ELONGATOR COMPLEX IN PICHIA INOSITOVORA TOXIN SENSITIVITY.
[10]	"A proteomics approach to understanding protein ubiquitination." Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P. Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-453, MASS SPECTROMETRY. Strain: SUB592.
[11]	"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] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[12]	"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].
[13]	"Molecular architecture, structure-function relationship, and importance of the Elp3 subunit for the RNA binding of holo-elongator." Petrakis T.G., Wittschieben B.O., Svejstrup J.Q. J. Biol. Chem. 279:32087-32092(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[14]	"Physical and functional interaction between Elongator and the chromatin-associated Kti12 protein." Petrakis T.G., Soegaard T.M.M., Erdjument-Bromage H., Tempst P., Svejstrup J.Q. J. Biol. Chem. 280:19454-19460(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH KTI12.
[15]	"Elp1p, the yeast homolog of the FD disease syndrome protein, negatively regulates exocytosis independently of transcriptional elongation." Rahl P.B., Chen C.Z., Collins R.N. Mol. Cell 17:841-853(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN EXOCYTOSIS REGULATION, SUBCELLULAR LOCATION.
[16]	"An early step in wobble uridine tRNA modification requires the Elongator complex." Huang B., Johansson M.J.O., Bystroem A.S. RNA 11:424-436(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN TRNA MODIFICATION.
[17]	"The Elongator subunit Elp3 contains a Fe4S4 cluster and binds S-adenosylmethionine." Paraskevopoulou C., Fairhurst S.A., Lowe D.J., Brick P., Onesti S. Mol. Microbiol. 59:795-806(2006) [PubMed] [Europe PMC] [Abstract] Cited for: S-ADENOSYLMETHIONINE-BINDING, MUTAGENESIS OF CYS-108; CYS-118 AND CYS-121.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U43281 Genomic DNA. Translation: AAB68213.1. BK006949 Genomic DNA. Translation: DAA11347.1.
PIR	S61980.
RefSeq	NP_015239.1. NM_001183900.1.
3D structure databases
ProteinModelPortal	Q02908.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2385N.
IntAct	Q02908. 16 interactions.
MINT	MINT-645857.
STRING	4932.YPL086C.
Proteomic databases
PaxDb	Q02908.
PeptideAtlas	Q02908.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YPL086C; YPL086C; YPL086C.
GeneID	856019.
KEGG	sce:YPL086C.
Organism-specific databases
CYGD	YPL086c.
SGD	S000006007. ELP3.
Phylogenomic databases
eggNOG	COG1243.
GeneTree	ENSGT00390000013141.
HOGENOM	HOG000227514.
KO	K07739.
OMA	GIQEVHH.
OrthoDB	EOG41CB4H.
Enzyme and pathway databases
BioCyc	YEAST:G3O-33992-MONOMER.
Gene expression databases
Genevestigator	Q02908.
GermOnline	YPL086C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.40.630.30. 1 hit. 3.80.30.20. 1 hit.
InterPro	IPR016181. Acyl_CoA_acyltransferase. IPR006638. Elp3/MiaB/NifB. IPR000182. GNAT_dom. IPR005910. Hist_AcTrfase_ELP3. IPR007197. rSAM. IPR023404. rSAM_horseshoe. [Graphical view]
Pfam	PF00583. Acetyltransf_1. 1 hit. PF04055. Radical_SAM. 1 hit. [Graphical view]
PIRSF	PIRSF005669. Hist_AcTrfase_ELP3. 1 hit.
SMART	SM00729. Elp3. 1 hit. [Graphical view]
SUPFAM	SSF55729. Acyl_CoA_acyltransferase. 1 hit.
TIGRFAMs	TIGR01211. ELP3. 1 hit.
PROSITE	PS51186. GNAT. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	980923.

Entry information

Entry name

ELP3_YEAST

Accession

Primary (citable) accession number: Q02908
Secondary accession number(s): D6W3T1

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 16, 2006
Last sequence update:	November 1, 1996
Last modified:	May 29, 2013
This is version 102 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome XVI

Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

SIMILARITY comments

Index of protein domains and families

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents