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Protein

Actin-related protein 4

Gene

ARP4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Chromatin interaction component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the INO80 complex which remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to gamma-H2A as a response to DNA damage.9 Publications

GO - Molecular functioni

  • chromatin binding Source: SGD
  • histone binding Source: SGD
  • nucleosomal histone binding Source: SGD

GO - Biological processi

  • chromatin organization Source: SGD
  • chromatin remodeling Source: SGD
  • DNA duplex unwinding Source: GOC
  • DNA repair Source: SGD
  • histone acetylation Source: SGD
  • kinetochore assembly Source: SGD
  • regulation of transcription, DNA-templated Source: SGD
  • regulation of transcription from RNA polymerase II promoter Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator

Keywords - Biological processi

DNA damage, DNA repair, Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-31538-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Actin-related protein 4
Alternative name(s):
Actin-like protein ARP4
Short name:
Actin-like protein 4
Gene namesi
Name:ARP4
Synonyms:ACT3
Ordered Locus Names:YJL081C
ORF Names:J1012
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJL081C.
SGDiS000003617. ARP4.

Subcellular locationi

GO - Cellular componenti

  • Ino80 complex Source: SGD
  • NuA4 histone acetyltransferase complex Source: SGD
  • nuclear chromatin Source: SGD
  • nucleus Source: SGD
  • Swr1 complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi23 – 231S → A: Lethal; when associated with D-161. Formamide-, hydroxyurea and UV-hypersensitivity, suppressor of TY phenotype; when associated with A-159. 1 Publication
Mutagenesisi155 – 1551C → Y: No histone acetyltransferase activity at 37 degrees Celsius. 1 Publication
Mutagenesisi159 – 1591D → A: Formamide-, hydroxyurea and UV-hypersensitivity, suppressor of TY phenotype; when associated with S-23. 1 Publication
Mutagenesisi161 – 1611G → D: Formamide-, hydroxyurea and UV-hypersensitivity, destabilization of ARP4, suppressor of TY phenotype and elevated levels of MSN2/MSN4-regulated genes. Lethal; when associated with A-23. 1 Publication
Mutagenesisi187 – 1871G → R: Defect in promoter association and change in chromatin structure. 1 Publication
Mutagenesisi455 – 4551G → S: No histone acetyltransferase activity at 37 degrees Celsius. Defect in promoter association and change in chromatin structure. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 489489Actin-related protein 4PRO_0000089103Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei349 – 3491PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP80428.
PeptideAtlasiP80428.

PTM databases

iPTMnetiP80428.

Interactioni

Subunit structurei

Component of the NuA4 histone acetyltransferase complex composed of at least ACT1, ARP4, EAF3, EAF5, EAF6, EAF7, EPL1, ESA1, SWC4, TRA1, VID21, YAF9 and YNG2. Component of the chromatin-remodeling INO80 complex, at least composed of ARP4, ARP5, ARP8, RVB1, RVB2, TAF14, NHP10, IES1, IES3, IES4, IES6, ACT1, IES2, IES5 and INO80. Component of the SWR1 chromatin remodeling complex composed of at least ACT1, ARP4, RVB1, RVB2, ARP6, YAF9, VPS71, VPS72, SWC3, SWC4, SWC5, SWC7 and SWR1, and perhaps BDF1. Interacts with histones H4 (HHF1 and HHF2), H3 (HHT1 and HHT2) and H2A (HTA1 and HTA2).6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ESA1Q0864910EBI-2939,EBI-6648

GO - Molecular functioni

  • histone binding Source: SGD
  • nucleosomal histone binding Source: SGD

Protein-protein interaction databases

BioGridi33675. 263 interactions.
DIPiDIP-2361N.
IntActiP80428. 54 interactions.
MINTiMINT-667718.

Structurei

Secondary structure

1
489
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi17 – 204Combined sources
Beta strandi23 – 308Combined sources
Beta strandi37 – 4913Combined sources
Helixi61 – 633Combined sources
Beta strandi69 – 768Combined sources
Beta strandi79 – 813Combined sources
Helixi83 – 9614Combined sources
Beta strandi108 – 1125Combined sources
Helixi118 – 12912Combined sources
Beta strandi135 – 1417Combined sources
Helixi142 – 1498Combined sources
Beta strandi153 – 1608Combined sources
Beta strandi165 – 1717Combined sources
Helixi177 – 1793Combined sources
Beta strandi181 – 1844Combined sources
Helixi187 – 19711Combined sources
Turni198 – 2003Combined sources
Beta strandi209 – 2113Combined sources
Beta strandi213 – 2153Combined sources
Helixi227 – 23610Combined sources
Helixi238 – 2458Combined sources
Helixi254 – 26310Combined sources
Beta strandi268 – 2714Combined sources
Beta strandi273 – 2753Combined sources
Beta strandi277 – 2804Combined sources
Helixi282 – 2909Combined sources
Turni291 – 2933Combined sources
Helixi297 – 2993Combined sources
Beta strandi308 – 3103Combined sources
Helixi385 – 39410Combined sources
Turni398 – 4003Combined sources
Helixi401 – 4055Combined sources
Beta strandi408 – 4125Combined sources
Helixi413 – 4164Combined sources
Helixi420 – 43112Combined sources
Helixi446 – 4494Combined sources
Helixi451 – 46010Combined sources
Helixi463 – 4675Combined sources
Beta strandi469 – 4713Combined sources
Helixi472 – 4765Combined sources
Helixi481 – 4866Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3QB0X-ray3.40A/B/C/D1-489[»]
ProteinModelPortaliP80428.
SMRiP80428. Positions 8-489.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the actin family. ARP4 subfamily.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00840000132076.
HOGENOMiHOG000233340.
InParanoidiP80428.
KOiK11400.
OMAiDGMTLSK.
OrthoDBiEOG7GJ6PB.

Family and domain databases

InterProiIPR004000. Actin.
IPR020902. Actin/actin-like_CS.
IPR027667. Arp4.
[Graphical view]
PANTHERiPTHR11937. PTHR11937. 3 hits.
PTHR11937:SF234. PTHR11937:SF234. 3 hits.
PfamiPF00022. Actin. 1 hit.
[Graphical view]
SMARTiSM00268. ACTIN. 1 hit.
[Graphical view]
PROSITEiPS01132. ACTINS_ACT_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P80428-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNAALQVYG GDEVSAVVID PGSYTTNIGY SGSDFPQSIL PSVYGKYTAD
60 70 80 90 100
EGNKKIFSEQ SIGIPRKDYE LKPIIENGLV IDWDTAQEQW QWALQNELYL
110 120 130 140 150
NSNSGIPALL TEPVWNSTEN RKKSLEVLLE GMQFEACYLA PTSTCVSFAA
160 170 180 190 200
GRPNCLVVDI GHDTCSVSPI VDGMTLSKST RRNFIAGKFI NHLIKKALEP
210 220 230 240 250
KEIIPLFAIK QRKPEFIKKT FDYEVDKSLY DYANNRGFFQ ECKETLCHIC
260 270 280 290 300
PTKTLEETKT ELSSTAKRSI ESPWNEEIVF DNETRYGFAE ELFLPKEDDI
310 320 330 340 350
PANWPRSNSG VVKTWRNDYV PLKRTKPSGV NKSDKKVTPT EEKEQEAVSK
360 370 380 390 400
STSPAANSAD TPNETGKRPL EEEKPPKENN ELIGLADLVY SSIMSSDVDL
410 420 430 440 450
RATLAHNVVL TGGTSSIPGL SDRLMTELNK ILPSLKFRIL TTGHTIERQY
460 470 480
QSWLGGSILT SLGTFHQLWV GKKEYEEVGV ERLLNDRFR
Length:489
Mass (Da):54,832
Last modified:February 1, 1995 - v1
Checksum:i6DE1C8938C6C3DBB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X75317 Genomic DNA. Translation: CAA53066.1.
X83502 Genomic DNA. Translation: CAA58489.1.
Z49356 Genomic DNA. Translation: CAA89374.1.
BK006943 Genomic DNA. Translation: DAA08718.1.
PIRiS47608.
RefSeqiNP_012454.1. NM_001181514.1.

Genome annotation databases

EnsemblFungiiYJL081C; YJL081C; YJL081C.
GeneIDi853364.
KEGGisce:YJL081C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X75317 Genomic DNA. Translation: CAA53066.1.
X83502 Genomic DNA. Translation: CAA58489.1.
Z49356 Genomic DNA. Translation: CAA89374.1.
BK006943 Genomic DNA. Translation: DAA08718.1.
PIRiS47608.
RefSeqiNP_012454.1. NM_001181514.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3QB0X-ray3.40A/B/C/D1-489[»]
ProteinModelPortaliP80428.
SMRiP80428. Positions 8-489.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33675. 263 interactions.
DIPiDIP-2361N.
IntActiP80428. 54 interactions.
MINTiMINT-667718.

PTM databases

iPTMnetiP80428.

Proteomic databases

MaxQBiP80428.
PeptideAtlasiP80428.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJL081C; YJL081C; YJL081C.
GeneIDi853364.
KEGGisce:YJL081C.

Organism-specific databases

EuPathDBiFungiDB:YJL081C.
SGDiS000003617. ARP4.

Phylogenomic databases

GeneTreeiENSGT00840000132076.
HOGENOMiHOG000233340.
InParanoidiP80428.
KOiK11400.
OMAiDGMTLSK.
OrthoDBiEOG7GJ6PB.

Enzyme and pathway databases

BioCyciYEAST:G3O-31538-MONOMER.

Miscellaneous databases

NextBioi973792.
PROiP80428.

Family and domain databases

InterProiIPR004000. Actin.
IPR020902. Actin/actin-like_CS.
IPR027667. Arp4.
[Graphical view]
PANTHERiPTHR11937. PTHR11937. 3 hits.
PTHR11937:SF234. PTHR11937:SF234. 3 hits.
PfamiPF00022. Actin. 1 hit.
[Graphical view]
SMARTiSM00268. ACTIN. 1 hit.
[Graphical view]
PROSITEiPS01132. ACTINS_ACT_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "An essential gene of Saccharomyces cerevisiae coding for an actin-related protein."
    Harata M., Karwan A., Wintersberger U.
    Proc. Natl. Acad. Sci. U.S.A. 91:8258-8262(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Erratum
    Harata M., Karwan A., Wintersberger U.
    Proc. Natl. Acad. Sci. U.S.A. 91:10757-10757(1994)
  3. "Sequence analysis of a 33.1 kb fragment from the left arm of Saccharomyces cerevisiae chromosome X, including putative proteins with leucine zippers, a fungal Zn(II)2-Cys6 binuclear cluster domain and a putative alpha 2-SCB-alpha 2 binding site."
    Miosga T., Schaaff-Gerstenschlaeger I., Chalwatzis N., Baur A., Boles E., Fournier C., Schmitt S., Velten C., Wilhelm N., Zimmermann F.K.
    Yeast 11:681-689(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription."
    Galarneau L., Nourani A., Boudreault A.A., Zhang Y., Heliot L., Allard S., Savard J., Lane W.S., Stillman D.J., Cote J.
    Mol. Cell 5:927-937(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 55-66; 202-210; 220-243; 269-296; 317-323; 378-430 AND 448-482, IDENTIFICATION IN THE NUA4 COMPLEX, INTERACTION WITH HISTONES H2A; H3 AND H4, MUTAGENESIS OF CYS-155 AND GLY-455, FUNCTION.
  7. "The actin-related protein Act3p of Saccharomyces cerevisiae is located in the nucleus."
    Weber V., Harata M., Hauser H., Wintersberger U.
    Mol. Biol. Cell 6:1263-1270(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  8. "A chromatin remodelling complex involved in transcription and DNA processing."
    Shen X., Mizuguchi G., Hamiche A., Wu C.
    Nature 406:541-544(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE INO80 COMPLEX, FUNCTION OF THE INO80 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  9. "Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae."
    Harata M., Zhang Y., Stillman D.J., Matsui D., Oma Y., Nishimori K., Mochizuki R.
    Nucleic Acids Res. 30:1743-1750(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF GLY-187 AND GLY-455.
  10. "Who's who among the Saccharomyces cerevisiae actin-related proteins? A classification and nomenclature proposal for a large family."
    Poch O., Winsor B.
    Yeast 13:1053-1058(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NOMENCLATURE.
  11. "Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair."
    Bird A.W., Yu D.Y., Pray-Grant M.G., Qiu Q., Harmon K.E., Megee P.C., Grant P.A., Smith M.M., Christman M.F.
    Nature 419:411-415(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "Involvement of actin-related proteins in ATP-dependent chromatin remodeling."
    Shen X., Ranallo R., Choi E., Wu C.
    Mol. Cell 12:147-155(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE INO80 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  13. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  14. Cited for: FUNCTION, IDENTIFICATION IN THE SWR1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  15. "Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites."
    Downs J.A., Allard S., Jobin-Robitaille O., Javaheri A., Auger A., Bouchard N., Kron S.J., Jackson S.P., Cote J.
    Mol. Cell 16:979-990(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  16. "The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes."
    Goerzer I., Schueller C., Heidenreich E., Krupanska L., Kuchler K., Wintersberger U.
    Mol. Microbiol. 50:1155-1171(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF SER-23; ASP-159 AND GLY-161.
  17. "A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin."
    Kobor M.S., Venkatasubrahmanyam S., Meneghini M.D., Gin J.W., Jennings J.L., Link A.J., Madhani H.D., Rine J.
    PLoS Biol. 2:587-599(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE SWR1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  18. "ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex."
    Mizuguchi G., Shen X., Landry J., Wu W.-H., Sen S., Wu C.
    Science 303:343-348(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SWR1 COMPLEX, FUNCTION OF THE SWR1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  19. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  20. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-349, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  21. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiARP4_YEAST
AccessioniPrimary (citable) accession number: P80428
Secondary accession number(s): D6VWA2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: May 11, 2016
This is version 143 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1070 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

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 one 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.