P53930 (AF9_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein AF-9 homolog

Gene names

Name:	YAF9
Ordered Locus Names:	YNL107W
ORF Names:	N1966

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	226 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histones H4 and H2A. The NuA4 complex is also involved in DNA repair. Yaf9 may also be required for viability in conditions in which the structural integrity of the spindle is compromised. Ref.5 Ref.6 Ref.10 Ref.11 Ref.13
Subunit structure	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. Component of the NuA4 histone acetyltransferase complex composed of at least ACT1, ARP4, YAF9, VID21, SWC4, EAF3, EAF5, EAF6, EAF7, EPL1, ESA1, TRA1 and YNG2. Interacts with SWC4. Ref.9
Subcellular location	Cytoplasm. Nucleus Ref.6 Ref.7 Ref.10.
Domain	The coiled-coil domain is required for assembly into the NuA4 complex.
Miscellaneous	Present with 259 molecules/cell in log phase SD medium. Ref.8
Sequence similarities	Contains 1 YEATS domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Domain	Coiled coil
Molecular function	Activator Chromatin regulator
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from direct assay. Source: SGD chromatin silencing at telomere Inferred from mutant phenotype Ref.10. Source: SGD histone exchange Inferred from mutant phenotype. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	NuA4 histone acetyltransferase complex Inferred from physical interaction Ref.10. Source: SGD Swr1 complex Inferred from direct assay Ref.13Ref.5. Source: SGD cytoplasm Inferred from direct assay Ref.7. Source: SGD
Molecular function	protein binding Inferred from physical interaction Ref.11. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
BDF1	P35817	3	EBI-28841,EBI-3493
EAF1	Q06337	2	EBI-28841,EBI-35867
ESA1	Q08649	6	EBI-28841,EBI-6648
SWC4	P53201	5	EBI-28841,EBI-23061
TRA1	P38811	4	EBI-28841,EBI-24638

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 226

226

Protein AF-9 homolog

PRO_0000215934

Regions

Domain

15 – 123

109

YEATS

Coiled coil

187 – 224

38

Potential

Experimental info

Sequence conflict

65

1

K → R in AAT93068. Ref.4

Secondary structure

1

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226

Helix Strand Turn

Details...

Beta strand

8 – 11

4

Beta strand

13 – 20

8

Beta strand

22 – 26

5

Beta strand

41 – 48

8

Turn

56 – 58

3

Beta strand

59 – 65

7

Beta strand

70 – 72

3

Beta strand

74 – 77

4

Beta strand

79 – 86

8

Beta strand

93 – 100

8

Helix

102 – 104

3

Beta strand

109 – 114

6

Beta strand

145 – 157

13

Helix

160 – 168

9

Sequences

	Sequence		Length	Mass (Da)
	P53930 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: 1FE08F72942061D1	FASTA	226	25,981
	10 20 30 40 50 60 MAPTISKRIK TLSVSRPIIY GNTAKKMGSV KPPNAPAEHT HLWTIFVRGP QNEDISYFIK 70 80 90 100 110 120 KVVFKLHDTY PNPVRSIEAP PFELTETGWG EFDINIKVYF VEEANEKVLN FYHRLRLHPY 130 140 150 160 170 180 ANPVPNSDNG NEQNTTDHNS KDAEVSSVYF DEIVFNEPNE EFFKILMSRP GNLLPSNKTD 190 200 210 220 DCVYSKQLEQ EEIDRIEIGI EKVDKEIDEL KQKLENLVKQ EAINGS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The DNA sequence of cosmid 14-13b from chromosome XIV of Saccharomyces cerevisiae reveals an unusually high number of overlapping open reading frames." de Antoni A., D'Angelo M., Dal Pero F., Sartorello F., Pandolfo D., Pallavicini A., Lanfranchi G., Valle G. Yeast 13:261-266(1997) [PubMed: 9090055] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed: 9169873] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1." Krogan N.J., Keogh M.-C., Datta N., Sawa C., Ryan O.W., Ding H., Haw R.A., Pootoolal J., Tong A., Canadien V., Richards D.P., Wu X., Emili A., Hughes T.R., Buratowski S., Greenblatt J.F. Mol. Cell 12:1565-1576(2003) [PubMed: 14690608] [Abstract] Cited for: IDENTIFICATION IN THE SWR1 COMPLEX, FUNCTION OF THE SWR1 COMPLEX, MASS SPECTROMETRY.
[6]	"Yaf9, a novel NuA4 histone acetyltransferase subunit, is required for the cellular response to spindle stress in yeast." Le Masson I., Yu D.Y., Jensen K., Chevalier A., Courbeyrette R., Boulard Y., Smith M.M., Mann C. Mol. Cell. Biol. 23:6086-6102(2003) [PubMed: 12917332] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, IDENTIFICATION IN THE NUA4 COMPLEX.
[7]	"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: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[8]	"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: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"Direct physical and functional interaction of the NuA4 complex components Yaf9p and Swc4p." Bittner C.B., Zeisig D.T., Zeisig B.B., Slany R.K. Eukaryot. Cell 3:976-983(2004) [PubMed: 15302830] [Abstract] Cited for: INTERACTION WITH SWC4.
[10]	"The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres." Zhang H., Richardson D.O., Roberts D.N., Utley R.T., Erdjument-Bromage H., Tempst P., Cote J., Cairns B.R. Mol. Cell. Biol. 24:9424-9436(2004) [PubMed: 15485911] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, IDENTIFICATION IN THE NUA4 COMPLEX, MASS SPECTROMETRY.
[11]	"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: 15045029] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE SWR1 COMPLEX, IDENTIFICATION IN THE NUA4 COMPLEX, MASS SPECTROMETRY.
[12]	"Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4." Krogan N.J., Baetz K., Keogh M.-C., Datta N., Sawa C., Kwok T.C.Y., Thompson N.J., Davey M.G., Pootoolal J., Hughes T.R., Emili A., Buratowski S., Hieter P., Greenblatt J.F. Proc. Natl. Acad. Sci. U.S.A. 101:13513-13518(2004) [PubMed: 15353583] [Abstract] Cited for: IDENTIFICATION IN THE NUA4 COMPLEX, MASS SPECTROMETRY.
[13]	"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: 14645854] [Abstract] Cited for: IDENTIFICATION IN THE SWR1 COMPLEX, FUNCTION OF THE SWR1 COMPLEX, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z69382 Genomic DNA. Translation: CAA93400.1.
Z71383 Genomic DNA. Translation: CAA95984.1.
AY693049 Genomic DNA. Translation: AAT93068.1.
BK006947 Genomic DNA. Translation: DAA10439.1.

PIR

S63048.

RefSeq

NP_014292.1. NM_001182945.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3FK3	X-ray	2.30	A/B/C	8-169	[»]
3RLS	X-ray	1.70	A/B	9-176	[»]

ProteinModelPortal

P53930.

SMR

P53930. Positions 9-176.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-4347N.

IntAct

P53930. 30 interactions.

MINT

MINT-515470.

STRING

P53930.

Proteomic databases

PeptideAtlas

P53930.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YNL107W; YNL107W; YNL107W.

GeneID

855616.

KEGG

sce:YNL107W.

NMPDR

fig|4932.3.peg.5362.

Organism-specific databases

CYGD

YNL107w.

SGD

S000005051. YAF9.

Phylogenomic databases

eggNOG

fuNOG08238.

GeneTree

EFGT00050000002502.

HOGENOM

HBG748014.

OMA

THLWTIF.

OrthoDB

EOG4WWVTQ.

Enzyme and pathway databases

BRENDA

2.3.1.48. 984.

Gene expression databases

ArrayExpress

P53930.

Genevestigator

P53930.

GermOnline

YNL107W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005033. YEATS.
[Graphical view]

KO

K11341.

PANTHER

PTHR23195. YEATS. 1 hit.

Pfam

PF03366. YEATS. 1 hit.
[Graphical view]

PROSITE

PS51037. YEATS. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

979801.

Entry information

Entry name

AF9_YEAST

Accession

Primary (citable) accession number: P53930
Secondary accession number(s): D6W173, Q6B1N1

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	December 14, 2011
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program