P11978 (SIR4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Regulatory protein SIR4

Alternative name(s):
Silent information regulator 4

Gene names

Name:	SIR4
Synonyms:	ASD1, STE9, UTH2
Ordered Locus Names:	YDR227W
ORF Names:	YD9934.12

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	1358 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The proteins SIR1 through SIR4 are required for transcriptional repression of the silent mating type loci, HML and HMR. The proteins SIR2 through SIR4 repress mulitple loci by modulating chromatin structure. Involves the compaction of chromatin fiber into a more condensed form. Ref.9
Subunit structure	Homodimer. Interacts with MPS3, RIS1, SIR1, SIR2, SIR3, YKU80 and RAP1 C-terminus. Ref.5 Ref.7 Ref.9
Subcellular location	Nucleus.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Coiled coil
Ligand	DNA-binding
Molecular function	Repressor
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	chromatin silencing Traceable author statement. Source: SGD double-strand break repair via nonhomologous end joining Inferred from direct assay. Source: SGD negative regulation of chromatin silencing involved in replicative cell aging Inferred from direct assay. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromatin silencing complex Inferred from direct assay. Source: SGD nuclear telomere cap complex Inferred from direct assay. Source: SGD nuclear telomeric heterochromatin Inferred from direct assay. Source: SGD
Molecular function	double-stranded DNA binding Inferred from direct assay. Source: SGD histone binding Traceable author statement. Source: SGD nucleosome binding Inferred from direct assay. Source: SGD structural constituent of chromatin Traceable author statement. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RAP1	P11938	2	EBI-17237,EBI-14821
SIR2	P06700	7	EBI-17237,EBI-17219
SIR3	P06701	7	EBI-17237,EBI-17230
YKU80	Q04437	2	EBI-17237,EBI-8224

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1358

1358

Regulatory protein SIR4

PRO_0000097769

Regions

Coiled coil

1271 – 1347

77

Amino acid modifications

Modified residue

62

1

Phosphothreonine Ref.10

Modified residue

274

1

Phosphoserine Ref.12

Modified residue

342

1

Phosphoserine Ref.12

Modified residue

692

1

Phosphoserine Ref.12

Modified residue

709

1

Phosphoserine Ref.12

Modified residue

711

1

Phosphoserine Ref.12

Modified residue

788

1

Phosphoserine Ref.12

Modified residue

1134

1

Phosphoserine Ref.11 Ref.12

Cross-link

1128

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) Ref.8

Natural variations

Natural variant

994

1

P → L.

Secondary structure

1

.

.

.

1358

Helix Strand Turn

Details...

Helix

1273 – 1343

71

Sequences

	Sequence		Length	Mass (Da)
	P11978 [UniParc]. Last modified October 1, 1989. Version 1. Checksum: 9C698765964F094E	FASTA	1,358	152,062
	10 20 30 40 50 60 MPNDNKTPNR SSTPKFTKKP VTPNDKIPER EEKSNEVKTP KIPLFTFAKS KNYSRPSTAI 70 80 90 100 110 120 HTSPHQPSDV KPTSHKQLQQ PKSSPLKKNN YNSFPHSNLE KISNSKLLSL LRSKTSAGRI 130 140 150 160 170 180 ESNNPSHDAS RSLASFEQTA FSRHAQQQTS TFNSKPVRTI VPISTSQTNN SFLSGVKSLL 190 200 210 220 230 240 SEEKIRDYSK EILGINLANE QPVLEKPLKK GSADIGASVI SLTKDKSIRK DTVEEKKEEK 250 260 270 280 290 300 LNIGKNFAHS DSLSVPKVSA GDSGISPEES KARSPGIAKP NAIQTEVYGI NEESTNERLE 310 320 330 340 350 360 INQEKPVKLD ENSANSTVAS ALDTNGTSAT TETLTSKKIV PSPKKVAIDQ DKITLHDEKT 370 380 390 400 410 420 LAPSKHQPIT SEQKMKEDAD LKRMEILKSP HLSKSPADRP QGRRNSRNFS TRDEETTKLA 430 440 450 460 470 480 FLVEYEGQEN NYNSTSRSTE KKNDMNTSAK NKNGENKKIG KRPPEIMSTE AHVNKVTEET 490 500 510 520 530 540 TKQIQSVRID GRKVLQKVQG ESHIDSRNNT LNVTPSKRPQ LGEIPNPMKK HKPNEGRTPN 550 560 570 580 590 600 ISNGTINIQK KLEPKEIVRD ILHTKESSNE AKKTIQNPLN KSQNTALPST HKVTQKKDIK 610 620 630 640 650 660 IGTNDLFQVE SAPKISSEID RENVKSKDEP VSKAVESKSL LNLFSNVLKA PFIKSESKPF 670 680 690 700 710 720 SSDALSKEKA NFLETIASTE KPENKTDKVS LSQPVSASKH EYSDNFPVSL SQPSKKSFAN 730 740 750 760 770 780 HTEDEQIEKK KICRGRMNTI ITHPGKMELV YVSDSDDSSS DNDSLTDLES LSSGESNEIK 790 800 810 820 830 840 VTNDLDTSAE KDQIQAGKWF DPVLDWRKSD RELTKNILWR IADKTTYDKE TITDLIEQGI 850 860 870 880 890 900 PKHSYLSGNP LTSVTNDICS VENYETSSAF FYQQVHKKDR LQYLPLYAVS TFENTNNTEK 910 920 930 940 950 960 NDVTNKNINI GKHSQEQNSS SAKPSQIPTV SSPLGFEETK LSTTPTKSNR RVSHSDTNSS 970 980 990 1000 1010 1020 KPKNTKENLS KSSWRQEWLA NLKLISVSLV DEFPSELSDS DRQIINEKMQ LLKDIFANNL 1030 1040 1050 1060 1070 1080 KSAISNNFRE SDIIILKGEI EDYPMSSEIK IYYNELQNKP DAKKARFWSF MKTQRFVSNM 1090 1100 1110 1120 1130 1140 GFDIQKSCEP VSISTSVKPH VVEPEHMADA KIMPKDILQI TKKPLMVKNV KPSSPPDVKS 1150 1160 1170 1180 1190 1200 LVQLSTMETK TLPEKKQFDS IFNSNKAKII PGNGKHASEN ISLSFSRPAS YGYFSVGKRV 1210 1220 1230 1240 1250 1260 PIVEDRRVKQ LDDITDSNTT EILTSVDVLG THSQTGTQQS NMYTSTQKTE LEIDNKDSVT 1270 1280 1290 1300 1310 1320 ECSKDMKEDG LSFVDIVLSK AASALDEKEK QLAVANEIIR SLSDEVMRNE IRITSLQGDL 1330 1340 1350 TFTKKCLENA RSQISEKDAK INKLMEKDFQ VNKEIKPY

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae." Marshall M., Mahoney D., Rose A., Hicks J.B., Broach J.R. Mol. Cell. Biol. 7:4441-4452(1987) [PubMed: 3325825] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Insertion site specificity of the transposon Tn3." Davies C.J., Hutchison C.A. III Nucleic Acids Res. 23:507-514(1995) [PubMed: 7885847] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV." Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T. , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Identification of a member of a DNA-dependent ATPase family that causes interference with silencing." Zhang Z., Buchman A.R. Mol. Cell. Biol. 17:5461-5472(1997) [PubMed: 9271422] [Abstract] Cited for: INTERACTION WITH RIS1.
[6]	"The molecular biology of the SIR proteins." Gasser S.M., Cockell M.M. Gene 279:1-16(2001) [PubMed: 11722841] [Abstract] Cited for: REVIEW.
[7]	"Separation-of-function mutants of yeast Ku80 reveal a Yku80p-Sir4p interaction involved in telomeric silencing." Roy R., Meier B., McAinsh A.D., Feldmann H.M., Jackson S.P. J. Biol. Chem. 279:86-94(2004) [PubMed: 14551211] [Abstract] Cited for: INTERACTION WITH YKU80.
[8]	"A proteomic strategy for gaining insights into protein sumoylation in yeast." Denison C., Rudner A.D., Gerber S.A., Bakalarski C.E., Moazed D., Gygi S.P. Mol. Cell. Proteomics 4:246-254(2005) [PubMed: 15542864] [Abstract] Cited for: SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-1128, MASS SPECTROMETRY.
[9]	"Telomere anchoring at the nuclear periphery requires the budding yeast Sad1-UNC-84 domain protein Mps3." Bupp J.M., Martin A.E., Stensrud E.S., Jaspersen S.L. J. Cell Biol. 179:845-854(2007) [PubMed: 18039933] [Abstract] Cited for: FUNCTION, INTERACTION WITH MPS3.
[10]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-62, MASS SPECTROMETRY.
[11]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1134, MASS SPECTROMETRY.
[12]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-274; SER-342; SER-692; SER-709; SER-711; SER-788 AND SER-1134, MASS SPECTROMETRY.
[13]	"Structure of the coiled-coil dimerization motif of Sir4 and its interaction with Sir3." Chang J.F., Hall B.E., Tanny J.C., Moazed D., Filman D., Ellenberger T. Structure 11:637-649(2003) [PubMed: 12791253] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 1271-1346.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M37249 Genomic DNA. Translation: AAA20881.1.
U13239 Genomic DNA. Translation: AAC33144.1.
Z48612 Genomic DNA. Translation: CAA88507.1.
BK006938 Genomic DNA. Translation: DAA12069.1.

PIR

A29360.

RefSeq

NP_010513.1. NM_001180535.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NYH	X-ray	3.10	A	1198-1358	[»]
1PL5	X-ray	2.50	A/S	1217-1358	[»]

ProteinModelPortal

P11978.

SMR

P11978. Positions 1271-1346.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-33N.

IntAct

P11978. 11 interactions.

MINT

MINT-622754.

STRING

P11978.

Proteomic databases

PeptideAtlas

P11978.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR227W; YDR227W; YDR227W.

GeneID

851813.

KEGG

sce:YDR227W.

NMPDR

fig|4932.3.peg.1270.

Organism-specific databases

CYGD

YDR227w.

SGD

S000002635. SIR4.

Phylogenomic databases

eggNOG

fuNOG15539.

OMA

TNDICSV.

OrthoDB

EOG47WRZJ.

Gene expression databases

ArrayExpress

P11978.

Genevestigator

P11978.

GermOnline

YDR227W. Saccharomyces cerevisiae.

Family and domain databases

KO

K11123.

ProtoNet

Search...

Other

NextBio

969671.

Entry information

Entry name

SIR4_YEAST

Accession

Primary (citable) accession number: P11978
Secondary accession number(s): D6VSK9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	October 1, 1989
Last modified:	December 14, 2011
This is version 111 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program