P06701 (SIR3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Regulatory protein SIR3

Alternative name(s):
Silent information regulator 3

Gene names

Name:	SIR3
Synonyms:	CMT1, MAR2, STE8
Ordered Locus Names:	YLR442C
ORF Names:	L9753.10

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	978 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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.
Subunit structure	Homodimer and interacts with SIR4 and RAP1 C-terminus. Interacts with MCM10. Ref.9
Subcellular location	Nucleus.
Post-translational modification	N-terminal acetylation by NatA is important for transcriptional silencing activity.
Miscellaneous	Present with 1400 molecules/cell in log phase SD medium. Ref.7
Sequence similarities	Contains 1 BAH domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Ligand	DNA-binding
Molecular function	Repressor
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	chromatin silencing at silent mating-type cassette Inferred from mutant phenotype. Source: SGD double-strand break repair via nonhomologous end joining Inferred from direct assay. Source: SGD heterochromatin assembly Inferred from mutant phenotype. Source: SGD negative regulation of chromatin silencing involved in replicative cell aging Inferred from direct assay. Source: SGD nuclear-transcribed mRNA catabolic process, non-stop decay Inferred from mutant phenotype. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromatin silencing complex Inferred from direct assay. Source: SGD mitochondrion 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 nucleolus Inferred from direct assay. Source: SGD
Molecular function	double-stranded DNA binding Inferred from direct assay. Source: SGD nucleosomal histone binding Inferred from direct assay. Source: SGD protein homodimerization activity Inferred from physical interaction. Source: SGD single-stranded DNA 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
itself		3	EBI-17230,EBI-17230
RAP1	P11938	2	EBI-17230,EBI-14821
SIR4	P11978	7	EBI-17230,EBI-17237

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 978

977

Regulatory protein SIR3

PRO_0000097768

Regions

Domain

48 – 188

141

BAH

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.8

Modified residue

502

1

Phosphoserine Ref.10

Experimental info

Mutagenesis

2

1

A → G: No acetylation, reduced silencing activity. Ref.8

Mutagenesis

2

1

A → Q: No acetylation, No silencing activity. Ref.8

Mutagenesis

2

1

A → S: No effect. Ref.8

Mutagenesis

2

1

A → T: Reduced silencing activity. Ref.8

Sequence conflict

74

1

I → T in AAT93176. Ref.4

Sequence conflict

331

1

P → S in CAA25668. Ref.1

Sequence conflict

335

1

T → P in CAA25668. Ref.1

Sequence conflict

405

1

S → G in CAA25668. Ref.1

Sequence conflict

421

1

K → Q in CAA25668. Ref.1

Sequence conflict

429 – 430

2

NE → KK in CAA25668. Ref.1

Sequence conflict

497

1

L → V in CAA25668. Ref.1

Sequence conflict

587

1

Q → R in CAA25668. Ref.1

Sequence conflict

597

1

I → V in CAA25668. Ref.1

Sequence conflict

669

1

E → D in CAA25668. Ref.1

Sequence conflict

704

1

R → G in CAA25668. Ref.1

Sequence conflict

712

1

S → T in CAA25668. Ref.1

Sequence conflict

726

1

D → N in CAA25668. Ref.1

Sequence conflict

828

1

L → F Ref.1

Sequence conflict

830

1

V → L Ref.1

Sequence conflict

925

1

Q → K in CAA25668. Ref.1

Secondary structure

1

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978

Helix Strand Turn

Details...

Beta strand

11 – 16

6

Beta strand

18 – 20

3

Beta strand

37 – 43

7

Turn

44 – 46

3

Beta strand

55 – 60

6

Turn

61 – 64

4

Beta strand

65 – 75

11

Beta strand

84 – 91

8

Helix

93 – 95

3

Helix

98 – 105

8

Helix

107 – 111

5

Helix

116 – 126

11

Beta strand

131 – 141

11

Helix

143 – 145

3

Beta strand

146 – 149

4

Beta strand

151 – 153

3

Turn

155 – 157

3

Turn

167 – 169

3

Beta strand

170 – 176

7

Helix

189 – 198

10

Helix

201 – 211

11

Sequences

	Sequence		Length	Mass (Da)
	P06701 [UniParc]. Last modified January 23, 2007. Version 6. Checksum: CA2503D7645397AC	FASTA	978	111,360
	10 20 30 40 50 60 MAKTLKDLDG WQVIITDDQG RVIDDNNRRR SRKRGGENVF LKRISDGLSF GKGESVIFND 70 80 90 100 110 120 NVTETYSVYL IHEIRLNTLN NVVEIWVFSY LRWFELKPKL YYEQFRPDLI KEDHPLEFYK 130 140 150 160 170 180 DKFFNEVNKS ELYLTAELSE IWLKDFIAVG QILPESQWND SSIDKIEDRD FLVRYACEPT 190 200 210 220 230 240 AEKFVPIDIF QIIRRVKEME PKQSDEYLKR VSVPVSGQKT NRQVMHKMGV ERSSKRLAKK 250 260 270 280 290 300 PSMKKIKIEP SADDDVNNGN IPSQRGTSTT HGSISPQEES VSPNISSASP SALTSPTDSS 310 320 330 340 350 360 KILQKRSISK ELIVSEEIPI NSSEQESDYE PNNETSVLSS KPGSKPEKTS TELVDGRENF 370 380 390 400 410 420 VYANNPEVSD DGGLEEETDE VSSESSDEAI IPVNKRRGAH GSELSSKIRK IHIQETQEFS 430 440 450 460 470 480 KNYTTETDNE MNGNGKPGIP RGNTKIHSMN ENPTPEKGNA KMIDFATLSK LKKKYQIILD 490 500 510 520 530 540 RFAPDNQVTD SSQLNKLTDE QSSLDVAGLE DKFRKACSSS GRETILSNFN ADINLEESIR 550 560 570 580 590 600 ESLQKRELLK SQVEDFTRIF LPIYDSLMSS QNKLFYITNA DDSTKFQLVN DVMDELITSS 610 620 630 640 650 660 ARKELPIFDY IHIDALELAG MDALYEKIWF AISKENLCGD ISLEALNFYI TNVPKAKKRK 670 680 690 700 710 720 TLILIQNPEN LLSEKILQYF EKWISSKNSK LSIICVGGHN VTIREQINIM PSLKAHFTEI 730 740 750 760 770 780 KLNKVDKNEL QQMIITRLKS LLKPFHVKVN DKKEMTIYNN IREGQNQKIP DNVIVINHKI 790 800 810 820 830 840 NNKITQLIAK NVANVSGSTE KAFKICEAAV EISKKDFVRK GGLQKGKLVV SQEMVPRYFS 850 860 870 880 890 900 EAINGFKDET ISKKIIGMSL LMRTFLYTLA QETEGTNRHT LALETVLIKM VKMLRDNPGY 910 920 930 940 950 960 KASKEIKKVI CGAWEPAITI EKLKQFSWIS VVNDLVGEKL VVVVLEEPSA SIMVELKLPL 970 EINYAFSMDE EFKNMDCI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of two genes required for the position-effect control of yeast mating-type genes." Shore D., Squire M., Nasmyth K.A. EMBO J. 3:2817-2823(1984) [PubMed: 6098447] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [PubMed: 9169871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[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]	"Activation of an MAP kinase cascade leads to Sir3p hyperphosphorylation and strengthens transcriptional silencing." Stone E.M., Pillus L. J. Cell Biol. 135:571-583(1996) [PubMed: 8909534] [Abstract] Cited for: PHOSPHORYLATION.
[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]	"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].
[8]	"Importance of the sir3 N terminus and its acetylation for yeast transcriptional silencing." Wang X., Connelly J.J., Wang C.L., Sternglanz R. Genetics 168:547-551(2004) [PubMed: 15454564] [Abstract] Cited for: MUTAGENESIS OF ALA-2, ACETYLATION AT ALA-2.
[9]	"Dual roles for Mcm10 in DNA replication initiation and silencing at the mating-type loci." Douglas N.L., Dozier S.K., Donato J.J. Mol. Biol. Rep. 32:197-204(2005) [PubMed: 16328881] [Abstract] Cited for: INTERACTION WITH MCM10.
[10]	"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-502, MASS SPECTROMETRY.
[11]	"Structure of the Sir3 protein bromo adjacent homology (BAH) domain from S. cerevisiae at 1.95 A resolution." Hou Z., Danzer J.R., Fox C.A., Keck J.L. Protein Sci. 15:1182-1186(2006) [PubMed: 16641491] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 2-229.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X01420 Genomic DNA. Translation: CAA25668.1.
U21094 Genomic DNA. Translation: AAB67522.1.
AY693157 Genomic DNA. Translation: AAT93176.1.
BK006945 Genomic DNA. Translation: DAA09743.1.

PIR

RGBYI3. S59410.

RefSeq

NP_013547.1. NM_001182330.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2FL7	X-ray	1.85	A	1-229	[»]
2FVU	X-ray	2.00	A/B	1-218	[»]
3OWT	X-ray	2.00	C	456-481	[»]
3TE6	X-ray	2.80	A/B	530-845	[»]
3TU4	X-ray	3.00	K/L	1-213	[»]

ProteinModelPortal

P06701.

SMR

P06701. Positions 8-215, 530-844.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-595N.

IntAct

P06701. 36 interactions.

MINT

MINT-673027.

STRING

P06701.

Proteomic databases

PeptideAtlas

P06701.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YLR442C; YLR442C; YLR442C.

GeneID

851163.

KEGG

sce:YLR442C.

NMPDR

fig|4932.3.peg.4578.

Organism-specific databases

SGD

S000004434. SIR3.

Phylogenomic databases

eggNOG

fuNOG05465.

OMA

YLIHEIR.

OrthoDB

EOG4H1F5T.

Gene expression databases

ArrayExpress

P06701.

Genevestigator

P06701.

GermOnline

YLR442C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR001025. BAH_dom.
[Graphical view]

KO

K11122.

Pfam

PF01426. BAH. 1 hit.
[Graphical view]

SMART

SM00439. BAH. 1 hit.
[Graphical view]

PROSITE

PS51038. BAH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

967960.

Entry information

Entry name

SIR3_YEAST

Accession

Primary (citable) accession number: P06701
Secondary accession number(s): D6VZ77, E9P924

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 110 of the entry and version 6 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program