P06700 (SIR2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
NAD-dependent histone deacetylase SIR2
EC=3.5.1.-

Alternative name(s):
Regulatory protein SIR2
Silent information regulator 2

Gene names

Name:	SIR2
Synonyms:	MAR1
Ordered Locus Names:	YDL042C
ORF Names:	D2714

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

General annotation (Comments)

Function	NAD-dependent deacetylase, which participates in a wide range of cellular events including chromosome silencing, chromosome segregation, DNA recombination and the determination of life span. Involved in transcriptional repression of the silent mating-type loci HML and HMR and telomeric silencing via its association with SIR3 and SIR4. Plays a central role in ribosomal DNA (rDNA) silencing via its association with the RENT complex, preventing hyperrecombination, and repressing transcription from foreign promoters, which contributes to extending life span. Probably represses transcription via the formation of heterochromatin structure, which involves the compaction of chromatin fiber into a more condensed form, although this complex in at least one case can still bind euchromatic levels of positive transcription regulators. Although it displays some NAD-dependent histone deacetylase activity on 'Lys-9' and 'Lys-14' of histone H3 and 'Lys-16' of histone H4 in vitro, such activity is unclear in vivo and may not be essential. Ref.6 Ref.7 Ref.8 Ref.16 Ref.22
Catalytic activity	NAD+ + an acetylprotein = nicotinamide + O-acetyl-ADP-ribose + a protein.
Cofactor	Binds 1 zinc ion per subunit By similarity.
Enzyme regulation	Its activity is increased by calorie restriction, which slows the pace of aging and increases maximum lifespan. Activated by resveratrol (3,5,4'-trihydroxy-trans-stilbene), which is found in red wine. Ref.18
Subunit structure	Homomultimer. Interacts with ESC8 and ZDS2. Component of the RENT complex, at least composed of SIR2, CDC14 and NET1. The RENT complex interacts with FOB1. Forms a complex with SIR3 and SIR4. Interacts with MCM10 and SLX5. Ref.9 Ref.12 Ref.14 Ref.16 Ref.20 Ref.22
Subcellular location	Nucleus › nucleolus. Note: Associated with nucleolar chromatin. Preferentially bound to the spacer regions of the rDNA repeats through its interaction with NET1. Ref.5
Miscellaneous	Its stability is directly linked to life span, which is extended when it is present in high dosage. Conversely, its absence shortens life span. Present with 3350 molecules/cell in log phase SD medium. Ref.17
Sequence similarities	Belongs to the sirtuin family. Contains 1 deacetylase sirtuin-type domain.
Caution	Was originally (Ref.6) thought to be an ADP-ribosyltransferase.

Ontologies

Keywords
Biological process	DNA damage DNA repair Transcription Transcription regulation
Cellular component	Nucleus
Ligand	Metal-binding NAD Zinc
Molecular function	Chromatin regulator Hydrolase Repressor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	chromatin assembly or disassembly Inferred from direct assay. Source: SGD chromatin silencing at rDNA Inferred from mutant phenotype. Source: SGD chromatin silencing at silent mating-type cassette Inferred from mutant phenotype. Source: SGD chromatin silencing at telomere Inferred from mutant phenotype. Source: SGD chronological cell aging Inferred from mutant phenotype. Source: SGD double-strand break repair via nonhomologous end joining Inferred from direct assay. Source: SGD negative regulation of DNA recombination Inferred from genetic interaction. Source: SGD negative regulation of DNA replication Inferred from mutant phenotype. Source: SGD negative regulation of chromatin silencing involved in replicative cell aging Traceable author statement. Source: SGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	RENT complex Inferred from direct assay Ref.10. Source: SGD nuclear telomere cap complex Inferred from direct assay. Source: SGD nuclear telomeric heterochromatin Inferred from direct assay. Source: SGD
Molecular function	NAD+ binding Inferred from electronic annotation. Source: InterPro NAD-dependent histone deacetylase activity (H3-K14 specific) Inferred from direct assay Ref.7. Source: SGD NAD-dependent histone deacetylase activity (H3-K9 specific) Inferred from direct assay Ref.7. Source: SGD NAD-dependent histone deacetylase activity (H4-K16 specific) Inferred from direct assay Ref.7. Source: SGD protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CDC14	Q00684	5	EBI-17219,EBI-4192
SIR4	P11978	7	EBI-17219,EBI-17237

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 562

562

NAD-dependent histone deacetylase SIR2

PRO_0000110280

Regions

Domain

245 – 529

285

Deacetylase sirtuin-type

Nucleotide binding

262 – 281

20

NAD By similarity

Nucleotide binding

344 – 348

5

NAD By similarity

Sites

Active site

364

1

Proton acceptor By similarity

Metal binding

372

1

Zinc By similarity

Metal binding

375

1

Zinc By similarity

Metal binding

396

1

Zinc By similarity

Metal binding

399

1

Zinc By similarity

Amino acid modifications

Modified residue

23

1

Phosphoserine Ref.21 Ref.23

Modified residue

400

1

Phosphotyrosine Ref.23

Experimental info

Mutagenesis

139

1

R → K: Defects in telomeric silencing. Ref.15

Mutagenesis

270

1

G → E: Defects in telomeric silencing. Ref.15

Mutagenesis

296

1

F → L: Defects in telomeric silencing. Ref.15

Secondary structure

1

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562

Helix Strand Turn

Details...

Beta strand

213 – 217

5

Helix

244 – 253

10

Beta strand

255 – 261

7

Beta strand

274 – 276

3

Helix

282 – 284

3

Helix

292 – 296

5

Helix

298 – 303

6

Helix

306 – 311

6

Helix

312 – 315

4

Helix

324 – 334

11

Beta strand

338 – 343

6

Helix

349 – 352

4

Turn

357 – 359

3

Beta strand

360 – 362

3

Beta strand

370 – 372

3

Turn

373 – 375

3

Helix

385 – 389

5

Turn

397 – 399

3

Helix

400 – 406

7

Beta strand

438 – 442

5

Helix

451 – 460

10

Turn

461 – 463

3

Beta strand

466 – 469

4

Helix

479 – 481

3

Helix

482 – 485

4

Beta strand

492 – 498

7

Beta strand

506 – 510

5

Helix

513 – 523

11

Helix

533 – 537

5

Beta strand

541 – 545

5

Beta strand

551 – 555

5

Sequences

	Sequence		Length	Mass (Da)
	P06700 [UniParc]. Last modified January 1, 1988. Version 1. Checksum: 52E6937533654586	FASTA	562	63,262
	10 20 30 40 50 60 MTIPHMKYAV SKTSENKVSN TVSPTQDKDA IRKQPDDIIN NDEPSHKKIK VAQPDSLRET 70 80 90 100 110 120 NTTDPLGHTK AALGEVASME LKPTNDMDPL AVSAASVVSM SNDVLKPETP KGPIIISKNP 130 140 150 160 170 180 SNGIFYGPSF TKRESLNARM FLKYYGAHKF LDTYLPEDLN SLYIYYLIKL LGFEVKDQAL 190 200 210 220 230 240 IGTINSIVHI NSQERVQDLG SAISVTNVED PLAKKQTVRL IKDLQRAINK VLCTRLRLSN 250 260 270 280 290 300 FFTIDHFIQK LHTARKILVL TGAGVSTSLG IPDFRSSEGF YSKIKHLGLD DPQDVFNYNI 310 320 330 340 350 360 FMHDPSVFYN IANMVLPPEK IYSPLHSFIK MLQMKGKLLR NYTQNIDNLE SYAGISTDKL 370 380 390 400 410 420 VQCHGSFATA TCVTCHWNLP GERIFNKIRN LELPLCPYCY KKRREYFPEG YNNKVGVAAS 430 440 450 460 470 480 QGSMSERPPY ILNSYGVLKP DITFFGEALP NKFHKSIRED ILECDLLICI GTSLKVAPVS 490 500 510 520 530 540 EIVNMVPSHV PQVLINRDPV KHAEFDLSLL GYCDDIAAMV AQKCGWTIPH KKWNDLKNKN 550 560 FKCQEKDKGV YVVTSDEHPK TL

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 sequence of a 36.7 kb segment on the left arm of chromosome IV from Saccharomyces cerevisiae reveals 20 non-overlapping open reading frames (ORFs) including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 new ORFs." Saren A.-M., Laamanen P., Lejarcegui J.B., Paulin L. Yeast 13:65-71(1997) [PubMed: 9046088] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[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 204508 / S288c.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Localization of Sir2p: the nucleolus as a compartment for silent information regulators." Gotta M., Strahl-Bolsinger S., Renauld H., Laroche T., Kennedy B.K., Grunstein M., Gasser S.M. EMBO J. 16:3243-3255(1997) [PubMed: 9214640] [Abstract] Cited for: SUBCELLULAR LOCATION.
[6]	"An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing." Tanny J.C., Dowd G.J., Huang J., Hilz H., Moazed D. Cell 99:735-745(1999) [PubMed: 10619427] [Abstract] Cited for: PRELIMINARY FUNCTION.
[7]	"Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase." Imai S., Armstrong C.M., Kaeberlein M., Guarente L. Nature 403:795-800(2000) [PubMed: 10693811] [Abstract] Cited for: FUNCTION.
[8]	"Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae." Tsukamoto Y., Kato J., Ikeda H. Nature 388:900-903(1997) [PubMed: 9278054] [Abstract] Cited for: FUNCTION.
[9]	"Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3." Moazed D., Kistler A., Axelrod A., Rine J., Johnson A.D. Proc. Natl. Acad. Sci. U.S.A. 94:2186-2191(1997) [PubMed: 9122169] [Abstract] Cited for: INTERACTION WITH SIR3 AND SIR4.
[10]	"Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex." Shou W., Seol J.H., Shevchenko A., Baskerville C., Moazed D., Chen Z.W.S., Jang J., Shevchenko A., Charbonneau H., Deshaies R.J. Cell 97:233-244(1999) [PubMed: 10219244] [Abstract] Cited for: IDENTIFICATION IN A RENT COMPLEX WITH CDC14.
[11]	"Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity." Straight A.F., Shou W., Dowd G.J., Turck C.W., Deshaies R.J., Johnson A.D., Moazed D. Cell 97:245-256(1999) [PubMed: 10219245] [Abstract] Cited for: IDENTIFICATION IN A RENT COMPLEX WITH NET1.
[12]	"Two paralogs involved in transcriptional silencing that antagonistically control yeast life span." Roy N., Runge K.W. Curr. Biol. 10:111-114(2000) [PubMed: 10662670] [Abstract] Cited for: INTERACTION WITH ZDS2.
[13]	"Silenced chromatin is permissive to activator binding and PIC recruitment." Sekinger E.A., Gross D.S. Cell 105:403-414(2001) [PubMed: 11348596] [Abstract] Cited for: MECHANISM OF TRANSCRIPTION REPRESSION.
[14]	"Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8." Cuperus G., Shore D. Genetics 162:633-645(2002) [PubMed: 12399377] [Abstract] Cited for: INTERACTION WITH ESC8.
[15]	"A unique class of conditional sir2 mutants displays distinct silencing defects in Saccharomyces cerevisiae." Garcia S.N., Pillus L. Genetics 162:721-736(2002) [PubMed: 12399383] [Abstract] Cited for: MUTAGENESIS OF ARG-139; GLY-270 AND PHE-296.
[16]	"Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing." Huang J., Moazed D. Genes Dev. 17:2162-2176(2003) [PubMed: 12923057] [Abstract] Cited for: FUNCTION, INTERACTION WITH FOB1.
[17]	"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].
[18]	"Small molecule activators of sirtuins extend Saccharomyces cerevisiae lifespan." Howitz K.T., Bitterman K.J., Cohen H.Y., Lamming D.W., Lavu S., Wood J.G., Zipkin R.E., Chung P., Kisielewski A., Zhang L.-L., Scherer B., Sinclair D.A. Nature 425:191-196(2003) [PubMed: 12939617] [Abstract] Cited for: ENZYME REGULATION.
[19]	"The molecular biology of the SIR proteins." Gasser S.M., Cockell M.M. Gene 279:1-16(2001) [PubMed: 11722841] [Abstract] Cited for: REVIEW.
[20]	"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.
[21]	"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-23, MASS SPECTROMETRY.
[22]	"Slx5 promotes transcriptional silencing and is required for robust growth in the absence of Sir2." Darst R.P., Garcia S.N., Koch M.R., Pillus L. Mol. Cell. Biol. 28:1361-1372(2008) [PubMed: 18086879] [Abstract] Cited for: FUNCTION, INTERACTION WITH SLX5/HEX3.
[23]	"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-23 AND TYR-400, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Web resources

Protein Spotlight

In vino vita? - Issue 40 of November 2003

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X01419 Genomic DNA. Translation: CAA25667.1.
Z71781 Genomic DNA. Translation: CAA96447.1.
Z74090 Genomic DNA. Translation: CAA98600.1.
BK006938 Genomic DNA. Translation: DAA11814.1.

PIR

RGBYS2. S05891.

RefSeq

NP_010242.1. NM_001180101.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2HJH	X-ray	1.85	A/B	209-562	[»]

ProteinModelPortal

P06700.

SMR

P06700. Positions 211-555.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-596N.

IntAct

P06700. 50 interactions.

MINT

MINT-509141.

STRING

P06700.

Proteomic databases

PeptideAtlas

P06700.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDL042C; YDL042C; YDL042C.

GeneID

851520.

KEGG

sce:YDL042C.

NMPDR

fig|4932.3.peg.982.

Organism-specific databases

CYGD

YDL042c.

SGD

S000002200. SIR2.

Phylogenomic databases

eggNOG

fuNOG07733.

GeneTree

EFGT00050000002392.

HOGENOM

HBG203103.

OMA

PVKHAEF.

OrthoDB

EOG4DZ53T.

Gene expression databases

ArrayExpress

P06700.

Genevestigator

P06700.

GermOnline

YDL042C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR003000. NAD-dep_deAcase_sirtuin.
IPR007654. NAD-dep_histone_deAcase_SIR2_N.
[Graphical view]

KO

K11121.

PANTHER

PTHR11085. SIR2. 1 hit.

Pfam

PF04574. DUF592. 1 hit.
PF02146. SIR2. 1 hit.
[Graphical view]

PROSITE

PS50305. SIRTUIN. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

968896.

Entry information

Entry name

SIR2_YEAST

Accession

Primary (citable) accession number: P06700
Secondary accession number(s): D6VRV4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 1, 1988
Last modified:	December 14, 2011
This is version 135 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program