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P53686

- HST2_YEAST

UniProt

P53686 - HST2_YEAST

Protein

NAD-dependent protein deacetylase HST2

Gene

HST2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 133 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    Functioni

    NAD-dependent histone deacetylase that is involved in nuclear silencing events. Derepresses subtelomeric silencing and increases repression in nucleolar (rDNA) silencing. Its function is negatively regulated by active nuclear export.5 Publications

    Catalytic activityi

    NAD+ + an acetylprotein = nicotinamide + O-acetyl-ADP-ribose + a protein.1 PublicationPROSITE-ProRule annotation

    Cofactori

    Binds 1 zinc ion per subunit.

    Enzyme regulationi

    Inhibited by ADP-ribose and nicotinamide.1 Publication

    Kineticsi

    1. KM=10.2 µM for NAD+4 Publications
    2. KM=0.92 µM for acetylated poly-L-lysine4 Publications
    3. KM=0.5 µM for a synthetic histone H3K14 acetyllysine peptide4 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei135 – 1351Proton acceptor1 PublicationPROSITE-ProRule annotation
    Metal bindingi143 – 1431Zinc4 PublicationsPROSITE-ProRule annotation
    Metal bindingi146 – 1461Zinc4 PublicationsPROSITE-ProRule annotation
    Metal bindingi170 – 1701Zinc4 PublicationsPROSITE-ProRule annotation
    Metal bindingi173 – 1731Zinc4 PublicationsPROSITE-ProRule annotation
    Binding sitei270 – 2701NAD; via amide nitrogen2 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi32 – 5221NAD2 PublicationsAdd
    BLAST
    Nucleotide bindingi115 – 1184NAD2 Publications
    Nucleotide bindingi223 – 2253NAD2 Publications
    Nucleotide bindingi248 – 2503NAD2 Publications

    GO - Molecular functioni

    1. NAD+ binding Source: InterPro
    2. NAD-dependent histone deacetylase activity Source: SGD
    3. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. chromatin silencing at rDNA Source: SGD
    2. chronological cell aging Source: SGD
    3. histone H4 deacetylation Source: UniProtKB
    4. negative regulation of chromatin silencing at telomere Source: SGD
    5. negative regulation of mitotic recombination Source: SGD
    6. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Hydrolase, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    Metal-binding, NAD, Zinc

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33934-MONOMER.
    SABIO-RKP53686.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NAD-dependent protein deacetylase HST2 (EC:3.5.1.-)
    Alternative name(s):
    Homologous to SIR2 protein 2
    Regulatory protein SIR2 homolog 2
    Gene namesi
    Name:HST2
    Ordered Locus Names:YPL015C
    ORF Names:LPA2C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XVI

    Organism-specific databases

    CYGDiYPL015c.
    SGDiS000005936. HST2.

    Subcellular locationi

    Cytoplasm. Nucleus
    Note: Shuttles between the nucleus and cytoplasm, but is largely cytoplasmic owing to efficient nuclear export. Nuclear exclusion is mediated by the exportin CRM1.

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. nucleus Source: SGD

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi117 – 1171I → A, D, H, W or Y: Nearly or completely catalytically inactive. 1 Publication
    Mutagenesisi117 – 1171I → F or V: Near wild-type activity for deacetylation. Increases slightly the KM for NAD(+) to 25 uM. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 357356NAD-dependent protein deacetylase HST2PRO_0000110282Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine1 Publication
    Modified residuei340 – 3401Phosphoserine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP53686.
    PaxDbiP53686.

    Expressioni

    Gene expression databases

    GenevestigatoriP53686.

    Interactioni

    Subunit structurei

    Homotrimer. Monomer. Homotrimeric in its unliganded state. Undergoes a trimer-monomer transition upon acetyl-lysine substrate binding.4 Publications

    Protein-protein interaction databases

    BioGridi36162. 37 interactions.
    IntActiP53686. 2 interactions.
    MINTiMINT-4504340.
    STRINGi4932.YPL015C.

    Structurei

    Secondary structure

    1
    357
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 64
    Helixi9 – 2113
    Beta strandi27 – 315
    Helixi33 – 397
    Beta strandi44 – 463
    Turni47 – 493
    Helixi51 – 533
    Helixi56 – 583
    Helixi63 – 675
    Helixi69 – 746
    Helixi77 – 8610
    Beta strandi88 – 903
    Helixi95 – 10511
    Beta strandi109 – 1146
    Helixi120 – 1234
    Helixi128 – 1303
    Beta strandi131 – 1333
    Beta strandi136 – 1438
    Turni144 – 1463
    Helixi153 – 1597
    Beta strandi161 – 1633
    Turni171 – 1733
    Beta strandi176 – 1816
    Helixi191 – 20818
    Beta strandi218 – 2236
    Turni230 – 2323
    Helixi233 – 2375
    Beta strandi242 – 2509
    Helixi254 – 2574
    Beta strandi264 – 2663
    Helixi270 – 28112
    Helixi284 – 2918
    Helixi304 – 31310

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Q14X-ray2.50A1-357[»]
    1Q17X-ray2.70A/B/C1-294[»]
    1Q1AX-ray1.50A5-293[»]
    1SZCX-ray1.75A1-294[»]
    1SZDX-ray1.50A1-294[»]
    2OD2X-ray2.00A1-294[»]
    2OD7X-ray2.00A1-294[»]
    2OD9X-ray2.05A1-294[»]
    2QQFX-ray2.00A1-294[»]
    2QQGX-ray2.05A1-294[»]
    ProteinModelPortaliP53686.
    SMRiP53686. Positions 5-293.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP53686.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini13 – 286274Deacetylase sirtuin-typePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the sirtuin family. Class I subfamily.Curated
    Contains 1 deacetylase sirtuin-type domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0846.
    GeneTreeiENSGT00740000115546.
    HOGENOMiHOG000085952.
    KOiK11121.
    OMAiFRPTIAH.
    OrthoDBiEOG7MWH64.

    Family and domain databases

    Gene3Di3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR003000. Sirtuin.
    IPR026591. Sirtuin_cat_small_dom.
    IPR017328. Sirtuin_class_I.
    IPR026590. Ssirtuin_cat_dom.
    [Graphical view]
    PANTHERiPTHR11085. PTHR11085. 1 hit.
    PfamiPF02146. SIR2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037938. SIR2_euk. 1 hit.
    SUPFAMiSSF52467. SSF52467. 1 hit.
    PROSITEiPS50305. SIRTUIN. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P53686-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSVSTASTEM SVRKIAAHMK SNPNAKVIFM VGAGISTSCG IPDFRSPGTG    50
    LYHNLARLKL PYPEAVFDVD FFQSDPLPFY TLAKELYPGN FRPSKFHYLL 100
    KLFQDKDVLK RVYTQNIDTL ERQAGVKDDL IIEAHGSFAH CHCIGCGKVY 150
    PPQVFKSKLA EHPIKDFVKC DVCGELVKPA IVFFGEDLPD SFSETWLNDS 200
    EWLREKITTS GKHPQQPLVI VVGTSLAVYP FASLPEEIPR KVKRVLCNLE 250
    TVGDFKANKR PTDLIVHQYS DEFAEQLVEE LGWQEDFEKI LTAQGGMGDN 300
    SKEQLLEIVH DLENLSLDQS EHESADKKDK KLQRLNGHDS DEDGASNSSS 350
    SQKAAKE 357
    Length:357
    Mass (Da):39,979
    Last modified:October 1, 1996 - v1
    Checksum:iED281E5B8241A4D0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U39063 Genomic DNA. Translation: AAA81035.1.
    U33335 Genomic DNA. Translation: AAB68090.1.
    AY693204 Genomic DNA. Translation: AAT93223.1.
    BK006949 Genomic DNA. Translation: DAA11413.1.
    PIRiS59678.
    RefSeqiNP_015310.1. NM_001183829.1.

    Genome annotation databases

    EnsemblFungiiYPL015C; YPL015C; YPL015C.
    GeneIDi856092.
    KEGGisce:YPL015C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U39063 Genomic DNA. Translation: AAA81035.1 .
    U33335 Genomic DNA. Translation: AAB68090.1 .
    AY693204 Genomic DNA. Translation: AAT93223.1 .
    BK006949 Genomic DNA. Translation: DAA11413.1 .
    PIRi S59678.
    RefSeqi NP_015310.1. NM_001183829.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1Q14 X-ray 2.50 A 1-357 [» ]
    1Q17 X-ray 2.70 A/B/C 1-294 [» ]
    1Q1A X-ray 1.50 A 5-293 [» ]
    1SZC X-ray 1.75 A 1-294 [» ]
    1SZD X-ray 1.50 A 1-294 [» ]
    2OD2 X-ray 2.00 A 1-294 [» ]
    2OD7 X-ray 2.00 A 1-294 [» ]
    2OD9 X-ray 2.05 A 1-294 [» ]
    2QQF X-ray 2.00 A 1-294 [» ]
    2QQG X-ray 2.05 A 1-294 [» ]
    ProteinModelPortali P53686.
    SMRi P53686. Positions 5-293.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36162. 37 interactions.
    IntActi P53686. 2 interactions.
    MINTi MINT-4504340.
    STRINGi 4932.YPL015C.

    Chemistry

    BindingDBi P53686.
    ChEMBLi CHEMBL5933.

    Proteomic databases

    MaxQBi P53686.
    PaxDbi P53686.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YPL015C ; YPL015C ; YPL015C .
    GeneIDi 856092.
    KEGGi sce:YPL015C.

    Organism-specific databases

    CYGDi YPL015c.
    SGDi S000005936. HST2.

    Phylogenomic databases

    eggNOGi COG0846.
    GeneTreei ENSGT00740000115546.
    HOGENOMi HOG000085952.
    KOi K11121.
    OMAi FRPTIAH.
    OrthoDBi EOG7MWH64.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33934-MONOMER.
    SABIO-RK P53686.

    Miscellaneous databases

    EvolutionaryTracei P53686.
    NextBioi 981122.
    PROi P53686.

    Gene expression databases

    Genevestigatori P53686.

    Family and domain databases

    Gene3Di 3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    InterProi IPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR003000. Sirtuin.
    IPR026591. Sirtuin_cat_small_dom.
    IPR017328. Sirtuin_class_I.
    IPR026590. Ssirtuin_cat_dom.
    [Graphical view ]
    PANTHERi PTHR11085. PTHR11085. 1 hit.
    Pfami PF02146. SIR2. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF037938. SIR2_euk. 1 hit.
    SUPFAMi SSF52467. SSF52467. 1 hit.
    PROSITEi PS50305. SIRTUIN. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression, and chromosome stability."
      Brachmann C.B., Sherman J.M., Devine S.E., Cameron E.E., Pillus L., Boeke J.D.
      Genes Dev. 9:2888-2902(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: S288c / YPH1.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
      Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
      , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
      Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. "The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases."
      Landry J., Sutton A., Tafrov S.T., Heller R.C., Stebbins J., Pillus L., Sternglanz R.
      Proc. Natl. Acad. Sci. U.S.A. 97:5807-5811(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. "Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose."
      Tanner K.G., Landry J., Sternglanz R., Denu J.M.
      Proc. Natl. Acad. Sci. U.S.A. 97:14178-14182(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    7. "A cytosolic NAD-dependent deacetylase, Hst2p, can modulate nucleolar and telomeric silencing in yeast."
      Perrod S., Cockell M.M., Laroche T., Renauld H., Ducrest A.L., Bonnard C., Gasser S.M.
      EMBO J. 20:197-209(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    10. "Substrate specificity and kinetic mechanism of the Sir2 family of NAD+-dependent histone/protein deacetylases."
      Borra M.T., Langer M.R., Slama J.T., Denu J.M.
      Biochemistry 43:9877-9887(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    11. "Nuclear export modulates the cytoplasmic Sir2 homologue Hst2."
      Wilson J.M., Le V.Q., Zimmerman C., Marmorstein R., Pillus L.
      EMBO Rep. 7:1247-1251(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    12. "Use of substrate analogs and mutagenesis to study substrate binding and catalysis in the Sir2 family of NAD-dependent protein deacetylases."
      Khan A.N., Lewis P.N.
      J. Biol. Chem. 281:11702-11711(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    13. "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-340, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Investigation of the catalytic mechanism of Sir2 enzyme with QM/MM approach: SN1 vs SN2?"
      Liang Z., Shi T., Ouyang S., Li H., Yu K., Zhu W., Luo C., Jiang H.
      J. Phys. Chem. B 114:11927-11933(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE.
    15. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    16. "Structure and autoregulation of the yeast Hst2 homolog of Sir2."
      Zhao K., Chai X., Clements A., Marmorstein R.
      Nat. Struct. Biol. 10:864-871(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH PEPTIDE SUBSTRATE; ZINC AND NAD.
    17. "Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide."
      Zhao K., Chai X., Marmorstein R.
      Structure 11:1403-1411(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 5-293 IN COMPLEX WITH SUBSTRATE ANALOG; PEPTIDE SUBSTRATE AND ZINC, SUBUNIT.
    18. "Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases."
      Zhao K., Harshaw R., Chai X., Marmorstein R.
      Proc. Natl. Acad. Sci. U.S.A. 101:8563-8568(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 1-294 IN COMPLEX WITH PEPTIDE SUBSTRATE; ZINC AND NAD.
    19. "Structural basis for nicotinamide inhibition and base exchange in Sir2 enzymes."
      Sanders B.D., Zhao K., Slama J.T., Marmorstein R.
      Mol. Cell 25:463-472(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 1-294 IN COMPLEX WITH PEPTIDE SUBSTRATE; NICOTINAMIDE AND ZINC, MUTAGENESIS OF 117, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiHST2_YEAST
    AccessioniPrimary (citable) accession number: P53686
    Secondary accession number(s): D6W3Z7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: October 1, 2014
    This is version 133 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 5260 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, 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 XVI
      Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

    External Data

    Dasty 3