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Q04636

- POB3_YEAST

UniProt

Q04636 - POB3_YEAST

Protein

FACT complex subunit POB3

Gene

POB3

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 118 (01 Oct 2014)
      Sequence version 1 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II. Transcription elongation is promoted by the repression of transcription initiation from cryptic sites. Also acts in establishing transcription initiation complexes and promotes SPT15/TBP-binding to a TATA box. Together with replication factor-A protein (RPA), FACT may play a role in nucleosome deposition during DNA replication.9 Publications

    GO - Molecular functioni

    1. DNA binding Source: InterPro
    2. protein binding Source: IntAct

    GO - Biological processi

    1. DNA-dependent DNA replication Source: SGD
    2. DNA repair Source: UniProtKB-KW
    3. DNA replication-independent nucleosome organization Source: SGD
    4. positive regulation of RNA polymerase II transcriptional preinitiation complex assembly Source: SGD
    5. regulation of transcription by chromatin organization Source: SGD
    6. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Biological processi

    DNA damage, DNA repair, DNA replication, Transcription, Transcription regulation

    Enzyme and pathway databases

    BioCyciYEAST:G3O-32664-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    FACT complex subunit POB3
    Alternative name(s):
    Facilitates chromatin transcription complex subunit POB3
    Gene namesi
    Name:POB3
    Ordered Locus Names:YML069W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIII

    Organism-specific databases

    CYGDiYML069w.
    SGDiS000004534. POB3.

    Subcellular locationi

    Nucleus. Chromosome
    Note: Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci.

    GO - Cellular componenti

    1. FACT complex Source: SGD
    2. nuclear chromatin Source: SGD
    3. replication fork protection complex Source: SGD

    Keywords - Cellular componenti

    Chromosome, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi20 – 201R → H in pob3-11; causes severe defects in rate of growth; when associated with C-109. 1 Publication
    Mutagenesisi78 – 781L → R in pob3-1; causes severe defects in rate of growth; when associated with K-419 and T-489. 1 Publication
    Mutagenesisi109 – 1091R → C in pob3-11; causes severe defects in rate of growth; when associated with H-20. 1 Publication
    Mutagenesisi308 – 3081Q → A or D: No effect. 1 Publication
    Mutagenesisi308 – 3081Q → K: Confers sensitivity to HU indicating a disturbed activity in DNA replication; confers a SPT- phenotype indicating a disturbed activity in transcription. 1 Publication
    Mutagenesisi308 – 3081Q → R: Confers sensitivity to HU indicating a disturbed activity in DNA replication. 1 Publication
    Mutagenesisi311 – 3111T → A: No change of sensitivity to HU; confers a SPT- phenotype indicating a disturbed activity in transcription. 1 Publication
    Mutagenesisi419 – 4191M → K in pob3-1; causes severe defects in rate of growth; when associated with R-78 and T-489. 1 Publication
    Mutagenesisi489 – 4891S → T in pob3-1; causes severe defects in rate of growth; when associated with R-78 and K-419. 1 Publication
    Mutagenesisi547 – 5471K → M in pob3-21; causes severe defects in rate of growth. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 552552FACT complex subunit POB3PRO_0000203250Add
    BLAST

    Proteomic databases

    MaxQBiQ04636.
    PaxDbiQ04636.
    PeptideAtlasiQ04636.

    Expressioni

    Gene expression databases

    GenevestigatoriQ04636.

    Interactioni

    Subunit structurei

    Forms a stable heterodimer with SPT16. The SPT16-POB3 dimer weakly associates with multiple molecules of NHP6 (NHP6A or NHP6B) to form the FACT (yFACT or SNP) complex. The FACT complex interacts with the CK2 (casein kinase II) complex subunits CKA1, CKA2, CKB1 and CKB2 and the components of the transcription machinery CHD1, CTR9, PAF1 and CDC73. The FACT complex interacts with the PAF1 complex. SPT16 interacts with SAS3 and POL1. Interacts directly with RFA1.9 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    RFA1P223363EBI-27863,EBI-14971
    SPT16P325589EBI-27863,EBI-4334

    Protein-protein interaction databases

    BioGridi35097. 188 interactions.
    DIPiDIP-4083N.
    IntActiQ04636. 46 interactions.
    MINTiMINT-559116.
    STRINGi4932.YML069W.

    Structurei

    Secondary structure

    552
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi1 – 1010
    Beta strandi17 – 226
    Beta strandi25 – 306
    Turni35 – 373
    Helixi38 – 414
    Beta strandi45 – 484
    Helixi49 – 513
    Beta strandi52 – 598
    Beta strandi61 – 7313
    Beta strandi75 – 817
    Helixi83 – 853
    Helixi86 – 9712
    Turni107 – 1104
    Beta strandi242 – 25211
    Beta strandi255 – 2617
    Beta strandi263 – 2697
    Beta strandi274 – 2785
    Helixi279 – 2813
    Beta strandi282 – 2898
    Beta strandi293 – 30816
    Beta strandi311 – 32111
    Beta strandi325 – 3295
    Helixi334 – 3407
    Turni341 – 3444
    Beta strandi347 – 3526
    Helixi353 – 36513
    Beta strandi384 – 3885
    Beta strandi391 – 3977
    Beta strandi399 – 40810
    Beta strandi410 – 4134
    Helixi414 – 4163
    Beta strandi417 – 4237
    Beta strandi434 – 4418
    Helixi442 – 4443
    Beta strandi447 – 4548
    Helixi455 – 4573
    Helixi458 – 46710

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GCJX-ray2.55A/B/C/D220-478[»]
    2GCLX-ray2.21A/B220-478[»]
    3F5RX-ray1.70A1-168[»]
    4PQ0X-ray1.65A232-473[»]
    ProteinModelPortaliQ04636.
    SMRiQ04636. Positions 1-178, 232-473.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ04636.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the SSRP1 family.Curated

    Phylogenomic databases

    eggNOGiCOG5165.
    GeneTreeiENSGT00560000076898.
    HOGENOMiHOG000180790.
    KOiK09272.
    OMAiIIQLDGF.
    OrthoDBiEOG7P2Z26.

    Family and domain databases

    Gene3Di2.30.29.30. 1 hit.
    InterProiIPR013719. DUF1747.
    IPR011993. PH_like_dom.
    IPR000969. SSrcognition.
    IPR024954. SSRP1_dom.
    [Graphical view]
    PfamiPF08512. Rtt106. 1 hit.
    PF03531. SSrecog. 2 hits.
    [Graphical view]
    PRINTSiPR00887. SSRCOGNITION.

    Sequencei

    Sequence statusi: Complete.

    Q04636-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSTDFDRIYL NQSKFSGRFR IADSGLGWKI STSGGSAANQ ARKPFLLPAT    50
    ELSTVQWSRG CRGYDLKINT KNQGVIQLDG FSQDDYNLIK NDFHRRFNIQ 100
    VEQREHSLRG WNWGKTDLAR NEMVFALNGK PTFEIPYARI NNTNLTSKNE 150
    VGIEFNIQDE EYQPAGDELV EMRFYIPGVI QTNVDENMTK KEESSNEVVP 200
    KKEDGAEGED VQMAVEEKSM AEAFYEELKE KADIGEVAGD AIVSFQDVFF 250
    TTPRGRYDID IYKNSIRLRG KTYEYKLQHR QIQRIVSLPK ADDIHHLLVL 300
    AIEPPLRQGQ TTYPFLVLQF QKDEETEVQL NLEDEDYEEN YKDKLKKQYD 350
    AKTHIVLSHV LKGLTDRRVI VPGEYKSKYD QCAVSCSFKA NEGYLYPLDN 400
    AFFFLTKPTL YIPFSDVSMV NISRAGQTST SSRTFDLEVV LRSNRGSTTF 450
    ANISKEEQQL LEQFLKSKNL RVKNEDREVQ ERLQTALGSD SDEEDINMGS 500
    AGEDDESVDE DFQVSSDNDA DEVAEEFDSD AALSDAEGGS DEERPSKKPK 550
    VE 552
    Length:552
    Mass (Da):62,994
    Last modified:November 1, 1997 - v1
    Checksum:i02C04F620C7B1450
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z38114 Genomic DNA. Translation: CAA86251.1.
    BK006946 Genomic DNA. Translation: DAA09828.1.
    PIRiS48328.
    RefSeqiNP_013642.1. NM_001182428.1.

    Genome annotation databases

    EnsemblFungiiYML069W; YML069W; YML069W.
    GeneIDi854933.
    KEGGisce:YML069W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z38114 Genomic DNA. Translation: CAA86251.1 .
    BK006946 Genomic DNA. Translation: DAA09828.1 .
    PIRi S48328.
    RefSeqi NP_013642.1. NM_001182428.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2GCJ X-ray 2.55 A/B/C/D 220-478 [» ]
    2GCL X-ray 2.21 A/B 220-478 [» ]
    3F5R X-ray 1.70 A 1-168 [» ]
    4PQ0 X-ray 1.65 A 232-473 [» ]
    ProteinModelPortali Q04636.
    SMRi Q04636. Positions 1-178, 232-473.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35097. 188 interactions.
    DIPi DIP-4083N.
    IntActi Q04636. 46 interactions.
    MINTi MINT-559116.
    STRINGi 4932.YML069W.

    Proteomic databases

    MaxQBi Q04636.
    PaxDbi Q04636.
    PeptideAtlasi Q04636.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YML069W ; YML069W ; YML069W .
    GeneIDi 854933.
    KEGGi sce:YML069W.

    Organism-specific databases

    CYGDi YML069w.
    SGDi S000004534. POB3.

    Phylogenomic databases

    eggNOGi COG5165.
    GeneTreei ENSGT00560000076898.
    HOGENOMi HOG000180790.
    KOi K09272.
    OMAi IIQLDGF.
    OrthoDBi EOG7P2Z26.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-32664-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q04636.
    NextBioi 977968.
    PROi Q04636.

    Gene expression databases

    Genevestigatori Q04636.

    Family and domain databases

    Gene3Di 2.30.29.30. 1 hit.
    InterProi IPR013719. DUF1747.
    IPR011993. PH_like_dom.
    IPR000969. SSrcognition.
    IPR024954. SSRP1_dom.
    [Graphical view ]
    Pfami PF08512. Rtt106. 1 hit.
    PF03531. SSrecog. 2 hits.
    [Graphical view ]
    PRINTSi PR00887. SSRCOGNITION.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein."
      Wittmeyer J., Formosa T.
      Mol. Cell. Biol. 17:4178-4190(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH POL1.
    4. "The yeast protein complex containing cdc68 and pob3 mediates core-promoter repression through the cdc68 N-terminal domain."
      Evans D.R.H., Brewster N.K., Xu Q., Rowley A., Altheim B.A., Johnston G.C., Singer R.A.
      Genetics 150:1393-1405(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SPT16.
    5. "Characterization of the CP complex, an abundant dimer of Cdc68 and Pob3 proteins that regulates yeast transcriptional activation and chromatin repression."
      Brewster N.K., Johnston G.C., Singer R.A.
      J. Biol. Chem. 273:21972-21979(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SPT16.
    6. "Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha."
      Wittmeyer J., Joss L., Formosa T.
      Biochemistry 38:8961-8971(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH SPT16, SUBCELLULAR LOCATION.
    7. "The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex."
      John S., Howe L., Tafrov S.T., Grant P.A., Sternglanz R., Workman J.L.
      Genes Dev. 14:1196-1208(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH SAS3.
    8. "POB3 is required for both transcription and replication in the yeast Saccharomyces cerevisiae."
      Schlesinger M.B., Formosa T.
      Genetics 155:1593-1606(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF ARG-20; LEU-78; ARG-109; MET-419; SER-489 AND LYS-547.
    9. "Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN."
      Formosa T., Eriksson P., Wittmeyer J., Ginn J., Yu Y., Stillman D.J.
      EMBO J. 20:3506-3517(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: ASSOCIATION OF THE SPT16-POB3 DIMER WITH NHP6A/B AND NUCLEOSOMES, FUNCTION OF THE FACT COMPLEX.
    10. "A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins modulates transcription."
      Brewster N.K., Johnston G.C., Singer R.A.
      Mol. Cell. Biol. 21:3491-3502(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: ASSOCIATION OF THE SPT16-POB3 DIMER WITH NHP6A/B.
    11. "The Paf1 complex physically and functionally associates with transcription elongation factors in vivo."
      Squazzo S.L., Costa P.J., Lindstrom D.L., Kumer K.E., Simic R., Jennings J.L., Link A.J., Arndt K.M., Hartzog G.A.
      EMBO J. 21:1764-1774(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH PAF1 COMPLEX.
    12. "Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: polymerase passage may degrade chromatin structure."
      Formosa T., Ruone S., Adams M.D., Olsen A.E., Eriksson P., Yu Y., Rhoades A.R., Kaufman P.D., Stillman D.J.
      Genetics 162:1557-1571(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE FACT COMPLEX.
    13. "RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach."
      Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A., Shilatifard A., Buratowski S., Greenblatt J.F.
      Mol. Cell. Biol. 22:6979-6992(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CHD1; CTR9; PAF1; CDC73; CKA1; CKA2; CKB1; CKB2 AND HISTONES.
    14. "Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes."
      Simic R., Lindstrom D.L., Tran H.G., Roinick K.L., Costa P.J., Johnson A.D., Hartzog G.A., Arndt K.M.
      EMBO J. 22:1846-1856(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CHD1.
    15. "Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes."
      Ruone S., Rhoades A.R., Formosa T.
      J. Biol. Chem. 278:45288-45295(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: ASSOCIATION OF THE SPT16-POB3 DIMER WITH NHP6A/B.
    16. "The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo."
      Mason P.B., Struhl K.
      Mol. Cell. Biol. 23:8323-8333(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE FACT COMPLEX, SUBCELLULAR LOCATION.
    17. Erratum
      Mason P.B., Struhl K.
      Mol. Cell. Biol. 24:6536-6536(2004)
    18. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    19. "Transcription elongation factors repress transcription initiation from cryptic sites."
      Kaplan C.D., Laprade L., Winston F.
      Science 301:1096-1099(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE FACT COMPLEX.
    20. "Transitions in RNA polymerase II elongation complexes at the 3' ends of genes."
      Kim M., Ahn S.-H., Krogan N.J., Greenblatt J.F., Buratowski S.
      EMBO J. 23:354-364(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    21. "Structural features of nucleosomes reorganized by yeast FACT and its HMG box component, Nhp6."
      Rhoades A.R., Ruone S., Formosa T.
      Mol. Cell. Biol. 24:3907-3917(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE FACT COMPLEX.
    22. "The yeast FACT complex has a role in transcriptional initiation."
      Biswas D., Yu Y., Prall M., Formosa T., Stillman D.J.
      Mol. Cell. Biol. 25:5812-5822(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF THE FACT COMPLEX.
    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] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    24. "The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition."
      Vandemark A.P., Blanksma M., Ferris E., Heroux A., Hill C.P., Formosa T.
      Mol. Cell 22:363-374(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 220-478, FUNCTION, INTERACTION WITH RFA1, MUTAGENESIS OF GLN-308 AND THR-311.

    Entry informationi

    Entry nameiPOB3_YEAST
    AccessioniPrimary (citable) accession number: Q04636
    Secondary accession number(s): D6VZA4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 118 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    In contrast to the orthologous protein in animals and plants, this protein does not contain a HMG box DNA-binding domain. This function may instead be provided by the HMG box of the associated NHP6A/NHP6B proteins in the FACT complex of yeast.
    Present with 22400 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 XIII
      Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

    External Data

    Dasty 3