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P49686

- NUP42_YEAST

UniProt

P49686 - NUP42_YEAST

Protein

Nucleoporin NUP42

Gene

NUP42

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 129 (01 Oct 2014)
      Sequence version 1 (01 Feb 1996)
      Previous versions | rss
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    Functioni

    Functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. Active directional transport is assured by both, a Phe-Gly (FG) repeat affinity gradient for these transport factors across the NPC and a transport cofactor concentration gradient across the nuclear envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in the nucleus, with GDP in the cytoplasm). NUP42 is specifically important for nuclear protein and mRNA export.8 Publications

    GO - Molecular functioni

    1. nucleocytoplasmic transporter activity Source: SGD
    2. protein binding Source: IntAct
    3. structural constituent of nuclear pore Source: SGD

    GO - Biological processi

    1. cellular response to salt stress Source: SGD
    2. mRNA export from nucleus in response to heat stress Source: SGD
    3. NLS-bearing protein import into nucleus Source: SGD
    4. poly(A)+ mRNA export from nucleus Source: SGD
    5. posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery Source: SGD
    6. transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery Source: SGD

    Keywords - Biological processi

    mRNA transport, Protein transport, Translocation, Transport

    Enzyme and pathway databases

    BioCyciYEAST:G3O-29780-MONOMER.

    Protein family/group databases

    TCDBi1.I.1.1.1. the nuclear pore complex (npc) family.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nucleoporin NUP42
    Alternative name(s):
    Nuclear pore protein NUP42
    Gene namesi
    Name:NUP42
    Synonyms:RIP1, UIP1
    Ordered Locus Names:YDR192C
    ORF Names:YD9346.04C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IV

    Organism-specific databases

    CYGDiYDR192c.
    SGDiS000002600. NUP42.

    Subcellular locationi

    GO - Cellular componenti

    1. nuclear membrane Source: UniProtKB-SubCell
    2. nuclear pore Source: SGD
    3. nuclear pore central transport channel Source: SGD
    4. nuclear pore cytoplasmic filaments Source: SGD

    Keywords - Cellular componenti

    Membrane, Nuclear pore complex, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 430430Nucleoporin NUP42PRO_0000204866Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei137 – 1371Phosphoserine1 Publication
    Modified residuei298 – 2981Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP49686.
    PaxDbiP49686.

    Expressioni

    Gene expression databases

    GenevestigatoriP49686.

    Interactioni

    Subunit structurei

    The nuclear pore complex (NPC) constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. The 55-60 MDa NPC is composed of at least 31 different subunits: ASM4, CDC31, GLE1, GLE2, NDC1, NIC96, NSP1, NUP1, NUP2, NUP100, NUP116, NUP120, NUP133, NUP145, NUP157, NUP159, NUP170, NUP188, NUP192, NUP42, NUP49, NUP53, NUP57, NUP60, NUP82, NUP84, NUP85, POM152, POM34, SEH1 and SEC1. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. NUP42 interacts with the NUP82 subcomplex (NUP82, NUP159, NSP1). It interacts directly with GLE1, and through its FG repeats with GFD1, the heterodimeric mRNA transport factor MEX67/MTR2, and the karyopherin CRM1.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    KAP95Q061422EBI-12310,EBI-9145
    NUP100Q026292EBI-12310,EBI-11698
    NUP116Q026302EBI-12310,EBI-11703
    NUP57P488372EBI-12310,EBI-12324

    Protein-protein interaction databases

    BioGridi32245. 84 interactions.
    DIPiDIP-2313N.
    IntActiP49686. 16 interactions.
    MINTiMINT-476904.
    STRINGi4932.YDR192C.

    Structurei

    3D structure databases

    ProteinModelPortaliP49686.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati2 – 54SXFG 1
    Repeati38 – 469SAFGXPXFG 1
    Repeati58 – 669SAFGXPXFG 2
    Repeati78 – 814SXFG 2
    Repeati90 – 989SAFGXPXFG 3
    Repeati112 – 1209SAFGXPXFG 4
    Repeati124 – 1252FG 1
    Repeati134 – 1352FG 2
    Repeati143 – 1519SAFGXPXFG 5
    Repeati168 – 1714SXFG 3
    Repeati182 – 1854SXFG 4
    Repeati200 – 2089SAFGXPXFG 6
    Repeati215 – 2184SXFG 5
    Repeati232 – 2354SXFG 6
    Repeati259 – 2624SXFG 7
    Repeati277 – 2804SXFG 8
    Repeati296 – 2972FG 3
    Repeati312 – 3154SXFG 9
    Repeati319 – 3224FG 4
    Repeati339 – 3402FG 5
    Repeati361 – 3644FG 6

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni121 – 230110Interactions with CRM1 and GFD1Add
    BLAST
    Regioni365 – 43066Interaction with GLE1Add
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi269 – 2735Poly-Asn
    Compositional biasi423 – 4264Poly-Pro

    Domaini

    Contains FG repeats. FG repeats are interaction sites for karyopherins (importins, exportins) and form probably an affinity gradient, guiding the transport proteins unidirectionally with their cargo through the NPC. FG repeat regions are highly flexible and lack ordered secondary structure. The overall conservation of FG repeats regarding exact sequence, spacing, and repeat unit length is limited. FG repeat types and their physico-chemical environment change across the NPC from the nucleoplasmic to the cytoplasmic side: SXFG/PXFG repeats are especially abundant in NUPs on the cytoplasmic side.

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiNOG12793.
    OMAiNNTTTGM.
    OrthoDBiEOG754HXQ.

    Sequencei

    Sequence statusi: Complete.

    P49686-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSAFGNPFTS GAKPNLSNTS GINPFTNNAA STNNMGGSAF GRPSFGTANT    50
    MTGGTTTSAF GMPQFGTNTG NTGNTSISAF GNTSNAAKPS AFGAPAFGSS 100
    APINVNPPST TSAFGAPSFG STGFGAMAAT SNPFGKSPGS MGSAFGQPAF 150
    GANKTAIPSS SVSNSNNSAF GAASNTPLTT TSPFGSLQQN ASQNASSTSS 200
    AFGKPTFGAA TNTQSPFGTI QNTSTSSGTG VSPFGTFGTN SNNKSPFSNL 250
    QSGAGAGSSP FGTTTSKANN NNNVGSSAFG TTNNQSPFSG GSGGTFGSAS 300
    NLNKNTNGNF QSSFGNKGFS FGITPQNDAN KVSQSNPSFG QTMPNTDPNI 350
    SLKSNGNATS FGFGQQQMNA TNVNANTATG KIRFVQGLSS EKDGILELAD 400
    LAEETLKIFR ANKFELGLVP DIPPPPALVA 430
    Length:430
    Mass (Da):42,778
    Last modified:February 1, 1996 - v1
    Checksum:i357F94914A5261F4
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti331 – 3311K → Q in AAA87033. (PubMed:7634338)Curated
    Sequence conflicti419 – 4191V → D in AAA87033. (PubMed:7634338)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U30614 Genomic DNA. Translation: AAA87033.1.
    Z48784 Genomic DNA. Translation: CAA88706.1.
    AY723779 Genomic DNA. Translation: AAU09696.1.
    BK006938 Genomic DNA. Translation: DAA12035.1.
    PIRiS52700.
    RefSeqiNP_010478.3. NM_001180500.3.

    Genome annotation databases

    EnsemblFungiiYDR192C; YDR192C; YDR192C.
    GeneIDi851774.
    KEGGisce:YDR192C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U30614 Genomic DNA. Translation: AAA87033.1 .
    Z48784 Genomic DNA. Translation: CAA88706.1 .
    AY723779 Genomic DNA. Translation: AAU09696.1 .
    BK006938 Genomic DNA. Translation: DAA12035.1 .
    PIRi S52700.
    RefSeqi NP_010478.3. NM_001180500.3.

    3D structure databases

    ProteinModelPortali P49686.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 32245. 84 interactions.
    DIPi DIP-2313N.
    IntActi P49686. 16 interactions.
    MINTi MINT-476904.
    STRINGi 4932.YDR192C.

    Protein family/group databases

    TCDBi 1.I.1.1.1. the nuclear pore complex (npc) family.

    Proteomic databases

    MaxQBi P49686.
    PaxDbi P49686.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YDR192C ; YDR192C ; YDR192C .
    GeneIDi 851774.
    KEGGi sce:YDR192C.

    Organism-specific databases

    CYGDi YDR192c.
    SGDi S000002600. NUP42.

    Phylogenomic databases

    eggNOGi NOG12793.
    OMAi NNTTTGM.
    OrthoDBi EOG754HXQ.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-29780-MONOMER.

    Miscellaneous databases

    NextBioi 969570.

    Gene expression databases

    Genevestigatori P49686.

    Family and domain databases

    ProtoNeti Search...

    Publicationsi

    1. "Identification of a novel nuclear pore-associated protein as a functional target of the HIV-1 Rev protein in yeast."
      Stutz F., Neville M., Rosbash M.
      Cell 82:495-506(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "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] [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 RNA export factor Gle1p is located on the cytoplasmic fibrils of the NPC and physically interacts with the FG-nucleoporin Rip1p, the DEAD-box protein Rat8p/Dbp5p and a new protein Ymr255p."
      Strahm Y., Fahrenkrog B., Zenklusen D., Rychner E., Kantor J., Rosbach M., Stutz F.
      EMBO J. 18:5761-5777(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH GLE1.
    6. "Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells."
      Hodge C.A., Colot H.V., Stafford P., Cole C.N.
      EMBO J. 18:5778-5788(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH CRM1 AND GFD1.
    7. "Binding of the Mex67p/Mtr2p heterodimer to FXFG, GLFG, and FG repeat nucleoporins is essential for nuclear mRNA export."
      Straesser K., Bassler J., Hurt E.C.
      J. Cell Biol. 150:695-706(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH MEX67/MTR2 HETERODIMER.
    8. "The yeast nuclear pore complex: composition, architecture, and transport mechanism."
      Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., Chait B.T.
      J. Cell Biol. 148:635-651(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, NPC SUBUNIT LOCATION.
    9. "Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways."
      Vainberg I.E., Dower K., Rosbash M.
      Mol. Cell. Biol. 20:3996-4005(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MRNA EXPORT.
    10. "Proteomic analysis of nucleoporin interacting proteins."
      Allen N.P., Huang L., Burlingame A., Rexach M.
      J. Biol. Chem. 276:29268-29274(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, NUCLEOPORIN INTERACTING PROTEINS.
    11. "A gradient of affinity for the karyopherin Kap95p along the yeast nuclear pore complex."
      Pyhtila B., Rexach M.
      J. Biol. Chem. 278:42699-42709(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, AFFINITY GRADIENT FOR KARYOPHERIN KAP95.
    12. "Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded."
      Denning D.P., Patel S.S., Uversky V., Fink A.L., Rexach M.
      Proc. Natl. Acad. Sci. U.S.A. 100:2450-2455(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, FG REPEAT STRUCTURE.
    13. "Minimal nuclear pore complexes define FG repeat domains essential for transport."
      Strawn L.A., Shen T.X., Shulga N., Goldfarb D.S., Wente S.R.
      Nat. Cell Biol. 6:197-206(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, FG REPEATS IN NPC TRANSPORT.
    14. "Peering through the pore: nuclear pore complex structure, assembly, and function."
      Suntharalingam M., Wente S.R.
      Dev. Cell 4:775-789(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    15. "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-137 AND SER-298, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiNUP42_YEAST
    AccessioniPrimary (citable) accession number: P49686
    Secondary accession number(s): D6VSH5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: February 1, 1996
    Last modified: October 1, 2014
    This is version 129 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    2. Yeast chromosome IV
      Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

    External Data

    Dasty 3