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P49686

- NUP42_YEAST

UniProt

P49686 - NUP42_YEAST

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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

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. 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
Complete GO annotation...

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 pore Source: SGD
  2. nuclear pore central transport channel Source: SGD
  3. nuclear pore cytoplasmic filaments Source: SGD
Complete GO annotation...

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. 85 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.
InParanoidiP49686.
OMAiNNTTTGM.
OrthoDBiEOG754HXQ.

Sequencei

Sequence statusi: Complete.

P49686-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSAFGNPFTS GAKPNLSNTS GINPFTNNAA STNNMGGSAF GRPSFGTANT
60 70 80 90 100
MTGGTTTSAF GMPQFGTNTG NTGNTSISAF GNTSNAAKPS AFGAPAFGSS
110 120 130 140 150
APINVNPPST TSAFGAPSFG STGFGAMAAT SNPFGKSPGS MGSAFGQPAF
160 170 180 190 200
GANKTAIPSS SVSNSNNSAF GAASNTPLTT TSPFGSLQQN ASQNASSTSS
210 220 230 240 250
AFGKPTFGAA TNTQSPFGTI QNTSTSSGTG VSPFGTFGTN SNNKSPFSNL
260 270 280 290 300
QSGAGAGSSP FGTTTSKANN NNNVGSSAFG TTNNQSPFSG GSGGTFGSAS
310 320 330 340 350
NLNKNTNGNF QSSFGNKGFS FGITPQNDAN KVSQSNPSFG QTMPNTDPNI
360 370 380 390 400
SLKSNGNATS FGFGQQQMNA TNVNANTATG KIRFVQGLSS EKDGILELAD
410 420 430
LAEETLKIFR ANKFELGLVP DIPPPPALVA
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. 85 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.
InParanoidi P49686.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 130 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