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P49686 (NUP42_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nucleoporin NUP42
Alternative name(s):
Nuclear pore protein NUP42
Gene names
Name:NUP42
Synonyms:RIP1, UIP1
Ordered Locus Names:YDR192C
ORF Names:YD9346.04C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length430 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.5 Ref.6 Ref.7 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13

Subunit structure

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. Ref.5 Ref.6 Ref.7 Ref.8

Subcellular location

Nucleusnuclear pore complex. Nucleus membrane; Peripheral membrane protein; Cytoplasmic side.

Domain

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.

Ontologies

Keywords
   Biological processmRNA transport
Protein transport
Translocation
Transport
   Cellular componentMembrane
Nuclear pore complex
Nucleus
   DomainRepeat
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processNLS-bearing protein import into nucleus

Inferred from genetic interaction Ref.13. Source: SGD

cellular response to salt stress

Inferred from mutant phenotype PubMed 22851651. Source: SGD

mRNA export from nucleus in response to heat stress

Inferred from mutant phenotype PubMed 18258809PubMed 9353254PubMed 9353255. Source: SGD

poly(A)+ mRNA export from nucleus

Inferred from genetic interaction Ref.7. Source: SGD

posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery

Inferred from mutant phenotype PubMed 20932479. Source: SGD

transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery

Inferred from mutant phenotype PubMed 20098417PubMed 20932479. Source: SGD

   Cellular_componentnuclear membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

nuclear pore

Inferred from direct assay Ref.5Ref.8Ref.1. Source: SGD

nuclear pore central transport channel

Inferred from direct assay PubMed 18046406. Source: SGD

nuclear pore cytoplasmic filaments

Inferred from direct assay Ref.5Ref.8. Source: SGD

   Molecular_functionnucleocytoplasmic transporter activity

Inferred from genetic interaction Ref.10. Source: SGD

protein binding

Inferred from physical interaction PubMed 17418788. Source: IntAct

structural constituent of nuclear pore

Inferred from physical interaction PubMed 17418788. Source: SGD

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 430430Nucleoporin NUP42
PRO_0000204866

Regions

Repeat2 – 54SXFG 1
Repeat38 – 469SAFGXPXFG 1
Repeat58 – 669SAFGXPXFG 2
Repeat78 – 814SXFG 2
Repeat90 – 989SAFGXPXFG 3
Repeat112 – 1209SAFGXPXFG 4
Repeat124 – 1252FG 1
Repeat134 – 1352FG 2
Repeat143 – 1519SAFGXPXFG 5
Repeat168 – 1714SXFG 3
Repeat182 – 1854SXFG 4
Repeat200 – 2089SAFGXPXFG 6
Repeat215 – 2184SXFG 5
Repeat232 – 2354SXFG 6
Repeat259 – 2624SXFG 7
Repeat277 – 2804SXFG 8
Repeat296 – 2972FG 3
Repeat312 – 3154SXFG 9
Repeat319 – 3224FG 4
Repeat339 – 3402FG 5
Repeat361 – 3644FG 6
Region121 – 230110Interactions with CRM1 and GFD1
Region365 – 43066Interaction with GLE1
Compositional bias269 – 2735Poly-Asn
Compositional bias423 – 4264Poly-Pro

Amino acid modifications

Modified residue1371Phosphoserine Ref.15
Modified residue2981Phosphoserine Ref.15

Experimental info

Sequence conflict3311K → Q in AAA87033. Ref.1
Sequence conflict4191V → D in AAA87033. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P49686 [UniParc].

Last modified February 1, 1996. Version 1.
Checksum: 357F94914A5261F4

FASTA43042,778
        10         20         30         40         50         60 
MSAFGNPFTS GAKPNLSNTS GINPFTNNAA STNNMGGSAF GRPSFGTANT MTGGTTTSAF 

        70         80         90        100        110        120 
GMPQFGTNTG NTGNTSISAF GNTSNAAKPS AFGAPAFGSS APINVNPPST TSAFGAPSFG 

       130        140        150        160        170        180 
STGFGAMAAT SNPFGKSPGS MGSAFGQPAF GANKTAIPSS SVSNSNNSAF GAASNTPLTT 

       190        200        210        220        230        240 
TSPFGSLQQN ASQNASSTSS AFGKPTFGAA TNTQSPFGTI QNTSTSSGTG VSPFGTFGTN 

       250        260        270        280        290        300 
SNNKSPFSNL QSGAGAGSSP FGTTTSKANN NNNVGSSAFG TTNNQSPFSG GSGGTFGSAS 

       310        320        330        340        350        360 
NLNKNTNGNF QSSFGNKGFS FGITPQNDAN KVSQSNPSFG QTMPNTDPNI SLKSNGNATS 

       370        380        390        400        410        420 
FGFGQQQMNA TNVNANTATG KIRFVQGLSS EKDGILELAD LAEETLKIFR ANKFELGLVP 

       430 
DIPPPPALVA 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U30614 Genomic DNA. Translation: AAA87033.1.
Z48784 Genomic DNA. Translation: CAA88706.1.
AY723779 Genomic DNA. Translation: AAU09696.1.
BK006938 Genomic DNA. Translation: DAA12035.1.
PIRS52700.
RefSeqNP_010478.3. NM_001180500.3.

3D structure databases

ProteinModelPortalP49686.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32245. 84 interactions.
DIPDIP-2313N.
IntActP49686. 16 interactions.
MINTMINT-476904.
STRING4932.YDR192C.

Protein family/group databases

TCDB1.I.1.1.1. the nuclear pore complex (npc) family.

Proteomic databases

MaxQBP49686.
PaxDbP49686.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYDR192C; YDR192C; YDR192C.
GeneID851774.
KEGGsce:YDR192C.

Organism-specific databases

CYGDYDR192c.
SGDS000002600. NUP42.

Phylogenomic databases

eggNOGNOG12793.
OMANNTTTGM.
OrthoDBEOG754HXQ.

Enzyme and pathway databases

BioCycYEAST:G3O-29780-MONOMER.

Gene expression databases

GenevestigatorP49686.

Family and domain databases

ProtoNetSearch...

Other

NextBio969570.

Entry information

Entry nameNUP42_YEAST
AccessionPrimary (citable) accession number: P49686
Secondary accession number(s): D6VSH5
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: June 11, 2014
This is version 128 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IV

Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD