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Protein

Nucleoporin NUP42

Gene

NUP42

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: 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

  • nucleocytoplasmic transporter activity Source: SGD
  • structural constituent of nuclear pore Source: SGD

GO - Biological processi

  • cellular response to salt stress Source: SGD
  • mRNA export from nucleus in response to heat stress Source: SGD
  • NLS-bearing protein import into nucleus Source: SGD
  • poly(A)+ mRNA export from nucleus Source: SGD
  • posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery Source: SGD
  • 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
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR192C.
SGDiS000002600. NUP42.

Subcellular locationi

GO - Cellular componenti

  • nuclear membrane Source: UniProtKB-SubCell
  • nuclear pore Source: SGD
  • nuclear pore central transport channel Source: SGD
  • nuclear pore cytoplasmic filaments Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Nuclear pore complex, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002048661 – 430Nucleoporin NUP42Add BLAST430

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei137PhosphoserineCombined sources1
Modified residuei298PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP49686.
PRIDEiP49686.

PTM databases

iPTMnetiP49686.

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
GLE1Q123154EBI-12310,EBI-7635
KAP95Q061422EBI-12310,EBI-9145
NUP100Q026292EBI-12310,EBI-11698
NUP116Q026302EBI-12310,EBI-11703
NUP57P488372EBI-12310,EBI-12324

Protein-protein interaction databases

BioGridi32245. 86 interactors.
DIPiDIP-2313N.
IntActiP49686. 16 interactors.
MINTiMINT-476904.

Structurei

3D structure databases

ProteinModelPortaliP49686.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati2 – 5SXFG 14
Repeati38 – 46SAFGXPXFG 19
Repeati58 – 66SAFGXPXFG 29
Repeati78 – 81SXFG 24
Repeati90 – 98SAFGXPXFG 39
Repeati112 – 120SAFGXPXFG 49
Repeati124 – 125FG 12
Repeati134 – 135FG 22
Repeati143 – 151SAFGXPXFG 59
Repeati168 – 171SXFG 34
Repeati182 – 185SXFG 44
Repeati200 – 208SAFGXPXFG 69
Repeati215 – 218SXFG 54
Repeati232 – 235SXFG 64
Repeati259 – 262SXFG 74
Repeati277 – 280SXFG 84
Repeati296 – 297FG 32
Repeati312 – 315SXFG 94
Repeati319 – 322FG 44
Repeati339 – 340FG 52
Repeati361 – 364FG 64

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni121 – 230Interactions with CRM1 and GFD1Add BLAST110
Regioni365 – 430Interaction with GLE11 PublicationAdd BLAST66

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi269 – 273Poly-Asn5
Compositional biasi423 – 426Poly-Pro4

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

InParanoidiP49686.
KOiK18716.
OMAiTIANTNQ.
OrthoDBiEOG092C0CCA.

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)DescriptionActionsGraphical viewLength
Sequence conflicti331K → Q in AAA87033 (PubMed:7634338).Curated1
Sequence conflicti419V → D in AAA87033 (PubMed:7634338).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP49686.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32245. 86 interactors.
DIPiDIP-2313N.
IntActiP49686. 16 interactors.
MINTiMINT-476904.

Protein family/group databases

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

PTM databases

iPTMnetiP49686.

Proteomic databases

MaxQBiP49686.
PRIDEiP49686.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YDR192C.
SGDiS000002600. NUP42.

Phylogenomic databases

InParanoidiP49686.
KOiK18716.
OMAiTIANTNQ.
OrthoDBiEOG092C0CCA.

Enzyme and pathway databases

BioCyciYEAST:G3O-29780-MONOMER.

Miscellaneous databases

PROiP49686.

Family and domain databases

ProtoNetiSearch...

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: November 30, 2016
This is version 148 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.