Nucleoporin NUP42 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P49686 (NUP42_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 106. History...

Clusters with 100%, 90%, 50% identity |

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Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	430 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Nucleus › nuclear 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 process	Protein transport Translocation Transport mRNA transport
Cellular component	Membrane Nuclear pore complex Nucleus
Domain	Repeat
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	mRNA export from nucleus in response to heat stress Inferred from mutant phenotype. 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. Source: SGD protein transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nuclear membrane Inferred from electronic annotation. Source: UniProtKB-SubCell nuclear pore Inferred from direct assay Ref.5 Ref.8 Ref.1. Source: SGD
Molecular function	protein binding Inferred from physical interaction. Source: IntAct structural molecule activity Traceable author statement. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct
KAP95	Q06142	2	EBI-12310,EBI-9145
NUP100	Q02629	2	EBI-12310,EBI-11698
NUP116	Q02630	2	EBI-12310,EBI-11703
NUP57	P48837	2	EBI-12310,EBI-12324

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 430

430

Nucleoporin NUP42

PRO_0000204866

Regions

Repeat

2 – 5

SXFG 1

Repeat

38 – 46

SAFGXPXFG 1

Repeat

58 – 66

SAFGXPXFG 2

Repeat

78 – 81

SXFG 2

Repeat

90 – 98

SAFGXPXFG 3

Repeat

112 – 120

SAFGXPXFG 4

Repeat

124 – 125

FG 1

Repeat

134 – 135

FG 2

Repeat

143 – 151

SAFGXPXFG 5

Repeat

168 – 171

SXFG 3

Repeat

182 – 185

SXFG 4

Repeat

200 – 208

SAFGXPXFG 6

Repeat

215 – 218

SXFG 5

Repeat

232 – 235

SXFG 6

Repeat

259 – 262

SXFG 7

Repeat

277 – 280

SXFG 8

Repeat

296 – 297

FG 3

Repeat

312 – 315

SXFG 9

Repeat

319 – 322

FG 4

Repeat

339 – 340

FG 5

Repeat

361 – 364

FG 6

Region

121 – 230

110

Interactions with CRM1 and GFD1

Region

365 – 430

Interaction with GLE1

Compositional bias

269 – 273

Poly-Asn

Compositional bias

423 – 426

Poly-Pro

Amino acid modifications

Modified residue

137

Phosphoserine Ref.15

Modified residue

298

Phosphoserine Ref.15

Experimental info

Sequence conflict

331

K → Q in AAA87033. Ref.1

Sequence conflict

419

V → D in AAA87033. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

P49686 [UniParc].

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

430

42,778

        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' referencesShow '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: 7634338] [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. Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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. LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [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: 10610322] [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: 10523319] [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: 10952996] [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: 10684247] [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: 10805742] [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: 11387327] [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: 12917401] [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: 12604785] [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: 15039779] [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: 12791264] [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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-137 AND SER-298, MASS SPECTROMETRY.
+	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.
PIR	S52700.
RefSeq	NP_010478.1. NM_001180500.1.
3D structure databases
ProteinModelPortal	P49686.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2313N.
IntAct	P49686. 17 interactions.
MINT	MINT-476904.
STRING	P49686.
Protein family/group databases
TCDB	9.A.14.1.1. nuclear pore complex (NPC) family.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YDR192C; YDR192C; YDR192C.
GeneID	851774.
KEGG	sce:YDR192C.
NMPDR	fig\|4932.3.peg.1230.
Organism-specific databases
CYGD	YDR192c.
SGD	S000002600. NUP42.
Phylogenomic databases
eggNOG	fuNOG11820.
GeneTree	EFGT00050000000035.
OMA	TIANTNQ.
OrthoDB	EOG4XWK6M.
Gene expression databases
ArrayExpress	P49686.
Genevestigator	P49686.
GermOnline	YDR192C. Saccharomyces cerevisiae.
Family and domain databases
ProtoNet	Search...
Other
NextBio	969570.

Entry information

Entry name

NUP42_YEAST

Accession

Primary (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:	December 14, 2011
This is version 106 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

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

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents