Nucleoporin NUP60 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P39705 (NUP60_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 100. History...

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

Documents (2) |

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 NUP60

Alternative name(s):
Nuclear pore protein NUP60

Gene names

Name:	NUP60
Synonyms:	FUN17
Ordered Locus Names:	YAR002W

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	539 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). Ref.6 Ref.7 Ref.9 Ref.10
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. Binds to NUP1 and NUP2 forming the nuclear basket and the distal ring. The interaction with NUP2 is GSP1-GTP-dependent. Interacts through its FG repeats with karyopherins, such as KAP123 and KAP95-SRP1 (KAP60). Also interacts with GSP1-GTP and SRM1 (PRP20), where NUP60 reduces SRM1 activity, thus inhibiting GSP1 guanine nucleotide dissociation. Ref.5 Ref.7
Subcellular location	Nucleus › nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Nucleoplasmic side. Note: Nuclear basket.
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.
Post-translational modification	Phosphorylated by CDC28. Ref.12 Ref.13 Ref.14 Ref.15 Ref.16 Ref.17
Miscellaneous	Present with 4590 molecules/cell in log phase SD medium. Ref.8

Ontologies

Keywords
Biological process	Protein transport Translocation Transport mRNA transport
Cellular component	Membrane Nuclear pore complex Nucleus
Domain	Coiled coil Repeat
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	NLS-bearing substrate import into nucleus Inferred from mutant phenotype Ref.7. Source: SGD double-strand break repair Inferred from mutant phenotype. Source: SGD intracellular mRNA localization Inferred from mutant phenotype. Source: SGD mRNA export from nucleus in response to heat stress Inferred from mutant phenotype. Source: SGD poly(A)+ mRNA export from nucleus Inferred from mutant phenotype. Source: SGD posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery Inferred from mutant phenotype. Source: SGD protein export from nucleus Inferred from mutant phenotype Ref.7. Source: SGD regulation of protein desumoylation Inferred from genetic interaction. Source: SGD telomere tethering at nuclear periphery Inferred from mutant phenotype. Source: SGD
Cellular component	nuclear membrane Inferred from electronic annotation. Source: UniProtKB-SubCell nuclear pore Inferred from direct assay Ref.5. Source: SGD
Molecular function	phospholipid binding Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction. Source: IntAct structural constituent of nuclear pore Traceable author statement Ref.7. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
KAP95	Q06142	4	EBI-20731,EBI-9145
NUP2	P32499	2	EBI-20731,EBI-12401

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 539

539

Nucleoporin NUP60

PRO_0000204879

Regions

Repeat

399 – 401

FXF 1

Repeat

427 – 429

FXF 2

Repeat

469 – 471

FXF 3

Repeat

509 – 511

FXF 4

Coiled coil

91 – 118

Potential

Amino acid modifications

Modified residue

Phosphoserine Ref.14 Ref.15 Ref.17

Modified residue

Phosphoserine Ref.15

Modified residue

Phosphoserine Ref.15 Ref.16

Modified residue

Phosphoserine Ref.14 Ref.16 Ref.17

Modified residue

162

Phosphoserine Ref.17

Modified residue

185

Phosphoserine Ref.16

Modified residue

207

Phosphoserine Ref.16

Modified residue

219

Phosphoserine Ref.17

Modified residue

300

Phosphoserine Ref.16

Modified residue

312

Phosphoserine Ref.16 Ref.17

Modified residue

322

Phosphoserine Ref.16

Modified residue

352

Phosphoserine Ref.16 Ref.17

Modified residue

360

Phosphoserine; by CHEK2 Ref.15 Ref.16 Ref.17

Modified residue

369

Phosphoserine Ref.15

Modified residue

374

Phosphoserine Ref.15

Modified residue

381

Phosphothreonine Ref.15 Ref.16 Ref.17

Modified residue

382

Phosphoserine Ref.13 Ref.15 Ref.16 Ref.17

Modified residue

400

Phosphoserine Ref.16

Modified residue

460

Phosphothreonine Ref.16 Ref.17

Modified residue

473

Phosphoserine Ref.16

Modified residue

478

Phosphoserine Ref.17

Modified residue

480

Phosphoserine Ref.15 Ref.16 Ref.17

Modified residue

483

Phosphoserine Ref.15 Ref.16 Ref.17

Sequences

Sequence

Length

Mass (Da)

Tools

P39705 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: B9A28494A358A3E3
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FASTA

539

59,039

        10         20         30         40         50         60 
MHRKSLRRAS ATVPSAPYRK QIISNAHNKP SLFSKIKTFF TQKDSARVSP RNNVANKQPR 

        70         80         90        100        110        120 
NESFNRRISS MPGGYFHSEI SPDSTVNRSV VVSAVGEARN DIENKEEEYD ETHETNISNA 

       130        140        150        160        170        180 
KLANFFSKKG NEPLSEIEIE GVMSLLQKSS KSMITSEGEQ KSAEGNNIDQ SLILKESGST 

       190        200        210        220        230        240 
PISISNAPTF NPKYDTSNAS MNTTLGSIGS RKYSFNYSSL PSPYKTTVYR YSAAKKIPDT 

       250        260        270        280        290        300 
YTANTSAQSI ASAKSVRSGV SKSAPSKKIS NTAAALVSLL DENDSKKNNA ASELANPYSS 

       310        320        330        340        350        360 
YVSQIRKHKR VSPNAAPRQE ISEEETTVKP LFQNVPEQGE EPMKQLNATK ISPSAPSKDS 

       370        380        390        400        410        420 
FTKYKPARSS SLRSNVVVAE TSPEKKDGGD KPPSSAFNFS FNTSRNVEPT ENAYKSENAP 

       430        440        450        460        470        480 
SASSKEFNFT NLQAKPLVGK PKTELTKGDS TPVQPDLSVT PQKSSSKGFV FNSVQKKSRS 

       490        500        510        520        530 
NLSQENDNEG KHISASIDND FSEEKAEEFD FNVPVVSKQL GNGLVDENKV EAFKSLYTF

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of the 42 kbp SPO7-CENI-CDC15 region." Clark M.W., Keng T., Storms R.K., Zhong W.-W., Fortin N., Zeng B., Delaney S., Ouellette B.F.F., Barton A.B., Kaback D.B., Bussey H. Yeast 10:535-541(1994) [PubMed: 7941740] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	"The nucleotide sequence of chromosome I from Saccharomyces cerevisiae." Bussey H., Kaback D.B., Zhong W.-W., Vo D.H., Clark M.W., Fortin N., Hall J., Ouellette B.F.F., Keng T., Barton A.B., Su Y., Davies C.J., Storms R.K. Proc. Natl. Acad. Sci. U.S.A. 92:3809-3813(1995) [PubMed: 7731988] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[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 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.
[6]	"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.
[7]	"The nucleoporin Nup60p functions as a Gsp1p-GTP-sensitive tether for Nup2p at the nuclear pore complex." Denning D.P., Mykytka B., Allen N.P., Huang L., Burlingame A., Rexach M. J. Cell Biol. 154:937-950(2001) [PubMed: 11535617] [Abstract] Cited for: FUNCTION, INTERACTION WITH GSP1-GTP; NUP2; SRM1; KAP123 AND KAP95-SRP1.
[8]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[9]	"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.
[10]	"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.
[11]	"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.
[12]	"Targets of the cyclin-dependent kinase Cdk1." Ubersax J.A., Woodbury E.L., Quang P.N., Paraz M., Blethrow J.D., Shah K., Shokat K.M., Morgan D.O. Nature 425:859-864(2003) [PubMed: 14574415] [Abstract] Cited for: PHOSPHORYLATION BY CDC28.
[13]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed: 15665377] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-382, MASS SPECTROMETRY. Strain: YAL6B.
[14]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10 AND SER-81, MASS SPECTROMETRY. Strain: ADR376.
[15]	"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry." Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F. Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10; SER-15; SER-49; SER-360; SER-369; SER-374; THR-381; SER-382; SER-480 AND SER-483, MASS SPECTROMETRY.
[16]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-49; SER-81; SER-185; SER-207; SER-300; SER-312; SER-322; SER-352; SER-360; THR-381; SER-382; SER-400; THR-460; SER-473; SER-480 AND SER-483, MASS SPECTROMETRY.
[17]	"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-10; SER-81; SER-162; SER-219; SER-312; SER-352; SER-360; THR-381; SER-382; THR-460; SER-478; SER-480 AND SER-483, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	L22015 Genomic DNA. Translation: AAC04957.1. AY692943 Genomic DNA. Translation: AAT92962.1. BK006935 Genomic DNA. Translation: DAA06986.1.
PIR	S40900.
RefSeq	NP_009401.1. NM_001178209.1.
3D structure databases
ProteinModelPortal	P39705.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5821N.
IntAct	P39705. 10 interactions.
MINT	MINT-629603.
STRING	P39705.
Protein family/group databases
TCDB	9.A.14.1.1. nuclear pore complex (NPC) family.
Proteomic databases
PeptideAtlas	P39705.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YAR002W; YAR002W; YAR002W.
GeneID	851263.
KEGG	sce:YAR002W.
NMPDR	fig\|4932.3.peg.85.
Organism-specific databases
CYGD	YAR002w.
SGD	S000000063. NUP60.
Phylogenomic databases
eggNOG	fuNOG10836.
OMA	IEYEGVM.
OrthoDB	EOG4ZSDCP.
Gene expression databases
ArrayExpress	P39705.
Genevestigator	P39705.
GermOnline	YAR002W. Saccharomyces cerevisiae.
Family and domain databases
ProtoNet	Search...
Other
NextBio	968225.

Entry information

Entry name

NUP60_YEAST

Accession

Primary (citable) accession number: P39705
Secondary accession number(s): D6VPL6

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	December 14, 2011
This is version 100 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

Yeast chromosome I

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

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

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protein family/group databases

Proteomic 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