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Nucleoporin NUP60 (Nuclear pore protein NUP60)

 NUP60_YEAST             Reviewed;         539 AA.
P39705; D6VPL6;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
01-FEB-1995, sequence version 1.
22-NOV-2017, entry version 150.
RecName: Full=Nucleoporin NUP60;
AltName: Full=Nuclear pore protein NUP60;
Name=NUP60; Synonyms=FUN17; OrderedLocusNames=YAR002W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204511 / S288c / AB972;
PubMed=7941740; DOI=10.1002/yea.320100413;
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.;
"Sequencing of chromosome I of Saccharomyces cerevisiae: analysis of
the 42 kbp SPO7-CENI-CDC15 region.";
Yeast 10:535-541(1994).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7731988; DOI=10.1073/pnas.92.9.3809;
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.;
"The nucleotide sequence of chromosome I from Saccharomyces
cerevisiae.";
Proc. Natl. Acad. Sci. U.S.A. 92:3809-3813(1995).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
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.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
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., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[5]
CHARACTERIZATION, AND NPC SUBUNIT LOCATION.
PubMed=10684247; DOI=10.1083/jcb.148.4.635;
Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y.,
Chait B.T.;
"The yeast nuclear pore complex: composition, architecture, and
transport mechanism.";
J. Cell Biol. 148:635-651(2000).
[6]
FUNCTION, AND NUCLEOPORIN INTERACTING PROTEINS.
PubMed=11387327; DOI=10.1074/jbc.M102629200;
Allen N.P., Huang L., Burlingame A., Rexach M.;
"Proteomic analysis of nucleoporin interacting proteins.";
J. Biol. Chem. 276:29268-29274(2001).
[7]
FUNCTION, AND INTERACTION WITH GSP1-GTP; NUP2; SRM1; KAP123 AND
KAP95-SRP1.
PubMed=11535617; DOI=10.1083/jcb.200101007;
Denning D.P., Mykytka B., Allen N.P., Huang L., Burlingame A.,
Rexach M.;
"The nucleoporin Nup60p functions as a Gsp1p-GTP-sensitive tether for
Nup2p at the nuclear pore complex.";
J. Cell Biol. 154:937-950(2001).
[8]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[9]
FUNCTION, AND FG REPEAT STRUCTURE.
PubMed=12604785; DOI=10.1073/pnas.0437902100;
Denning D.P., Patel S.S., Uversky V., Fink A.L., Rexach M.;
"Disorder in the nuclear pore complex: the FG repeat regions of
nucleoporins are natively unfolded.";
Proc. Natl. Acad. Sci. U.S.A. 100:2450-2455(2003).
[10]
FUNCTION, AND FG REPEATS IN NPC TRANSPORT.
PubMed=15039779; DOI=10.1038/ncb1097;
Strawn L.A., Shen T.X., Shulga N., Goldfarb D.S., Wente S.R.;
"Minimal nuclear pore complexes define FG repeat domains essential for
transport.";
Nat. Cell Biol. 6:197-206(2004).
[11]
REVIEW.
PubMed=12791264; DOI=10.1016/S1534-5807(03)00162-X;
Suntharalingam M., Wente S.R.;
"Peering through the pore: nuclear pore complex structure, assembly,
and function.";
Dev. Cell 4:775-789(2003).
[12]
PHOSPHORYLATION BY CDC28.
PubMed=14574415; DOI=10.1038/nature02062;
Ubersax J.A., Woodbury E.L., Quang P.N., Paraz M., Blethrow J.D.,
Shah K., Shokat K.M., Morgan D.O.;
"Targets of the cyclin-dependent kinase Cdk1.";
Nature 425:859-864(2003).
[13]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=YAL6B;
PubMed=15665377; DOI=10.1074/mcp.M400219-MCP200;
Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J.,
Mann M., Jensen O.N.;
"Quantitative phosphoproteomics applied to the yeast pheromone
signaling pathway.";
Mol. Cell. Proteomics 4:310-327(2005).
[14]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10 AND SER-81, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[15]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10; SER-49; SER-360;
SER-374; SER-480 AND SER-483, AND IDENTIFICATION BY MASS SPECTROMETRY
[LARGE SCALE ANALYSIS].
PubMed=17287358; DOI=10.1073/pnas.0607084104;
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.;
"Analysis of phosphorylation sites on proteins from Saccharomyces
cerevisiae by electron transfer dissociation (ETD) mass
spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10; SER-81; SER-352 AND
THR-460, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[17]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10; SER-81; SER-89;
SER-162; SER-171; SER-214; SER-222; SER-352 AND SER-382, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- 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). {ECO:0000269|PubMed:11387327,
ECO:0000269|PubMed:11535617, ECO:0000269|PubMed:12604785,
ECO:0000269|PubMed:15039779}.
-!- SUBUNIT: 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. {ECO:0000269|PubMed:11535617}.
-!- INTERACTION:
Q06142:KAP95; NbExp=3; IntAct=EBI-20731, EBI-9145;
P32499:NUP2; NbExp=2; IntAct=EBI-20731, EBI-12401;
-!- 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.
-!- PTM: Phosphorylated by CDC28. {ECO:0000269|PubMed:14574415}.
-!- MISCELLANEOUS: Present with 4590 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; L22015; AAC04957.1; -; Genomic_DNA.
EMBL; AY692943; AAT92962.1; -; Genomic_DNA.
EMBL; BK006935; DAA06986.1; -; Genomic_DNA.
PIR; S40900; S40900.
RefSeq; NP_009401.1; NM_001178209.1.
ProteinModelPortal; P39705; -.
BioGrid; 31790; 342.
DIP; DIP-5821N; -.
IntAct; P39705; 12.
MINT; MINT-629603; -.
STRING; 4932.YAR002W; -.
TCDB; 1.I.1.1.1; the eukaryotic nuclear pore complex (e-npc) family.
iPTMnet; P39705; -.
MaxQB; P39705; -.
PRIDE; P39705; -.
DNASU; 851263; -.
EnsemblFungi; YAR002W; YAR002W; YAR002W.
GeneID; 851263; -.
KEGG; sce:YAR002W; -.
EuPathDB; FungiDB:YAR002W; -.
SGD; S000000063; NUP60.
InParanoid; P39705; -.
KO; K18718; -.
OMA; ETHETNI; -.
OrthoDB; EOG092C2FN5; -.
BioCyc; YEAST:G3O-28867-MONOMER; -.
PRO; PR:P39705; -.
Proteomes; UP000002311; Chromosome I.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
GO; GO:0005643; C:nuclear pore; IDA:SGD.
GO; GO:0044613; C:nuclear pore central transport channel; IDA:SGD.
GO; GO:0044615; C:nuclear pore nuclear basket; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0005487; F:nucleocytoplasmic transporter activity; IGI:SGD.
GO; GO:0005543; F:phospholipid binding; IDA:SGD.
GO; GO:0017056; F:structural constituent of nuclear pore; IMP:SGD.
GO; GO:0030466; P:chromatin silencing at silent mating-type cassette; IMP:SGD.
GO; GO:0051276; P:chromosome organization; IMP:SGD.
GO; GO:0006302; P:double-strand break repair; IMP:SGD.
GO; GO:0008298; P:intracellular mRNA localization; IMP:SGD.
GO; GO:0031990; P:mRNA export from nucleus in response to heat stress; IMP:SGD.
GO; GO:0006607; P:NLS-bearing protein import into nucleus; IMP:SGD.
GO; GO:0006913; P:nucleocytoplasmic transport; IMP:SGD.
GO; GO:0016973; P:poly(A)+ mRNA export from nucleus; IMP:SGD.
GO; GO:0000973; P:posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery; IMP:SGD.
GO; GO:0006611; P:protein export from nucleus; IMP:SGD.
GO; GO:0060188; P:regulation of protein desumoylation; IGI:SGD.
GO; GO:0034398; P:telomere tethering at nuclear periphery; IMP:SGD.
GO; GO:0000972; P:transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery; IMP:SGD.
InterPro; IPR034432; Nup60.
PANTHER; PTHR28284; PTHR28284; 1.
1: Evidence at protein level;
Coiled coil; Complete proteome; Membrane; mRNA transport;
Nuclear pore complex; Nucleus; Phosphoprotein; Protein transport;
Reference proteome; Repeat; Translocation; Transport.
CHAIN 1 539 Nucleoporin NUP60.
/FTId=PRO_0000204879.
REPEAT 399 401 FXF 1.
REPEAT 427 429 FXF 2.
REPEAT 469 471 FXF 3.
REPEAT 509 511 FXF 4.
COILED 91 118 {ECO:0000255}.
MOD_RES 10 10 Phosphoserine.
{ECO:0000244|PubMed:17287358,
ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 49 49 Phosphoserine.
{ECO:0000244|PubMed:17287358}.
MOD_RES 81 81 Phosphoserine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 89 89 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 162 162 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 171 171 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 214 214 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 222 222 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 352 352 Phosphoserine.
{ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 360 360 Phosphoserine.
{ECO:0000244|PubMed:17287358}.
MOD_RES 374 374 Phosphoserine.
{ECO:0000244|PubMed:17287358}.
MOD_RES 382 382 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 460 460 Phosphothreonine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 480 480 Phosphoserine.
{ECO:0000244|PubMed:17287358}.
MOD_RES 483 483 Phosphoserine.
{ECO:0000244|PubMed:17287358}.
SEQUENCE 539 AA; 59039 MW; B9A28494A358A3E3 CRC64;
MHRKSLRRAS ATVPSAPYRK QIISNAHNKP SLFSKIKTFF TQKDSARVSP RNNVANKQPR
NESFNRRISS MPGGYFHSEI SPDSTVNRSV VVSAVGEARN DIENKEEEYD ETHETNISNA
KLANFFSKKG NEPLSEIEIE GVMSLLQKSS KSMITSEGEQ KSAEGNNIDQ SLILKESGST
PISISNAPTF NPKYDTSNAS MNTTLGSIGS RKYSFNYSSL PSPYKTTVYR YSAAKKIPDT
YTANTSAQSI ASAKSVRSGV SKSAPSKKIS NTAAALVSLL DENDSKKNNA ASELANPYSS
YVSQIRKHKR VSPNAAPRQE ISEEETTVKP LFQNVPEQGE EPMKQLNATK ISPSAPSKDS
FTKYKPARSS SLRSNVVVAE TSPEKKDGGD KPPSSAFNFS FNTSRNVEPT ENAYKSENAP
SASSKEFNFT NLQAKPLVGK PKTELTKGDS TPVQPDLSVT PQKSSSKGFV FNSVQKKSRS
NLSQENDNEG KHISASIDND FSEEKAEEFD FNVPVVSKQL GNGLVDENKV EAFKSLYTF


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