NUP53_YEAST
ID NUP53_YEAST Reviewed; 475 AA.
AC Q03790; D6VZX4;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 182.
DE RecName: Full=Nucleoporin NUP53;
DE AltName: Full=Nuclear pore protein NUP53;
GN Name=NUP53; OrderedLocusNames=YMR153W; ORFNames=YM8520.02;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP FUNCTION, SUBCOMPLEX WITH NUP170 AND ASM4, INTERACTION WITH KARYOPHERIN
RP PSE1, AND PHOSPHORYLATION.
RX PubMed=9864357; DOI=10.1083/jcb.143.7.1813;
RA Marelli M., Aitchison J.D., Wozniak R.W.;
RT "Specific binding of the karyopherin Kap121p to a subunit of the nuclear
RT pore complex containing Nup53p, Nup59p, and Nup170p.";
RL J. Cell Biol. 143:1813-1830(1998).
RN [4]
RP FUNCTION, IDENTIFICATION IN THE NUCLEAR PORE COMPLEX, AND SUBCELLULAR
RP LOCATION.
RX PubMed=10684247; DOI=10.1083/jcb.148.4.635;
RA Rout M.P., Aitchison J.D., Suprapto A., Hjertaas K., Zhao Y., Chait B.T.;
RT "The yeast nuclear pore complex: composition, architecture, and transport
RT mechanism.";
RL J. Cell Biol. 148:635-651(2000).
RN [5]
RP FUNCTION, AND DE NOVO NPC ASSEMBLY.
RX PubMed=11352933; DOI=10.1083/jcb.153.4.709;
RA Marelli M., Lusk C.P., Chan H., Aitchison J.D., Wozniak R.W.;
RT "A link between the synthesis of nucleoporins and the biogenesis of the
RT nuclear envelope.";
RL J. Cell Biol. 153:709-724(2001).
RN [6]
RP FUNCTION, AND DOMAIN PSE1 BINDING.
RX PubMed=12403813; DOI=10.1083/jcb.200203079;
RA Lusk C.P., Makhnevych T., Marelli M., Aitchison J.D., Wozniak R.W.;
RT "Karyopherins in nuclear pore biogenesis: a role for Kap121p in the
RT assembly of Nup53p into nuclear pore complexes.";
RL J. Cell Biol. 159:267-278(2002).
RN [7]
RP FUNCTION, AND CELL CYCLE-DEPENDENT INTERACTION WITH MAD1-MAD2 COMPLEX.
RX PubMed=12473689; DOI=10.1083/jcb.200205068;
RA Iouk T., Kerscher O., Scott R.J., Basrai M.A., Wozniak R.W.;
RT "The yeast nuclear pore complex functionally interacts with components of
RT the spindle assembly checkpoint.";
RL J. Cell Biol. 159:807-819(2002).
RN [8]
RP FUNCTION, MITOTIC PSE1 TRANSPORT INHIBITION, AND NPC ASSEMBLY.
RX PubMed=14697200; DOI=10.1016/s0092-8674(03)00986-3;
RA Makhnevych T., Lusk C.P., Anderson A.M., Aitchison J.D., Wozniak R.W.;
RT "Cell cycle regulated transport controlled by alterations in the nuclear
RT pore complex.";
RL Cell 115:813-823(2003).
RN [9]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [10]
RP FUNCTION, AND FG REPEAT STRUCTURE.
RX PubMed=12604785; DOI=10.1073/pnas.0437902100;
RA Denning D.P., Patel S.S., Uversky V., Fink A.L., Rexach M.;
RT "Disorder in the nuclear pore complex: the FG repeat regions of
RT nucleoporins are natively unfolded.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:2450-2455(2003).
RN [11]
RP INTERACTION.
RX PubMed=10688190; DOI=10.1038/35001009;
RA Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R.,
RA Lockshon D., Narayan V., Srinivasan M., Pochart P., Qureshi-Emili A.,
RA Li Y., Godwin B., Conover D., Kalbfleisch T., Vijayadamodar G., Yang M.,
RA Johnston M., Fields S., Rothberg J.M.;
RT "A comprehensive analysis of protein-protein interactions in Saccharomyces
RT cerevisiae.";
RL Nature 403:623-627(2000).
RN [12]
RP INTERACTION.
RX PubMed=11283351; DOI=10.1073/pnas.061034498;
RA Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y.;
RT "A comprehensive two-hybrid analysis to explore the yeast protein
RT interactome.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4569-4574(2001).
RN [13]
RP REVIEW.
RX PubMed=12791264; DOI=10.1016/s1534-5807(03)00162-x;
RA Suntharalingam M., Wente S.R.;
RT "Peering through the pore: nuclear pore complex structure, assembly, and
RT function.";
RL Dev. Cell 4:775-789(2003).
RN [14]
RP PHOSPHORYLATION BY CDC28.
RX PubMed=14574415; DOI=10.1038/nature02062;
RA Ubersax J.A., Woodbury E.L., Quang P.N., Paraz M., Blethrow J.D., Shah K.,
RA Shokat K.M., Morgan D.O.;
RT "Targets of the cyclin-dependent kinase Cdk1.";
RL Nature 425:859-864(2003).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-101 AND SER-438, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-297, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [18]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: Functions as a component of the nuclear pore complex (NPC).
CC NPC components, collectively referred to as nucleoporins (NUPs), can
CC play the role of both NPC structural components and of docking or
CC interaction partners for transiently associated nuclear transport
CC factors. Active directional transport is assured by both, a Phe-Gly
CC (FG) repeat affinity gradient for these transport factors across the
CC NPC and a transport cofactor concentration gradient across the nuclear
CC envelope (GSP1 and GSP2 GTPases associated predominantly with GTP in
CC the nucleus, with GDP in the cytoplasm). NUP53 may play an important
CC role in cell cycle regulation by inhibiting PSE1 transport functions
CC during mitosis and sequestration of MAD1-MAD2 in a cell cycle-dependent
CC manner. It also seems to play an important role in de novo NPC assembly
CC by associating with nuclear membranes and driving their proliferation.
CC {ECO:0000269|PubMed:10684247, ECO:0000269|PubMed:11352933,
CC ECO:0000269|PubMed:12403813, ECO:0000269|PubMed:12473689,
CC ECO:0000269|PubMed:12604785, ECO:0000269|PubMed:14697200,
CC ECO:0000269|PubMed:9864357}.
CC -!- SUBUNIT: Component of the nuclear pore complex (NPC). NPC constitutes
CC the exclusive means of nucleocytoplasmic transport. NPCs allow the
CC passive diffusion of ions and small molecules and the active, nuclear
CC transport receptor-mediated bidirectional transport of macromolecules
CC such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal
CC subunits across the nuclear envelope. Due to its 8-fold rotational
CC symmetry, all subunits are present with 8 copies or multiples thereof.
CC NUP53 interacts with MAD1-MAD2. During mitosis NUP53 changes its
CC binding partner within the NPC from NUP170 to NIC96, exposing a high
CC affinity binding site for the karyopherin PSE1, and retaining it in the
CC NPC, while MAD2 is released. It forms a subcomplex with ASM4 and NDC1.
CC {ECO:0000269|PubMed:10684247, ECO:0000269|PubMed:10688190,
CC ECO:0000269|PubMed:11283351, ECO:0000269|PubMed:9864357}.
CC -!- INTERACTION:
CC Q03790; P34077: NIC96; NbExp=3; IntAct=EBI-27321, EBI-12056;
CC Q03790; P38181: NUP170; NbExp=5; IntAct=EBI-27321, EBI-11756;
CC Q03790; Q03790: NUP53; NbExp=3; IntAct=EBI-27321, EBI-27321;
CC -!- SUBCELLULAR LOCATION: Nucleus, nuclear pore complex
CC {ECO:0000269|PubMed:10684247}. Nucleus membrane; Peripheral membrane
CC protein; Cytoplasmic side. Nucleus membrane; Peripheral membrane
CC protein; Nucleoplasmic side. Note=Symmetric distribution.
CC -!- DOMAIN: Contains FG repeats. FG repeats are interaction sites for
CC karyopherins (importins, exportins) and form probably an affinity
CC gradient, guiding the transport proteins unidirectionally with their
CC cargo through the NPC. FG repeat regions are highly flexible and lack
CC ordered secondary structure. The overall conservation of FG repeats
CC regarding exact sequence, spacing, and repeat unit length is limited.
CC FG repeat types and their physico-chemical environment change across
CC the NPC from the nucleoplasmic to the cytoplasmic side.
CC {ECO:0000269|PubMed:12403813}.
CC -!- DOMAIN: The RRM Nup35-type domain might be involved in the control of
CC mitosis. {ECO:0000269|PubMed:12403813}.
CC -!- PTM: Phosphorylated by CDC28. {ECO:0000269|PubMed:14574415,
CC ECO:0000269|PubMed:9864357}.
CC -!- MISCELLANEOUS: Present with 2060 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; Z49705; CAA89789.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA10048.1; -; Genomic_DNA.
DR PIR; S54511; S54511.
DR RefSeq; NP_013873.1; NM_001182656.1.
DR PDB; 3W3Y; X-ray; 2.80 A; B=401-448.
DR PDB; 5UAZ; X-ray; 1.75 A; A/B=247-355.
DR PDB; 7N85; EM; 7.60 A; U/W=1-475.
DR PDB; 7N9F; EM; 37.00 A; U/W=1-475.
DR PDBsum; 3W3Y; -.
DR PDBsum; 5UAZ; -.
DR PDBsum; 7N85; -.
DR PDBsum; 7N9F; -.
DR AlphaFoldDB; Q03790; -.
DR SMR; Q03790; -.
DR BioGRID; 35328; 208.
DR ComplexPortal; CPX-824; Nuclear pore complex.
DR DIP; DIP-1467N; -.
DR IntAct; Q03790; 25.
DR MINT; Q03790; -.
DR STRING; 4932.YMR153W; -.
DR MoonDB; Q03790; Predicted.
DR TCDB; 1.I.1.1.1; the nuclear pore complex (npc) family.
DR iPTMnet; Q03790; -.
DR MaxQB; Q03790; -.
DR PaxDb; Q03790; -.
DR PRIDE; Q03790; -.
DR DNASU; 855184; -.
DR EnsemblFungi; YMR153W_mRNA; YMR153W; YMR153W.
DR GeneID; 855184; -.
DR KEGG; sce:YMR153W; -.
DR SGD; S000004762; NUP53.
DR VEuPathDB; FungiDB:YMR153W; -.
DR eggNOG; ENOG502QWFW; Eukaryota.
DR GeneTree; ENSGT00390000005923; -.
DR HOGENOM; CLU_024892_0_0_1; -.
DR InParanoid; Q03790; -.
DR OMA; TIHEHTP; -.
DR BioCyc; YEAST:G3O-32843-MON; -.
DR PRO; PR:Q03790; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q03790; protein.
DR GO; GO:0005635; C:nuclear envelope; IC:ComplexPortal.
DR GO; GO:0031965; C:nuclear membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005643; C:nuclear pore; IDA:SGD.
DR GO; GO:0044613; C:nuclear pore central transport channel; IDA:SGD.
DR GO; GO:0044615; C:nuclear pore nuclear basket; IDA:SGD.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0005543; F:phospholipid binding; IDA:SGD.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:SGD.
DR GO; GO:0017056; F:structural constituent of nuclear pore; IPI:SGD.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0006607; P:NLS-bearing protein import into nucleus; IMP:SGD.
DR GO; GO:0006999; P:nuclear pore organization; IGI:SGD.
DR GO; GO:0006913; P:nucleocytoplasmic transport; IC:ComplexPortal.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:SGD.
DR GO; GO:0006606; P:protein import into nucleus; IGI:SGD.
DR GO; GO:0034501; P:protein localization to kinetochore; IMP:SGD.
DR GO; GO:0007088; P:regulation of mitotic nuclear division; IMP:SGD.
DR GO; GO:0060188; P:regulation of protein desumoylation; IMP:SGD.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0072417; P:response to spindle checkpoint signaling; IMP:SGD.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR017389; Nucleoporin_NUP53.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR007846; RRM_NUP35_dom.
DR PANTHER; PTHR21527; PTHR21527; 1.
DR Pfam; PF05172; Nup35_RRM; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS51472; RRM_NUP35; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cell cycle; Cell division; Membrane; Mitosis;
KW mRNA transport; Nuclear pore complex; Nucleus; Phosphoprotein;
KW Protein transport; Reference proteome; Repeat; Translocation; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..475
FT /note="Nucleoporin NUP53"
FT /id="PRO_0000204871"
FT REPEAT 124..125
FT /note="FG 1"
FT /evidence="ECO:0000269|PubMed:12604785"
FT DOMAIN 247..352
FT /note="RRM Nup35-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00804"
FT REPEAT 264..265
FT /note="FG 2"
FT /evidence="ECO:0000269|PubMed:12604785"
FT REPEAT 273..274
FT /note="FG 3"
FT /evidence="ECO:0000269|PubMed:12604785"
FT REPEAT 470..471
FT /note="FG 4"
FT /evidence="ECO:0000269|PubMed:12604785"
FT REGION 1..83
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 89..108
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 190..209
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 222..244
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 405..438
FT /note="PSE1 binding"
FT REGION 449..475
FT /note="Required for nuclear membrane association and
FT proliferation"
FT COMPBIAS 1..45
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 91..108
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES 101
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 297
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 438
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:5UAZ"
FT STRAND 252..256
FT /evidence="ECO:0007829|PDB:5UAZ"
FT HELIX 260..262
FT /evidence="ECO:0007829|PDB:5UAZ"
FT HELIX 263..271
FT /evidence="ECO:0007829|PDB:5UAZ"
FT HELIX 281..283
FT /evidence="ECO:0007829|PDB:5UAZ"
FT STRAND 313..319
FT /evidence="ECO:0007829|PDB:5UAZ"
FT HELIX 321..328
FT /evidence="ECO:0007829|PDB:5UAZ"
FT TURN 329..332
FT /evidence="ECO:0007829|PDB:5UAZ"
FT STRAND 333..335
FT /evidence="ECO:0007829|PDB:5UAZ"
FT STRAND 338..344
FT /evidence="ECO:0007829|PDB:5UAZ"
FT HELIX 347..352
FT /evidence="ECO:0007829|PDB:5UAZ"
SQ SEQUENCE 475 AA; 52619 MW; 2ECE0C561D27E523 CRC64;
MADLQKQENS SRFTNVSVIA PESQGQHEQQ KQQEQLEQQK QPTGLLKGLN GFPSAPQPLF
MEDPPSTVSG ELNDNPAWFN NPRKRAIPNS IIKRSNGQSL SPVRSDSADV PAFSNSNGFN
NVTFGSKKDP RILKNVSPND NNSANNNAHS SDLGTVVFDS NEAPPKTSLA DWQKEDGIFS
SKTDNIEDPN LSSNITFDGK PTATPSPFRP LEKTSRILNF FDKNTKTTPN TASSEASAGS
KEGASTNWDD HAIIIFGYPE TIANSIILHF ANFGEILEDF RVIKDFKKLN SKNMSKSPSL
TAQKYPIYTG DGWVKLTYKS ELSKSRALQE NGIIMNGTLI GCVSYSPAAL KQLASLKKSE
EIINNKTSSQ TSLSSKDLSN YRKTEGIFEK AKAKAVTSKV RNAEFKVSKN STSFKNPRRL
EIKDGRSLFL RNRGKIHSGV LSSIESDLKK REQASKSKKS WLNRLNNWLF GWNDL
