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Protein

Nucleoporin NUP53

Gene

NUP53

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). NUP53 may play an important role in cell cycle regulation by inhibiting PSE1 transport functions during mitosis and sequestration of MAD1-MAD2 in a cell cycle-dependent manner. It also seems to play an important role in de novo NPC assembly by associating with nuclear membranes and driving their proliferation.6 Publications

GO - Molecular functioni

  • nucleocytoplasmic transporter activity Source: SGD
  • nucleotide binding Source: InterPro
  • phospholipid binding Source: SGD
  • single-stranded DNA binding Source: SGD

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • mitotic nuclear division Source: UniProtKB-KW
  • mRNA transport Source: UniProtKB-KW
  • NLS-bearing protein import into nucleus Source: SGD
  • nuclear pore organization Source: SGD
  • positive regulation of transcription, DNA-templated Source: SGD
  • protein import into nucleus Source: SGD
  • protein localization to kinetochore Source: SGD
  • regulation of mitotic nuclear division Source: SGD
  • regulation of protein desumoylation Source: SGD
  • response to spindle checkpoint signaling Source: SGD
Complete GO annotation...

Keywords - Biological processi

Cell cycle, Cell division, Mitosis, mRNA transport, Protein transport, Translocation, Transport

Enzyme and pathway databases

BioCyciYEAST:G3O-32843-MONOMER.

Protein family/group databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoporin NUP53
Alternative name(s):
Nuclear pore protein NUP53
Gene namesi
Name:NUP53
Ordered Locus Names:YMR153W
ORF Names:YM8520.02
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR153W.
SGDiS000004762. NUP53.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Membrane, Nuclear pore complex, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources
Chaini2 – 475474Nucleoporin NUP53PRO_0000204871Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineCombined sources
Modified residuei101 – 1011PhosphoserineCombined sources
Modified residuei297 – 2971PhosphoserineCombined sources
Modified residuei438 – 4381PhosphoserineCombined sources

Post-translational modificationi

Phosphorylated by CDC28.2 Publications

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ03790.

PTM databases

iPTMnetiQ03790.

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. NUP53 interacts with MAD1-MAD2. During mitosis NUP53 changes its binding partner within the NPC from NUP170 to NIC96, exposing a high affinity binding site for the karyopherin PSE1, and retaining it in the NPC, while MAD2 is released. It forms a subcomplex with ASM4 and NDC1.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
NUP170P381815EBI-27321,EBI-11756

Protein-protein interaction databases

BioGridi35328. 104 interactions.
DIPiDIP-1467N.
IntActiQ03790. 24 interactions.
MINTiMINT-398434.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3W3YX-ray2.80B401-448[»]
ProteinModelPortaliQ03790.
SMRiQ03790. Positions 252-353.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati124 – 1252FG 11 Publication
Domaini247 – 352106RRM Nup35-typePROSITE-ProRule annotationAdd
BLAST
Repeati264 – 2652FG 21 Publication
Repeati273 – 2742FG 31 Publication
Repeati470 – 4712FG 41 Publication

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni405 – 43834PSE1 bindingAdd
BLAST
Regioni449 – 47527Required for nuclear membrane association and proliferationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi24 – 4118Gln-richAdd
BLAST
Compositional biasi115 – 14733Asn-richAdd
BLAST

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.1 Publication
The RRM Nup35-type domain might be involved in the control of mitosis.1 Publication

Sequence similaritiesi

Contains 1 RRM Nup35-type domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00530000067349.
HOGENOMiHOG000113890.
InParanoidiQ03790.
KOiK14313.
OMAiTRNENTI.
OrthoDBiEOG7S4XG6.

Family and domain databases

InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR007846. RRM_NUP35_dom.
[Graphical view]
PfamiPF05172. Nup35_RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS51472. RRM_NUP35. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q03790-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADLQKQENS SRFTNVSVIA PESQGQHEQQ KQQEQLEQQK QPTGLLKGLN
60 70 80 90 100
GFPSAPQPLF MEDPPSTVSG ELNDNPAWFN NPRKRAIPNS IIKRSNGQSL
110 120 130 140 150
SPVRSDSADV PAFSNSNGFN NVTFGSKKDP RILKNVSPND NNSANNNAHS
160 170 180 190 200
SDLGTVVFDS NEAPPKTSLA DWQKEDGIFS SKTDNIEDPN LSSNITFDGK
210 220 230 240 250
PTATPSPFRP LEKTSRILNF FDKNTKTTPN TASSEASAGS KEGASTNWDD
260 270 280 290 300
HAIIIFGYPE TIANSIILHF ANFGEILEDF RVIKDFKKLN SKNMSKSPSL
310 320 330 340 350
TAQKYPIYTG DGWVKLTYKS ELSKSRALQE NGIIMNGTLI GCVSYSPAAL
360 370 380 390 400
KQLASLKKSE EIINNKTSSQ TSLSSKDLSN YRKTEGIFEK AKAKAVTSKV
410 420 430 440 450
RNAEFKVSKN STSFKNPRRL EIKDGRSLFL RNRGKIHSGV LSSIESDLKK
460 470
REQASKSKKS WLNRLNNWLF GWNDL
Length:475
Mass (Da):52,619
Last modified:November 1, 1997 - v1
Checksum:i2ECE0C561D27E523
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49705 Genomic DNA. Translation: CAA89789.1.
BK006946 Genomic DNA. Translation: DAA10048.1.
PIRiS54511.
RefSeqiNP_013873.1. NM_001182656.1.

Genome annotation databases

EnsemblFungiiYMR153W; YMR153W; YMR153W.
GeneIDi855184.
KEGGisce:YMR153W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49705 Genomic DNA. Translation: CAA89789.1.
BK006946 Genomic DNA. Translation: DAA10048.1.
PIRiS54511.
RefSeqiNP_013873.1. NM_001182656.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3W3YX-ray2.80B401-448[»]
ProteinModelPortaliQ03790.
SMRiQ03790. Positions 252-353.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35328. 104 interactions.
DIPiDIP-1467N.
IntActiQ03790. 24 interactions.
MINTiMINT-398434.

Protein family/group databases

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

PTM databases

iPTMnetiQ03790.

Proteomic databases

MaxQBiQ03790.

Protocols and materials databases

DNASUi855184.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR153W; YMR153W; YMR153W.
GeneIDi855184.
KEGGisce:YMR153W.

Organism-specific databases

EuPathDBiFungiDB:YMR153W.
SGDiS000004762. NUP53.

Phylogenomic databases

GeneTreeiENSGT00530000067349.
HOGENOMiHOG000113890.
InParanoidiQ03790.
KOiK14313.
OMAiTRNENTI.
OrthoDBiEOG7S4XG6.

Enzyme and pathway databases

BioCyciYEAST:G3O-32843-MONOMER.

Miscellaneous databases

NextBioi978644.
PROiQ03790.

Family and domain databases

InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR007846. RRM_NUP35_dom.
[Graphical view]
PfamiPF05172. Nup35_RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 2 hits.
PROSITEiPS51472. RRM_NUP35. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p."
    Marelli M., Aitchison J.D., Wozniak R.W.
    J. Cell Biol. 143:1813-1830(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCOMPLEX WITH NUP170 AND ASM4, INTERACTION WITH KARYOPHERIN PSE1, PHOSPHORYLATION.
  4. "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] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, NPC SUBUNIT LOCATION.
  5. "A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope."
    Marelli M., Lusk C.P., Chan H., Aitchison J.D., Wozniak R.W.
    J. Cell Biol. 153:709-724(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DE NOVO NPC ASSEMBLY.
  6. "Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes."
    Lusk C.P., Makhnevych T., Marelli M., Aitchison J.D., Wozniak R.W.
    J. Cell Biol. 159:267-278(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN PSE1 BINDING.
  7. "The yeast nuclear pore complex functionally interacts with components of the spindle assembly checkpoint."
    Iouk T., Kerscher O., Scott R.J., Basrai M.A., Wozniak R.W.
    J. Cell Biol. 159:807-819(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CELL CYCLE-DEPENDENT INTERACTION WITH MAD1-MAD2 COMPLEX.
  8. "Cell cycle regulated transport controlled by alterations in the nuclear pore complex."
    Makhnevych T., Lusk C.P., Anderson A.M., Aitchison J.D., Wozniak R.W.
    Cell 115:813-823(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MITOTIC PSE1 TRANSPORT INHIBITION, NPC ASSEMBLY.
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "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] [Europe PMC] [Abstract]
    Cited for: FUNCTION, FG REPEAT STRUCTURE.
  11. Cited for: INTERACTION.
  12. "A comprehensive two-hybrid analysis to explore the yeast protein interactome."
    Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y.
    Proc. Natl. Acad. Sci. U.S.A. 98:4569-4574(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION.
  13. "Peering through the pore: nuclear pore complex structure, assembly, and function."
    Suntharalingam M., Wente S.R.
    Dev. Cell 4:775-789(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  14. Cited for: PHOSPHORYLATION BY CDC28.
  15. "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] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  16. "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] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-101 AND SER-438, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-297, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  18. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS], IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNUP53_YEAST
AccessioniPrimary (citable) accession number: Q03790
Secondary accession number(s): D6VZX4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: May 11, 2016
This is version 137 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2060 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: 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.