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P13084

- NPM_RAT

UniProt

P13084 - NPM_RAT

Protein

Nucleophosmin

Gene

Npm1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 123 (01 Oct 2014)
      Sequence version 1 (01 Jan 1990)
      Previous versions | rss
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    Functioni

    Involved in diverse cellular processes such as ribosome biogenesis, centrosome duplication, protein chaperoning, histone assembly, cell proliferation, and regulation of tumor suppressors p53/TP53 and ARF. Binds ribosome presumably to drive ribosome nuclear export. Acts as a chaperonin for the core histones H3, H2B and H4. Stimulates APEX1 endonuclease activity on apurinic/apyrimidinic (AP) double-stranded DNA but inhibits APEX1 endonuclease activity on AP single-stranded RNA. May exert a control of APEX1 endonuclease activity within nucleoli devoted to repair AP on rDNA and the removal of oxidized rRNA molecules By similarity. Associated with nucleolar ribonucleoprotein structures and bind single-stranded nucleic acids. In concert with BRCA2, regulates centrosome duplication. Regulates centriole duplication: phosphorylation by PLK2 is able to trigger centriole replication By similarity. Negatively regulates the activation of EIF2AK2/PKR and suppresses apoptosis through inhibition of EIF2AK2/PKR autophosphorylation By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei55 – 551Interaction between pentamersBy similarity
    Sitei80 – 801Interaction between pentamersBy similarity

    GO - Molecular functioni

    1. DNA binding Source: RGD
    2. enzyme binding Source: RGD
    3. NF-kappaB binding Source: UniProtKB
    4. phosphatidylinositol-3,4,5-trisphosphate binding Source: RGD
    5. protein kinase inhibitor activity Source: UniProtKB
    6. RNA binding Source: UniProtKB-KW
    7. unfolded protein binding Source: UniProtKB

    GO - Biological processi

    1. cell aging Source: UniProtKB
    2. centrosome cycle Source: UniProtKB
    3. DNA repair Source: UniProtKB
    4. negative regulation of apoptotic process Source: UniProtKB
    5. negative regulation of cell proliferation Source: UniProtKB
    6. negative regulation of protein kinase activity by regulation of protein phosphorylation Source: UniProtKB
    7. positive regulation of catalytic activity Source: RGD
    8. positive regulation of DNA metabolic process Source: RGD
    9. positive regulation of DNA replication Source: RGD
    10. positive regulation of translation Source: UniProtKB
    11. protein homooligomerization Source: RGD
    12. regulation of centriole replication Source: UniProtKB
    13. regulation of eIF2 alpha phosphorylation by dsRNA Source: UniProtKB
    14. regulation of endodeoxyribonuclease activity Source: UniProtKB
    15. regulation of endoribonuclease activity Source: UniProtKB
    16. regulation of neuron apoptotic process Source: RGD

    Keywords - Molecular functioni

    Chaperone

    Keywords - Ligandi

    DNA-binding, RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nucleophosmin
    Short name:
    NPM
    Alternative name(s):
    Nucleolar phosphoprotein B23
    Nucleolar protein NO38
    Numatrin
    Gene namesi
    Name:Npm1
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 10

    Organism-specific databases

    RGDi3192. Npm1.

    Subcellular locationi

    Nucleusnucleolus. Nucleusnucleoplasm By similarity. Cytoplasmcytoskeletonmicrotubule organizing centercentrosome By similarity
    Note: Generally nucleolar, but is translocated to the nucleoplasm in case of serum starvation or treatment with anticancer drugs. Colocalizes with the methylated form of RPS10 in the granular component (GC) region of the nucleolus. Colocalized with nucleolin and APEX1 in nucleoli. NEK2 is required for its localization to the centrosome during mitosis By similarity.By similarity

    GO - Cellular componenti

    1. centrosome Source: UniProtKB
    2. cytoplasm Source: UniProtKB
    3. nucleolus Source: RGD
    4. nucleoplasm Source: UniProtKB-SubCell
    5. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Cytoskeleton, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 292292NucleophosminPRO_0000219483Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionineBy similarity
    Modified residuei4 – 41Phosphoserine; by PLK1 and PLK2By similarity
    Modified residuei10 – 101PhosphoserineBy similarity
    Modified residuei32 – 321N6-acetyllysineBy similarity
    Modified residuei70 – 701PhosphoserineBy similarity
    Modified residuei75 – 751PhosphothreonineBy similarity
    Modified residuei95 – 951PhosphothreonineBy similarity
    Modified residuei125 – 1251Phosphoserine; by CDK2
    Modified residuei139 – 1391PhosphoserineBy similarity
    Modified residuei150 – 1501N6-acetyllysineBy similarity
    Modified residuei154 – 1541N6-acetyllysineBy similarity
    Modified residuei198 – 1981Phosphothreonine; by CDK1 and CDK2By similarity
    Modified residuei211 – 2111N6-acetyllysineBy similarity
    Modified residuei217 – 2171Phosphothreonine; by CDK1By similarity
    Modified residuei225 – 2251PhosphoserineBy similarity
    Modified residuei227 – 2271N6-acetyllysineBy similarity
    Modified residuei228 – 2281N6-acetyllysine; alternateBy similarity
    Cross-linki228 – 228Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateBy similarity
    Modified residuei232 – 2321Phosphothreonine; by CDK1By similarity
    Modified residuei235 – 2351Phosphothreonine; by CDK1By similarity
    Modified residuei240 – 2401PhosphoserineBy similarity
    Modified residuei241 – 2411PhosphoserineBy similarity
    Modified residuei248 – 2481N6-acetyllysineBy similarity
    Modified residuei252 – 2521PhosphoserineBy similarity
    Modified residuei255 – 2551N6-acetyllysineBy similarity
    Modified residuei258 – 2581PhosphoserineBy similarity
    Cross-linki261 – 261Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
    Modified residuei265 – 2651N6-acetyllysineBy similarity
    Modified residuei271 – 2711N6-acetyllysineBy similarity
    Modified residuei277 – 2771PhosphothreonineBy similarity
    Modified residuei290 – 2901N6-acetyllysineBy similarity

    Post-translational modificationi

    Acetylated at C-terminal lysine residues, thereby increasing affinity to histones.By similarity
    ADP-ribosylated.By similarity
    Phosphorylated at Ser-4 by PLK1 and PLK2. Phosphorylation at Ser-4 by PLK2 in S phase is required for centriole duplication and is sufficient to trigger centriole replication. Phosphorylation at Ser-4 by PLK1 takes place during mitosis. Phosphorylated by CDK2 at Ser-125 and Thr-198. Phosphorylation at Thr-198 may trigger initiation of centrosome duplication. Phosphorylated by CDK1 at Thr-198, Thr-217, Thr-232 and Thr-235 during cell mitosis. When these four sites are phosphorated, RNA-binding activity seem to be abolished. May be phosphorylated at Ser-70 by NEK2. The Thr-198 phosphorylated form has higher affinity for ROCK2 By similarity.By similarity
    Sumoylated by ARF.By similarity
    The N-terminus is blocked.

    Keywords - PTMi

    Acetylation, ADP-ribosylation, Disulfide bond, Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    PaxDbiP13084.
    PRIDEiP13084.

    2D gel databases

    World-2DPAGE0004:P13084.

    PTM databases

    PhosphoSiteiP13084.

    Expressioni

    Gene expression databases

    GenevestigatoriP13084.

    Interactioni

    Subunit structurei

    Decamer formed by two pentameric rings associated in a head-to-head fashion. Disulfide-linked dimers under certain conditions. The SWAP complex consists of NPM1, NCL, PARP1 and SWAP70. Interacts with NSUN2 and SENP3. Interacts with the methylated form of RPS10. Interacts (via N-terminal domain) with APEX1; the interaction is RNA-dependent and decreases in hydrogen peroxide-damaged cells. Interacts with NEK2. Interacts with ROCK2 and BRCA2 By similarity. Interacts with RPGR. Interacts with CENPW By similarity. Interacts with EIF2AK2/PKR By similarity.By similarity

    Protein-protein interaction databases

    BioGridi247531. 2 interactions.
    IntActiP13084. 1 interaction.
    MINTiMINT-4587645.

    Structurei

    3D structure databases

    ProteinModelPortaliP13084.
    SMRiP13084. Positions 15-118, 241-292.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 185185Required for interaction with SENP3By similarityAdd
    BLAST
    Regioni1 – 117117Necessary for interaction with APEX1By similarityAdd
    BLAST
    Regioni241 – 29252Required for nucleolar localizationBy similarityAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi152 – 1576Nuclear localization signalSequence Analysis
    Motifi190 – 1967Nuclear localization signalSequence Analysis

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi1 – 99Met-rich
    Compositional biasi120 – 13213Asp/Glu-rich (acidic)Add
    BLAST
    Compositional biasi158 – 18730Asp/Glu-rich (highly acidic)Add
    BLAST

    Sequence similaritiesi

    Belongs to the nucleoplasmin family.Curated

    Phylogenomic databases

    eggNOGiNOG79897.
    GeneTreeiENSGT00440000034554.
    HOGENOMiHOG000013061.
    HOVERGENiHBG001860.
    InParanoidiP13084.
    KOiK11276.
    OMAiNCFRTED.
    OrthoDBiEOG79W97G.
    PhylomeDBiP13084.
    TreeFamiTF327704.

    Family and domain databases

    Gene3Di2.60.120.340. 1 hit.
    InterProiIPR004301. Nucleoplasmin.
    IPR024057. Nucleoplasmin_core_dom.
    [Graphical view]
    PANTHERiPTHR22747. PTHR22747. 1 hit.
    SUPFAMiSSF69203. SSF69203. 1 hit.

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform B23.1 (identifier: P13084-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MEDSMDMDMS PLRPQNYLFG CELKADKDYH FKVDNDENEH QLSLRTVSLG    50
    AGAKDELHIV EAEAMNYEGS PIKVTLATLK MSVQPTVSLG GFEITPPVVL 100
    RLKCGSGPVH ISGQHLVAVE EDAESEDEDE EDVKLLGMSG KRSAPGGGNK 150
    VPQKKVKLDE DDDEDDEDDE DDEDDDDDDF DEEETEEKVP VKKSVRDTPA 200
    KNAQKSNQNG KDLKPSTPRS KGQESFKKQE KTPKTPKGPS SVEDIKAKMQ 250
    ASIEKGGSLP KVEAKFINYV KNCFRMTDQE AIQDLWQWRK SL 292
    Length:292
    Mass (Da):32,560
    Last modified:January 1, 1990 - v1
    Checksum:i1372A474F9ED2457
    GO
    Isoform B23.2 (identifier: P13084-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         256-292: GGSLPKVEAKFINYVKNCFRMTDQEAIQDLWQWRKSL → AH

    Show »
    Length:257
    Mass (Da):28,385
    Checksum:i7271F6D962A63D6C
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei256 – 29237GGSLP…WRKSL → AH in isoform B23.2. 2 PublicationsVSP_003617Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J03969 mRNA. Translation: AAA40796.1.
    M37039
    , M37035, M37036, M37037, M37038 Genomic DNA. Translation: AAA41730.1.
    M37041
    , M37035, M37036, M37037, M37038, M37040 Genomic DNA. Translation: AAA41731.1.
    M25062 Genomic DNA. Translation: AAA40795.1.
    J04943 mRNA. Translation: AAA40794.1.
    J04944 Genomic DNA. Translation: AAA40793.1.
    BC060579 mRNA. Translation: AAH60579.1.
    BC088088 mRNA. Translation: AAH88088.1.
    PIRiA28939.
    A36089.
    B36089. A34168.
    RefSeqiNP_037124.1. NM_012992.4. [P13084-1]
    UniGeneiRn.54537.

    Genome annotation databases

    EnsembliENSRNOT00000006591; ENSRNOP00000006591; ENSRNOG00000004616. [P13084-1]
    ENSRNOT00000064744; ENSRNOP00000062356; ENSRNOG00000004616. [P13084-2]
    GeneIDi25498.
    KEGGirno:25498.
    UCSCiRGD:3192. rat. [P13084-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J03969 mRNA. Translation: AAA40796.1 .
    M37039
    , M37035 , M37036 , M37037 , M37038 Genomic DNA. Translation: AAA41730.1 .
    M37041
    , M37035 , M37036 , M37037 , M37038 , M37040 Genomic DNA. Translation: AAA41731.1 .
    M25062 Genomic DNA. Translation: AAA40795.1 .
    J04943 mRNA. Translation: AAA40794.1 .
    J04944 Genomic DNA. Translation: AAA40793.1 .
    BC060579 mRNA. Translation: AAH60579.1 .
    BC088088 mRNA. Translation: AAH88088.1 .
    PIRi A28939.
    A36089.
    B36089. A34168.
    RefSeqi NP_037124.1. NM_012992.4. [P13084-1 ]
    UniGenei Rn.54537.

    3D structure databases

    ProteinModelPortali P13084.
    SMRi P13084. Positions 15-118, 241-292.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 247531. 2 interactions.
    IntActi P13084. 1 interaction.
    MINTi MINT-4587645.

    PTM databases

    PhosphoSitei P13084.

    2D gel databases

    World-2DPAGE 0004:P13084.

    Proteomic databases

    PaxDbi P13084.
    PRIDEi P13084.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000006591 ; ENSRNOP00000006591 ; ENSRNOG00000004616 . [P13084-1 ]
    ENSRNOT00000064744 ; ENSRNOP00000062356 ; ENSRNOG00000004616 . [P13084-2 ]
    GeneIDi 25498.
    KEGGi rno:25498.
    UCSCi RGD:3192. rat. [P13084-1 ]

    Organism-specific databases

    CTDi 4869.
    RGDi 3192. Npm1.

    Phylogenomic databases

    eggNOGi NOG79897.
    GeneTreei ENSGT00440000034554.
    HOGENOMi HOG000013061.
    HOVERGENi HBG001860.
    InParanoidi P13084.
    KOi K11276.
    OMAi NCFRTED.
    OrthoDBi EOG79W97G.
    PhylomeDBi P13084.
    TreeFami TF327704.

    Miscellaneous databases

    NextBioi 606897.
    PROi P13084.

    Gene expression databases

    Genevestigatori P13084.

    Family and domain databases

    Gene3Di 2.60.120.340. 1 hit.
    InterProi IPR004301. Nucleoplasmin.
    IPR024057. Nucleoplasmin_core_dom.
    [Graphical view ]
    PANTHERi PTHR22747. PTHR22747. 1 hit.
    SUPFAMi SSF69203. SSF69203. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "cDNA and deduced primary structure of rat protein B23, a nucleolar protein containing highly conserved sequences."
      Chang J.-H., Dumbar T.S., Olson M.O.J.
      J. Biol. Chem. 263:12824-12827(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS B23.1 AND B23.2), PARTIAL PROTEIN SEQUENCE.
    2. "A single gene codes for two forms of rat nucleolar protein B23 mRNA."
      Chang J.-H., Olson M.O.J.
      J. Biol. Chem. 264:11732-11737(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM B23.2).
    3. "Structure of the gene for rat nucleolar protein B23."
      Chang J.-H., Olson M.O.J.
      J. Biol. Chem. 265:18227-18233(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS B23.1 AND B23.2).
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM B23.1).
      Tissue: Pituitary and Thymus.
    5. Lubec G., Chen W.-Q.
      Submitted (APR-2007) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 55-101; 238-246 AND 266-271, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: Sprague-Dawley.
      Tissue: Hippocampus.

    Entry informationi

    Entry nameiNPM_RAT
    AccessioniPrimary (citable) accession number: P13084
    Secondary accession number(s): Q63698, Q64269
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 1, 1990
    Last modified: October 1, 2014
    This is version 123 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3