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P13084

- NPM_RAT

UniProt

P13084 - NPM_RAT

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Protein

Nucleophosmin

Gene

Npm1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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. rRNA binding Source: Ensembl
  7. unfolded protein binding Source: UniProtKB

GO - Biological processi

  1. cell aging Source: UniProtKB
  2. cell growth Source: Ensembl
  3. cell volume homeostasis Source: Ensembl
  4. centrosome cycle Source: UniProtKB
  5. DNA repair Source: UniProtKB
  6. negative regulation of apoptotic process Source: UniProtKB
  7. negative regulation of cell proliferation Source: UniProtKB
  8. negative regulation of mRNA splicing, via spliceosome Source: Ensembl
  9. negative regulation of protein kinase activity by regulation of protein phosphorylation Source: UniProtKB
  10. positive regulation of catalytic activity Source: RGD
  11. positive regulation of cell proliferation Source: Ensembl
  12. positive regulation of centrosome duplication Source: Ensembl
  13. positive regulation of DNA metabolic process Source: RGD
  14. positive regulation of DNA replication Source: RGD
  15. positive regulation of protein kinase activity Source: Ensembl
  16. positive regulation of translation Source: UniProtKB
  17. protein homooligomerization Source: RGD
  18. protein localization Source: Ensembl
  19. regulation of centriole replication Source: UniProtKB
  20. regulation of DNA damage response, signal transduction by p53 class mediator Source: Ensembl
  21. regulation of eIF2 alpha phosphorylation by dsRNA Source: UniProtKB
  22. regulation of endodeoxyribonuclease activity Source: UniProtKB
  23. regulation of endoribonuclease activity Source: UniProtKB
  24. regulation of neuron apoptotic process Source: RGD
  25. ribosomal large subunit biogenesis Source: Ensembl
  26. ribosomal large subunit export from nucleus Source: Ensembl
  27. ribosomal small subunit biogenesis Source: Ensembl
  28. ribosomal small subunit export from nucleus Source: Ensembl
  29. rRNA export from nucleus Source: Ensembl
Complete GO annotation...

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. cytosol Source: Ensembl
  4. granular component Source: Ensembl
  5. large ribosomal subunit Source: Ensembl
  6. nuclear speck Source: Ensembl
  7. nucleolus Source: RGD
  8. nucleus Source: UniProtKB
  9. small ribosomal subunit Source: Ensembl
Complete GO annotation...

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

        10         20         30         40         50
MEDSMDMDMS PLRPQNYLFG CELKADKDYH FKVDNDENEH QLSLRTVSLG
60 70 80 90 100
AGAKDELHIV EAEAMNYEGS PIKVTLATLK MSVQPTVSLG GFEITPPVVL
110 120 130 140 150
RLKCGSGPVH ISGQHLVAVE EDAESEDEDE EDVKLLGMSG KRSAPGGGNK
160 170 180 190 200
VPQKKVKLDE DDDEDDEDDE DDEDDDDDDF DEEETEEKVP VKKSVRDTPA
210 220 230 240 250
KNAQKSNQNG KDLKPSTPRS KGQESFKKQE KTPKTPKGPS SVEDIKAKMQ
260 270 280 290
ASIEKGGSLP KVEAKFINYV KNCFRMTDQE AIQDLWQWRK SL
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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

« Hide 'large scale' publications
  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 29, 2014
This is version 124 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