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P13084 (NPM_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 121. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nucleophosmin

Short name=NPM
Alternative name(s):
Nucleolar phosphoprotein B23
Nucleolar protein NO38
Numatrin
Gene names
Name:Npm1
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length292 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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.

Subcellular location

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.

Post-translational modification

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.

Sumoylated by ARF By similarity.

The N-terminus is blocked.

Sequence similarities

Belongs to the nucleoplasmin family.

Ontologies

Keywords
   Cellular componentCytoplasm
Cytoskeleton
Nucleus
   Coding sequence diversityAlternative splicing
   LigandDNA-binding
RNA-binding
   Molecular functionChaperone
   PTMAcetylation
ADP-ribosylation
Disulfide bond
Isopeptide bond
Phosphoprotein
Ubl conjugation
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processDNA repair

Inferred from sequence or structural similarity. Source: UniProtKB

cell aging

Inferred from sequence or structural similarity. Source: UniProtKB

centrosome cycle

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of apoptotic process

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of cell proliferation

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of protein kinase activity by regulation of protein phosphorylation

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of DNA metabolic process

Inferred from direct assay PubMed 11481036. Source: RGD

positive regulation of DNA replication

Inferred from direct assay PubMed 11481036. Source: RGD

positive regulation of catalytic activity

Inferred from direct assay PubMed 11481036. Source: RGD

positive regulation of translation

Inferred from sequence or structural similarity. Source: UniProtKB

protein homooligomerization

Inferred from direct assay PubMed 8611572. Source: RGD

regulation of centriole replication

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of eIF2 alpha phosphorylation by dsRNA

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of endodeoxyribonuclease activity

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of endoribonuclease activity

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of neuron apoptotic process

Inferred from mutant phenotype PubMed 15893727. Source: RGD

   Cellular_componentcentrosome

Inferred from sequence or structural similarity. Source: UniProtKB

cytoplasm

Inferred from sequence or structural similarity. Source: UniProtKB

nucleolus

Inferred from direct assay PubMed 12450141. Source: RGD

nucleoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functionDNA binding

Inferred from direct assay PubMed 8611572. Source: RGD

NF-kappaB binding

Inferred from sequence or structural similarity. Source: UniProtKB

RNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

enzyme binding

Inferred from direct assay PubMed 11481036. Source: RGD

phosphatidylinositol-3,4,5-trisphosphate binding

Inferred from physical interaction PubMed 15893727. Source: RGD

protein kinase inhibitor activity

Inferred from sequence or structural similarity. Source: UniProtKB

unfolded protein binding

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform B23.1 (identifier: P13084-1)

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.
Isoform B23.2 (identifier: P13084-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 292292Nucleophosmin
PRO_0000219483

Regions

Region1 – 185185Required for interaction with SENP3 By similarity
Region1 – 117117Necessary for interaction with APEX1 By similarity
Region241 – 29252Required for nucleolar localization By similarity
Motif152 – 1576Nuclear localization signal Potential
Motif190 – 1967Nuclear localization signal Potential
Compositional bias1 – 99Met-rich
Compositional bias120 – 13213Asp/Glu-rich (acidic)
Compositional bias158 – 18730Asp/Glu-rich (highly acidic)

Sites

Site551Interaction between pentamers By similarity
Site801Interaction between pentamers By similarity

Amino acid modifications

Modified residue11N-acetylmethionine By similarity
Modified residue41Phosphoserine; by PLK1 and PLK2 By similarity
Modified residue101Phosphoserine By similarity
Modified residue321N6-acetyllysine By similarity
Modified residue701Phosphoserine By similarity
Modified residue751Phosphothreonine By similarity
Modified residue951Phosphothreonine By similarity
Modified residue1251Phosphoserine; by CDK2
Modified residue1391Phosphoserine By similarity
Modified residue1501N6-acetyllysine By similarity
Modified residue1541N6-acetyllysine By similarity
Modified residue1981Phosphothreonine; by CDK1 and CDK2 By similarity
Modified residue2111N6-acetyllysine By similarity
Modified residue2171Phosphothreonine; by CDK1 By similarity
Modified residue2251Phosphoserine By similarity
Modified residue2271N6-acetyllysine By similarity
Modified residue2281N6-acetyllysine; alternate By similarity
Modified residue2321Phosphothreonine; by CDK1 By similarity
Modified residue2351Phosphothreonine; by CDK1 By similarity
Modified residue2401Phosphoserine By similarity
Modified residue2411Phosphoserine By similarity
Modified residue2481N6-acetyllysine By similarity
Modified residue2521Phosphoserine By similarity
Modified residue2551N6-acetyllysine By similarity
Modified residue2581Phosphoserine By similarity
Modified residue2651N6-acetyllysine By similarity
Modified residue2711N6-acetyllysine By similarity
Modified residue2771Phosphothreonine By similarity
Modified residue2901N6-acetyllysine By similarity
Cross-link228Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate By similarity
Cross-link261Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) By similarity

Natural variations

Alternative sequence256 – 29237GGSLP…WRKSL → AH in isoform B23.2.
VSP_003617

Sequences

Sequence LengthMass (Da)Tools
Isoform B23.1 [UniParc].

Last modified January 1, 1990. Version 1.
Checksum: 1372A474F9ED2457

FASTA29232,560
        10         20         30         40         50         60 
MEDSMDMDMS PLRPQNYLFG CELKADKDYH FKVDNDENEH QLSLRTVSLG AGAKDELHIV 

        70         80         90        100        110        120 
EAEAMNYEGS PIKVTLATLK MSVQPTVSLG GFEITPPVVL RLKCGSGPVH ISGQHLVAVE 

       130        140        150        160        170        180 
EDAESEDEDE EDVKLLGMSG KRSAPGGGNK VPQKKVKLDE DDDEDDEDDE DDEDDDDDDF 

       190        200        210        220        230        240 
DEEETEEKVP VKKSVRDTPA KNAQKSNQNG KDLKPSTPRS KGQESFKKQE KTPKTPKGPS 

       250        260        270        280        290 
SVEDIKAKMQ ASIEKGGSLP KVEAKFINYV KNCFRMTDQE AIQDLWQWRK SL 

« Hide

Isoform B23.2 [UniParc].

Checksum: 7271F6D962A63D6C
Show »

FASTA25728,385

References

« Hide 'large scale' references
[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J03969 mRNA. Translation: AAA40796.1.
M37039 expand/collapse EMBL AC list , M37035, M37036, M37037, M37038 Genomic DNA. Translation: AAA41730.1.
M37041 expand/collapse EMBL AC list , 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.
PIRA28939.
A36089.
A34168. B36089.
RefSeqNP_037124.1. NM_012992.4. [P13084-1]
UniGeneRn.54537.

3D structure databases

ProteinModelPortalP13084.
SMRP13084. Positions 15-118, 241-292.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid247531. 2 interactions.
MINTMINT-4587645.

PTM databases

PhosphoSiteP13084.

2D gel databases

World-2DPAGE0004:P13084.

Proteomic databases

PaxDbP13084.
PRIDEP13084.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000006591; ENSRNOP00000006591; ENSRNOG00000004616. [P13084-1]
ENSRNOT00000064744; ENSRNOP00000062356; ENSRNOG00000004616. [P13084-2]
GeneID25498.
KEGGrno:25498.
UCSCRGD:3192. rat. [P13084-1]

Organism-specific databases

CTD4869.
RGD3192. Npm1.

Phylogenomic databases

eggNOGNOG79897.
GeneTreeENSGT00440000034554.
HOGENOMHOG000013061.
HOVERGENHBG001860.
InParanoidP13084.
KOK11276.
OMANCFRTED.
OrthoDBEOG79W97G.
PhylomeDBP13084.
TreeFamTF327704.

Gene expression databases

GenevestigatorP13084.

Family and domain databases

Gene3D2.60.120.340. 1 hit.
InterProIPR004301. Nucleoplasmin.
IPR024057. Nucleoplasmin_core_dom.
[Graphical view]
PANTHERPTHR22747. PTHR22747. 1 hit.
SUPFAMSSF69203. SSF69203. 1 hit.
ProtoNetSearch...

Other

NextBio606897.
PROP13084.

Entry information

Entry nameNPM_RAT
AccessionPrimary (citable) accession number: P13084
Secondary accession number(s): Q63698, Q64269
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: May 14, 2014
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families