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Protein

Nucleolar protein 3

Gene

NPL3

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

Required for pre-rRNA processing and nuclear import as well as mitochondrial protein targeting. Binds to poly(A).

GO - Molecular functioni

  1. eukaryotic initiation factor 4G binding Source: SGD
  2. identical protein binding Source: IntAct
  3. mRNA binding Source: SGD
  4. nucleotide binding Source: InterPro
  5. poly(A) binding Source: SGD
  6. RNA polymerase II core binding Source: SGD

GO - Biological processi

  1. mRNA export from nucleus Source: SGD
  2. mRNA splicing, via spliceosome Source: SGD
  3. negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled Source: SGD
  4. negative regulation of translation Source: SGD
  5. positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  6. rRNA processing Source: UniProtKB-KW
  7. translational termination Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-29970-MONOMER.
ReactomeiREACT_294700. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleolar protein 3
Alternative name(s):
Mitochondrial targeting suppressor 1 protein
Nuclear polyadenylated RNA-binding protein 1
Gene namesi
Name:NPL3
Synonyms:MTR13, MTS1, NAB1, NOP3
Ordered Locus Names:YDR432W
ORF Names:D9461.19
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome IV

Organism-specific databases

CYGDiYDR432w.
EuPathDBiFungiDB:YDR432W.
SGDiS000002840. NPL3.

Subcellular locationi

  1. Nucleusnucleolus 2 Publications

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. nucleolus Source: UniProtKB-SubCell
  3. nucleus Source: SGD
  4. ribonucleoprotein complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 414414Nucleolar protein 3PRO_0000081676Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei182 – 1821Phosphoserine1 Publication
Modified residuei224 – 2241Phosphoserine3 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ01560.
PaxDbiQ01560.
PeptideAtlasiQ01560.

Expressioni

Gene expression databases

GenevestigatoriQ01560.

Interactioni

Subunit structurei

Interacts with RRP6.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
itself2EBI-12114,EBI-12114
HMT1P380749EBI-12114,EBI-8394
RPL25P044562EBI-12114,EBI-15308
RSP5P399402EBI-12114,EBI-16219

Protein-protein interaction databases

BioGridi32489. 1114 interactions.
DIPiDIP-6464N.
IntActiQ01560. 35 interactions.
MINTiMINT-600838.
STRINGi4932.YDR432W.

Structurei

Secondary structure

1
414
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi125 – 1295Combined sources
Helixi138 – 1458Combined sources
Turni146 – 1483Combined sources
Beta strandi153 – 1575Combined sources
Beta strandi160 – 1645Combined sources
Helixi168 – 17811Combined sources
Beta strandi189 – 1924Combined sources
Beta strandi200 – 2056Combined sources
Helixi213 – 22311Combined sources
Beta strandi228 – 2314Combined sources
Beta strandi236 – 2383Combined sources
Beta strandi241 – 2477Combined sources
Helixi248 – 25710Combined sources
Beta strandi261 – 2633Combined sources
Beta strandi266 – 2738Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JVONMR-A116-201[»]
2JVRNMR-A193-282[»]
2OSQNMR-A121-194[»]
2OSRNMR-A194-280[»]
ProteinModelPortaliQ01560.
SMRiQ01560. Positions 121-280.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ01560.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini125 – 19571RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini200 – 27576RRM 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi280 – 398119Arg/Gly-richAdd
BLAST

Sequence similaritiesi

Belongs to the RRM GAR family.Curated
Contains 2 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0724.
GeneTreeiENSGT00700000104103.
InParanoidiQ01560.
KOiK14651.
OMAiPEGCSWQ.
OrthoDBiEOG7QVMDQ.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q01560-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEAQETHVE QLPESVVDAP VEEQHQEPPQ APDAPQEPQV PQESAPQESA
60 70 80 90 100
PQEPPAPQEQ NDVPPPSNAP IYEGEESHSV QDYQEAHQHH QPPEPQPYYP
110 120 130 140 150
PPPPGEHMHG RPPMHHRQEG ELSNTRLFVR PFPLDVQESE LNEIFGPFGP
160 170 180 190 200
MKEVKILNGF AFVEFEEAES AAKAIEEVHG KSFANQPLEV VYSKLPAKRY
210 220 230 240 250
RITMKNLPEG CSWQDLKDLA RENSLETTFS SVNTRDFDGT GALEFPSEEI
260 270 280 290 300
LVEALERLNN IEFRGSVITV ERDDNPPPIR RSNRGGFRGR GGFRGGFRGG
310 320 330 340 350
FRGGFSRGGF GGPRGGFGGP RGGYGGYSRG GYGGYSRGGY GGSRGGYDSP
360 370 380 390 400
RGGYDSPRGG YSRGGYGGPR NDYGPPRGSY GGSRGGYDGP RGDYGPPRDA
410
YRTRDAPRER SPTR
Length:414
Mass (Da):45,407
Last modified:July 1, 1993 - v1
Checksum:i024439E4B6578787
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X66019 Genomic DNA. Translation: CAA46817.1.
M86731 Genomic DNA. Translation: AAA34818.1.
X70951 Genomic DNA. Translation: CAA50291.1.
U33007 Genomic DNA. Translation: AAB64865.1.
BK006938 Genomic DNA. Translation: DAA12270.1.
PIRiJN0866.
RefSeqiNP_010720.3. NM_001180740.3.

Genome annotation databases

EnsemblFungiiYDR432W; YDR432W; YDR432W.
GeneIDi852042.
KEGGisce:YDR432W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X66019 Genomic DNA. Translation: CAA46817.1.
M86731 Genomic DNA. Translation: AAA34818.1.
X70951 Genomic DNA. Translation: CAA50291.1.
U33007 Genomic DNA. Translation: AAB64865.1.
BK006938 Genomic DNA. Translation: DAA12270.1.
PIRiJN0866.
RefSeqiNP_010720.3. NM_001180740.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JVONMR-A116-201[»]
2JVRNMR-A193-282[»]
2OSQNMR-A121-194[»]
2OSRNMR-A194-280[»]
ProteinModelPortaliQ01560.
SMRiQ01560. Positions 121-280.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32489. 1114 interactions.
DIPiDIP-6464N.
IntActiQ01560. 35 interactions.
MINTiMINT-600838.
STRINGi4932.YDR432W.

Proteomic databases

MaxQBiQ01560.
PaxDbiQ01560.
PeptideAtlasiQ01560.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR432W; YDR432W; YDR432W.
GeneIDi852042.
KEGGisce:YDR432W.

Organism-specific databases

CYGDiYDR432w.
EuPathDBiFungiDB:YDR432W.
SGDiS000002840. NPL3.

Phylogenomic databases

eggNOGiCOG0724.
GeneTreeiENSGT00700000104103.
InParanoidiQ01560.
KOiK14651.
OMAiPEGCSWQ.
OrthoDBiEOG7QVMDQ.

Enzyme and pathway databases

BioCyciYEAST:G3O-29970-MONOMER.
ReactomeiREACT_294700. mRNA Splicing - Minor Pathway.

Miscellaneous databases

EvolutionaryTraceiQ01560.
NextBioi970290.
PROiQ01560.

Gene expression databases

GenevestigatoriQ01560.

Family and domain databases

Gene3Di3.30.70.330. 2 hits.
InterProiIPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF00076. RRM_1. 2 hits.
[Graphical view]
SMARTiSM00360. RRM. 2 hits.
[Graphical view]
PROSITEiPS50102. RRM. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "NOP3 is an essential yeast protein which is required for pre-rRNA processing."
    Russell I.D., Tollervey D.
    J. Cell Biol. 119:737-747(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "A mutant nuclear protein with similarity to RNA binding proteins interferes with nuclear import in yeast."
    Bossie M.A., Dehoratious C., Barcelo G., Silver P.
    Mol. Biol. Cell 3:875-893(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The Saccharomyces cerevisiae MTS1 gene encodes a putative RNA-binding protein involved in mitochondrial protein targeting."
    Ellis E.M., Reid G.A.
    Gene 132:175-183(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "Characterization of nuclear polyadenylated RNA-binding proteins in Saccharomyces cerevisiae."
    Wilson S.M., Datar K.V., Paddy M.R., Swedlow J.R., Swanson M.S.
    J. Cell Biol. 127:1173-1184(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, BINDING TO POLYADENYLATED RNA.
  7. "A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p."
    Burkard K.T.D., Butler J.S.
    Mol. Cell. Biol. 20:604-616(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RRP6.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-224, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  11. "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-182 AND SER-224, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "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-224, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNOP3_YEAST
AccessioniPrimary (citable) accession number: Q01560
Secondary accession number(s): D6VT60
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 1, 1993
Last modified: April 29, 2015
This is version 160 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 78700 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 IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3

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 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.