Nucleolar protein 3 - Saccharomyces cerevisiae (Baker's yeast)

Names and origin

Protein names

Recommended name:
    Nucleolar protein 3
Alternative name(s):
    Mitochondrial targeting suppressor 1 protein
    Nuclear polyadenylated RNA-binding protein 1

Gene names

Name:	NPL3
Synonyms:	MTR13, MTS1, NAB1, NOP3
Ordered Locus Names:	YDR432W
ORF Names:	D9461.19

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	414 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Required for pre-rRNA processing and nuclear import as well as mitochondrial protein targeting. Binds to poly(A).
Subunit structure	Interacts with RRP6. Ref.6
Subcellular location	Nucleus › nucleolus. Ref.5 Ref.8
Miscellaneous	Present with 78700 molecules/cell in log phase SD medium. Ref.9
Sequence similarities	Belongs to the RRM GAR family. Contains 2 RRM (RNA recognition motif) domains.

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Ontologies

Keywords
Biological process	Ribosome biogenesis rRNA processing
Cellular component	Nucleus
Domain	Repeat
Ligand	RNA-binding
Molecular function	Ribonucleoprotein
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	mRNA export from nucleus Inferred from genetic interaction. Source: SGD nuclear mRNA splicing, via spliceosome Inferred from genetic interaction. Source: SGD positive regulation of RNA elongation Inferred from direct assay. Source: SGD pseudohyphal growth Inferred from mutant phenotype. Source: SGD rRNA processing Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription termination Inferred from mutant phenotype. Source: SGD
Cellular component	cytoplasm Inferred from mutant phenotype. Source: SGD nucleolus Inferred from electronic annotation. Source: UniProtKB-SubCell ribonucleoprotein complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	RNA polymerase II transcription elongation factor activity Inferred from direct assay. Source: SGD poly(A) binding Ref.5 Inferred from direct assay. Source: SGD protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
	P43582	1	EBI-12114,EBI-22766
AUS1	Q08409	1	EBI-12114,EBI-35723
HMT1	P38074	2	EBI-12114,EBI-8394
MLP1	Q02455	1	EBI-12114,EBI-11009
PRP40	P33203	1	EBI-12114,EBI-701
RSP5	P39940	1	EBI-12114,EBI-16219
URN1	Q06525	1	EBI-12114,EBI-35138

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 414

414

Nucleolar protein 3

PRO_0000081676

Regions

Domain

125 – 195

71

RRM 1

Domain

200 – 275

76

RRM 2

Compositional bias

280 – 398

119

Arg/Gly-rich

Amino acid modifications

Modified residue

182

1

Phosphoserine Ref.13

Modified residue

224

1

Phosphoserine Ref.13 Ref.10 Ref.11 Ref.12

Modified residue

227

1

Phosphothreonine Ref.12

Modified residue

228

1

Phosphothreonine Ref.13

Modified residue

356

1

Phosphoserine Ref.7

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Sequences

Sequence

Length

Mass (Da)

Tools

Q01560-1 [UniParc].

Last modified July 1, 1993. Version 1.
Checksum: 024439E4B6578787
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FASTA

414

45,407

        10         20         30         40         50         60 
MSEAQETHVE QLPESVVDAP VEEQHQEPPQ APDAPQEPQV PQESAPQESA PQEPPAPQEQ 

        70         80         90        100        110        120 
NDVPPPSNAP IYEGEESHSV QDYQEAHQHH QPPEPQPYYP PPPPGEHMHG RPPMHHRQEG 

       130        140        150        160        170        180 
ELSNTRLFVR PFPLDVQESE LNEIFGPFGP MKEVKILNGF AFVEFEEAES AAKAIEEVHG 

       190        200        210        220        230        240 
KSFANQPLEV VYSKLPAKRY RITMKNLPEG CSWQDLKDLA RENSLETTFS SVNTRDFDGT 

       250        260        270        280        290        300 
GALEFPSEEI LVEALERLNN IEFRGSVITV ERDDNPPPIR RSNRGGFRGR GGFRGGFRGG 

       310        320        330        340        350        360 
FRGGFSRGGF GGPRGGFGGP RGGYGGYSRG GYGGYSRGGY GGSRGGYDSP RGGYDSPRGG 

       370        380        390        400        410 
YSRGGYGGPR NDYGPPRGSY GGSRGGYDGP RGDYGPPRDA YRTRDAPRER SPTR

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 1429834] [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: 1392078] [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: 8224861] [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. Zaccaria P. Nature 387:75-78(1997) [PubMed: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"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: 7962083] [Abstract] Cited for: SUBCELLULAR LOCATION, BINDING TO POLYADENYLATED RNA.
[6]	"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: 10611239] [Abstract] Cited for: INTERACTION WITH RRP6.
[7]	"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae." Ficarro S.B., McCleland M.L., Stukenberg P.T., Burke D.J., Ross M.M., Shabanowitz J., Hunt D.F., White F.M. Nat. Biotechnol. 20:301-305(2002) [PubMed: 11875433] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-356, MASS SPECTROMETRY.
[8]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[9]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[10]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed: 15665377] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-224, MASS SPECTROMETRY.
[11]	"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: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-224, MASS SPECTROMETRY.
[12]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-224 AND THR-227, MASS SPECTROMETRY.
[13]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-182; SER-224 AND THR-228, MASS SPECTROMETRY.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

X66019 Genomic DNA. Translation: CAA46817.1.
M86731 Genomic DNA. Translation: AAA34818.1.
X70951 Genomic DNA. Translation: CAA50291.1.
U33007 Genomic DNA. Translation: AAB64865.1.

PIR

JN0866.

RefSeq

NP_010720.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2JVO	NMR	-	A	114-201	[»]
2JVR	NMR	-	A	193-282	[»]
2OSQ	NMR	-	A	121-194	[»]
2OSR	NMR	-	A	194-280	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:6464N.

IntAct

Q01560. 35 interactions.

Proteomic databases

PeptideAtlas

Q01560.

PRIDE

Q01560.

Genome annotation databases

Ensembl

YDR432W. Saccharomyces cerevisiae. [Contig view]

GeneID

852042.

GenomeReviews

Gene locus YDR432W in contig Z71256_GR.

KEGG

sce:YDR432W.

NMPDR

fig|4932.3.peg.1493.

Organism-specific databases

CYGD

YDR432w.

SGD

S000002840. NPL3.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

Q01560.

OMA

Q01560. GGYDSPR.

Gene expression databases

GermOnline

YDR432W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000504. RRM_RNP1.
[Graphical view]

Pfam

PF00076. RRM_1. 2 hits.
[Graphical view]

SMART

SM00360. RRM. 2 hits.
[Graphical view]

PROSITE

PS50102. RRM. 2 hits.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

970290.

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Entry information

Entry name

NOP3_YEAST

Accession

Primary (citable) accession number: Q01560

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 1, 1993
Last modified:	June 16, 2009
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents