Q01560 (NOP3_YEAST) Reviewed, UniProtKB/Swiss-Prot

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 (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	414 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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.7
Subcellular location	Nucleus › nucleolus Ref.6 Ref.9.
Miscellaneous	Present with 78700 molecules/cell in log phase SD medium. Ref.10
Sequence similarities	Belongs to the RRM GAR family. Contains 2 RRM (RNA recognition motif) domains.

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 Reference proteome
Gene Ontology (GO)
Biological process	mRNA export from nucleus Inferred from genetic interaction. Source: SGD negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled Inferred from mutant phenotype. Source: SGD nuclear mRNA splicing, via spliceosome Inferred from mutant phenotype. Source: SGD positive regulation of transcription elongation from RNA polymerase II promoter Inferred from mutant phenotype. Source: SGD rRNA processing Inferred from electronic annotation. Source: UniProtKB-KW translational 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 core binding Inferred from physical interaction. Source: SGD nucleotide binding Inferred from electronic annotation. Source: InterPro poly(A) RNA binding Inferred from direct assay Ref.6. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
AIR1	P40507	3	EBI-12114,EBI-25083
HMT1	P38074	6	EBI-12114,EBI-8394
RSP5	P39940	2	EBI-12114,EBI-16219

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.14

Modified residue

224

1

Phosphoserine Ref.11 Ref.12 Ref.13 Ref.14

Modified residue

227

1

Phosphothreonine Ref.13

Modified residue

228

1

Phosphothreonine Ref.14

Modified residue

356

1

Phosphoserine Ref.8

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

414

Helix Strand Turn

Details...

Beta strand

125 – 129

5

Helix

138 – 144

7

Beta strand

153 – 156

4

Beta strand

161 – 164

4

Helix

168 – 178

11

Beta strand

189 – 192

4

Sequences

	Sequence		Length	Mass (Da)
	Q01560 [UniParc]. Last modified July 1, 1993. Version 1. Checksum: 024439E4B6578787	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

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. , 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: 9169867] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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: 7962083] [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: 10611239] [Abstract] Cited for: INTERACTION WITH RRP6.
[8]	"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. Strain: 2124.
[9]	"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].
[10]	"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].
[11]	"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. Strain: YAL6B.
[12]	"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. Strain: ADR376.
[13]	"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.
[14]	"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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

JN0866.

RefSeq

NP_010720.1. NM_001180740.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

Q01560.

SMR

Q01560. Positions 121-280.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6464N.

IntAct

Q01560. 31 interactions.

MINT

MINT-600838.

STRING

Q01560.

Proteomic databases

PeptideAtlas

Q01560.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YDR432W; YDR432W; YDR432W.

GeneID

852042.

KEGG

sce:YDR432W.

NMPDR

fig|4932.3.peg.1493.

Organism-specific databases

CYGD

YDR432w.

SGD

S000002840. NPL3.

Phylogenomic databases

eggNOG

fuNOG12461.

GeneTree

EFGT00050000000572.

OMA

DDNPPPI.

OrthoDB

EOG4BP4N7.

Gene expression databases

ArrayExpress

Q01560.

Genevestigator

Q01560.

GermOnline

YDR432W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]

Gene3D

G3DSA:3.30.70.330. a_b_plait_nuc_bd. 2 hits.

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

NextBio

970290.

Entry information

Entry name

NOP3_YEAST

Accession

Primary (citable) accession number: Q01560
Secondary accession number(s): D6VT60

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1993
Last sequence update:	July 1, 1993
Last modified:	January 25, 2012
This is version 123 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program