Q99383 (HRP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nuclear polyadenylated RNA-binding protein 4

Alternative name(s):
Cleavage factor IB
Short name=CFIB

Gene names

Name:	HRP1
Synonyms:	NAB4, NAB5
Ordered Locus Names:	YOL123W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	534 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	RNA-binding protein, which is involved in the polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with the cleavage factor CFIA complex and the cleavage and polyadenylation factor (CPF) complex. May be involved in regulation of poly(A) site selection. Is involved in nonsense-mediated mRNA decay. Seems to bind to a RNA downstream sequence element (DSE) located 3' of a nonsense codon and may mark the transcript for decay. Ref.6 Ref.7 Ref.9 Ref.10
Subunit structure	Interacts with NAM7. Ref.9
Subcellular location	Cytoplasm. Nucleus Ref.6 Ref.11.
Sequence similarities	Contains 2 RRM (RNA recognition motif) domains.

Ontologies

Keywords
Biological process	Nonsense-mediated mRNA decay mRNA processing
Cellular component	Cytoplasm Nucleus
Domain	Repeat
Ligand	RNA-binding
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	mRNA cleavage Inferred from direct assay Ref.10. Source: SGD mRNA polyadenylation Inferred from direct assay Ref.10. Source: SGD nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasmic stress granule Inferred from direct assay PubMed 18981231. Source: SGD mRNA cleavage factor complex Inferred from physical interaction Ref.10. Source: SGD
Molecular_function	mRNA binding Inferred from direct assay PubMed 15703440PubMed 17684230. Source: SGD nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
NAB2	P32505	3	EBI-11783,EBI-11770

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 534

534

Nuclear polyadenylated RNA-binding protein 4

PRO_0000081658

Regions

Domain

159 – 241

83

RRM 1

Domain

243 – 320

78

RRM 2

Amino acid modifications

Modified residue

2

1

Phosphoserine Ref.12 Ref.13 Ref.14

Modified residue

3

1

Phosphoserine Ref.12 Ref.13 Ref.14

Modified residue

34

1

Phosphoserine Ref.14

Modified residue

184

1

Phosphothreonine Ref.14

Modified residue

206

1

Phosphoserine Ref.14

Modified residue

458

1

Phosphothreonine Ref.14

Modified residue

460

1

Phosphoserine Ref.14

Modified residue

462

1

Phosphoserine Ref.14

Secondary structure

1

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534

Helix Strand Turn

Details...

Helix

157 – 159

3

Beta strand

160 – 163

4

Helix

172 – 179

8

Turn

180 – 182

3

Beta strand

185 – 189

5

Turn

194 – 196

3

Beta strand

203 – 209

7

Helix

211 – 218

8

Beta strand

223 – 226

4

Helix

236 – 241

6

Beta strand

243 – 250

8

Helix

256 – 264

9

Beta strand

265 – 267

3

Beta strand

270 – 273

4

Beta strand

277 – 281

5

Beta strand

284 – 293

10

Helix

294 – 302

9

Beta strand

304 – 306

3

Beta strand

308 – 311

4

Beta strand

313 – 317

5

Sequences

	Sequence		Length	Mass (Da)
	Q99383 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: 1B231069437B093D	FASTA	534	59,650
	10 20 30 40 50 60 MSSDEEDFND IYGDDKPTTT EEVKKEEEQN KAGSGTSQLD QLAALQALSS SLNKLNNPNS 70 80 90 100 110 120 NNSSSNNSNQ DTSSSKQDGT ANDKEGSNED TKNEKKQESA TSANANANAS SAGPSGLPWE 130 140 150 160 170 180 QLQQTMSQFQ QPSSQSPPQQ QVTQTKEERS KADLSKESCK MFIGGLNWDT TEDNLREYFG 190 200 210 220 230 240 KYGTVTDLKI MKDPATGRSR GFGFLSFEKP SSVDEVVKTQ HILDGKVIDP KRAIPRDEQD 250 260 270 280 290 300 KTGKIFVGGI GPDVRPKEFE EFFSQWGTII DAQLMLDKDT GQSRGFGFVT YDSADAVDRV 310 320 330 340 350 360 CQNKFIDFKD RKIEIKRAEP RHMQQKSSNN GGNNGGNNMN RRGGNFGNQG DFNQMYQNPM 370 380 390 400 410 420 MGGYNPMMNP QAMTDYYQKM QEYYQQMQKQ TGMDYTQMYQ QQMQQMAMMM PGFAMPPNAM 430 440 450 460 470 480 TLNQPQQDSN ATQGSPAPSD SDNNKSNDVQ TIGNTSNTDS GSPPLNLPNG PKGPSQYNDD 490 500 510 520 530 HNSGYGYNRD RGDRDRNDRD RDYNHRSGGN HRRNGRGGRG GYNRRNNGYH PYNR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	Oberdorf A.M., Anderson J.T., Devore D.R., Swanson M.S. Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Potential RNA binding proteins in Saccharomyces cerevisiae identified as suppressors of temperature-sensitive mutations in NPL3." Henry M., Borland C.Z., Bossie M., Silver P.A. Genetics 142:103-115(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	"DNA sequence analysis of a 10 624 bp fragment of the left arm of chromosome XV from Saccharomyces cerevisiae reveals a RNA binding protein, a mitochondrial protein, two ribosomal proteins and two new open reading frames." Lafuente M.J., Gamo F.-J., Gancedo C. Yeast 12:1041-1045(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[4]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV." Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K. Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3'-end formation in yeast." Kessler M.M., Henry M.F., Shen E., Zhao J., Gross S., Silver P.A., Moore C.L. Genes Dev. 11:2545-2556(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 182-189 AND 245-257, FUNCTION, RNA-BINDING, SUBCELLULAR LOCATION.
[7]	"Control of cleavage site selection during mRNA 3' end formation by a yeast hnRNP." Minvielle-Sebastia L., Beyer K., Krecic A.M., Hector R.E., Swanson M.S., Keller W. EMBO J. 17:7454-7468(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"A specific RNA-protein interaction at yeast polyadenylation efficiency elements." Chen S., Hyman L.E. Nucleic Acids Res. 26:4965-4974(1998) [PubMed] [Europe PMC] [Abstract] Cited for: RNA-BINDING.
[9]	"The yeast hnRNP-like protein Hrp1/Nab4 marks a transcript for nonsense-mediated mRNA decay." Gonzalez C.I., Ruiz-Echevarria M.J., Vasudevan S., Henry M.F., Peltz S.W. Mol. Cell 5:489-499(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN NMD, INTERACTION WITH NAM7.
[10]	"Five subunits are required for reconstitution of the cleavage and polyadenylation activities of Saccharomyces cerevisiae cleavage factor I." Gross S., Moore C. Proc. Natl. Acad. Sci. U.S.A. 98:6080-6085(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN PRE-MRNA 3'-END FORMATION.
[11]	"Coupling of termination, 3' processing, and mRNA export." Hammell C.M., Gross S., Zenklusen D., Heath C.V., Stutz F., Moore C., Cole C.N. Mol. Cell. Biol. 22:6441-6457(2002) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION.
[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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2 AND SER-3, 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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2 AND SER-3, 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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2; SER-3; SER-34; THR-184; SER-206; THR-458; SER-460 AND SER-462, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U35737 Genomic DNA. Translation: AAA79097.1.
U38535 Genomic DNA. Translation: AAB18142.1.
X95258 Genomic DNA. Translation: CAA64546.1.
Z74865 Genomic DNA. Translation: CAA99142.1.
BK006948 Genomic DNA. Translation: DAA10661.1.

PIR

S66820.

RefSeq

NP_014518.1. NM_001183377.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CJK	NMR	-	A	156-322	[»]
2KM8	NMR	-	C	156-322	[»]

ProteinModelPortal

Q99383.

SMR

Q99383. Positions 117-322.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1371N.

IntAct

Q99383. 31 interactions.

MINT

MINT-395353.

Proteomic databases

PaxDb

Q99383.

PeptideAtlas

Q99383.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YOL123W; YOL123W; YOL123W.

GeneID

853997.

KEGG

sce:YOL123W.

Organism-specific databases

CYGD

YOL123w.

SGD

S000005483. HRP1.

Phylogenomic databases

eggNOG

COG0724.

GeneTree

ENSGT00700000104255.

HOGENOM

HOG000248803.

KO

K14411.

OMA

AREEQDK.

OrthoDB

EOG4TF3VC.

Gene expression databases

Genevestigator

Q99383.

GermOnline

YOL123W. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

3.30.70.330. 2 hits.

InterPro

IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[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

EvolutionaryTrace

Q99383.

NextBio

975491.

Entry information

Entry name

HRP1_YEAST

Accession

Primary (citable) accession number: Q99383
Secondary accession number(s): D6W1U5, Q02741

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 112 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program