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Nuclear polyadenylated RNA-binding protein 4 (Cleavage factor IB) (CFIB)

 HRP1_YEAST              Reviewed;         534 AA.
Q99383; D6W1U5; Q02741;
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 1.
25-OCT-2017, entry version 155.
RecName: Full=Nuclear polyadenylated RNA-binding protein 4;
AltName: Full=Cleavage factor IB;
Short=CFIB;
Name=HRP1; Synonyms=NAB4, NAB5; OrderedLocusNames=YOL123W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Oberdorf A.M., Anderson J.T., Devore D.R., Swanson M.S.;
Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8770588;
Henry M., Borland C.Z., Bossie M., Silver P.A.;
"Potential RNA binding proteins in Saccharomyces cerevisiae identified
as suppressors of temperature-sensitive mutations in NPL3.";
Genetics 142:103-115(1996).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=8896268;
DOI=10.1002/(SICI)1097-0061(199609)12:10B<1041::AID-YEA989>3.3.CO;2-9;
Lafuente M.J., Gamo F.-J., Gancedo C.;
"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.";
Yeast 12:1041-1045(1996).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169874;
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.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
Nature 387:98-102(1997).
[5]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[6]
PROTEIN SEQUENCE OF 182-189 AND 245-257, FUNCTION, RNA-BINDING, AND
SUBCELLULAR LOCATION.
PubMed=9334319; DOI=10.1101/gad.11.19.2545;
Kessler M.M., Henry M.F., Shen E., Zhao J., Gross S., Silver P.A.,
Moore C.L.;
"Hrp1, a sequence-specific RNA-binding protein that shuttles between
the nucleus and the cytoplasm, is required for mRNA 3'-end formation
in yeast.";
Genes Dev. 11:2545-2556(1997).
[7]
FUNCTION.
PubMed=9857200; DOI=10.1093/emboj/17.24.7454;
Minvielle-Sebastia L., Beyer K., Krecic A.M., Hector R.E.,
Swanson M.S., Keller W.;
"Control of cleavage site selection during mRNA 3' end formation by a
yeast hnRNP.";
EMBO J. 17:7454-7468(1998).
[8]
RNA-BINDING.
PubMed=9776761; DOI=10.1093/nar/26.21.4965;
Chen S., Hyman L.E.;
"A specific RNA-protein interaction at yeast polyadenylation
efficiency elements.";
Nucleic Acids Res. 26:4965-4974(1998).
[9]
FUNCTION IN NMD, AND INTERACTION WITH NAM7.
PubMed=10882134; DOI=10.1016/S1097-2765(00)80443-8;
Gonzalez C.I., Ruiz-Echevarria M.J., Vasudevan S., Henry M.F.,
Peltz S.W.;
"The yeast hnRNP-like protein Hrp1/Nab4 marks a transcript for
nonsense-mediated mRNA decay.";
Mol. Cell 5:489-499(2000).
[10]
FUNCTION IN PRE-MRNA 3'-END FORMATION.
PubMed=11344258; DOI=10.1073/pnas.101046598;
Gross S., Moore C.;
"Five subunits are required for reconstitution of the cleavage and
polyadenylation activities of Saccharomyces cerevisiae cleavage factor
I.";
Proc. Natl. Acad. Sci. U.S.A. 98:6080-6085(2001).
[11]
SUBCELLULAR LOCATION.
PubMed=12192043; DOI=10.1128/MCB.22.18.6441-6457.2002;
Hammell C.M., Gross S., Zenklusen D., Heath C.V., Stutz F., Moore C.,
Cole C.N.;
"Coupling of termination, 3' processing, and mRNA export.";
Mol. Cell. Biol. 22:6441-6457(2002).
[12]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2 AND SER-3, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2; SER-3; SER-206;
THR-458 AND SER-462, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE
SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[14]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-2; SER-3 AND SER-462,
AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- 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 an RNA downstream sequence
element (DSE) located 3' of a nonsense codon and may mark the
transcript for decay. {ECO:0000269|PubMed:10882134,
ECO:0000269|PubMed:11344258, ECO:0000269|PubMed:9334319,
ECO:0000269|PubMed:9857200}.
-!- SUBUNIT: Interacts with NAM7. {ECO:0000269|PubMed:10882134}.
-!- INTERACTION:
P38217:KAP104; NbExp=4; IntAct=EBI-11783, EBI-9152;
P25298:RNA14; NbExp=2; IntAct=EBI-11783, EBI-15632;
-!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
-----------------------------------------------------------------------
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Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; U35737; AAA79097.1; -; Genomic_DNA.
EMBL; U38535; AAB18142.1; -; Genomic_DNA.
EMBL; X95258; CAA64546.1; -; Genomic_DNA.
EMBL; Z74865; CAA99142.1; -; Genomic_DNA.
EMBL; BK006948; DAA10661.1; -; Genomic_DNA.
PIR; S66820; S66820.
RefSeq; NP_014518.1; NM_001183377.1.
PDB; 2CJK; NMR; -; A=156-322.
PDB; 2KM8; NMR; -; C=156-322.
PDBsum; 2CJK; -.
PDBsum; 2KM8; -.
ProteinModelPortal; Q99383; -.
SMR; Q99383; -.
BioGrid; 34252; 319.
DIP; DIP-1371N; -.
IntAct; Q99383; 34.
MINT; MINT-395353; -.
STRING; 4932.YOL123W; -.
iPTMnet; Q99383; -.
MaxQB; Q99383; -.
PRIDE; Q99383; -.
EnsemblFungi; YOL123W; YOL123W; YOL123W.
GeneID; 853997; -.
KEGG; sce:YOL123W; -.
EuPathDB; FungiDB:YOL123W; -.
SGD; S000005483; HRP1.
GeneTree; ENSGT00900000140835; -.
HOGENOM; HOG000248803; -.
InParanoid; Q99383; -.
KO; K14411; -.
OMA; DYTIMKD; -.
OrthoDB; EOG092C3SCB; -.
BioCyc; YEAST:G3O-33519-MONOMER; -.
Reactome; R-SCE-450408; AUF1 (hnRNP D0) binds and destabilizes mRNA.
EvolutionaryTrace; Q99383; -.
PRO; PR:Q99383; -.
Proteomes; UP000002311; Chromosome XV.
GO; GO:0005737; C:cytoplasm; IDA:SGD.
GO; GO:0010494; C:cytoplasmic stress granule; IDA:SGD.
GO; GO:0005849; C:mRNA cleavage factor complex; IPI:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0003729; F:mRNA binding; IDA:SGD.
GO; GO:0003723; F:RNA binding; IDA:SGD.
GO; GO:0006378; P:mRNA polyadenylation; IDA:SGD.
GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
GO; GO:0098789; P:pre-mRNA cleavage required for polyadenylation; IDA:SGD.
GO; GO:0072423; P:response to DNA damage checkpoint signaling; IMP:SGD.
CDD; cd12577; RRM1_Hrp1p; 1.
CDD; cd12330; RRM2_Hrp1p; 1.
InterPro; IPR034156; Hrp1_RRM1.
InterPro; IPR034155; Hrp1_RRM2.
InterPro; IPR035979; RBD_domain_sf.
InterPro; IPR000504; RRM_dom.
Pfam; PF00076; RRM_1; 2.
SMART; SM00360; RRM; 2.
SUPFAM; SSF54928; SSF54928; 2.
PROSITE; PS50102; RRM; 2.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing;
mRNA processing; Nonsense-mediated mRNA decay; Nucleus;
Phosphoprotein; Reference proteome; Repeat; RNA-binding.
CHAIN 1 534 Nuclear polyadenylated RNA-binding
protein 4.
/FTId=PRO_0000081658.
DOMAIN 159 241 RRM 1. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
DOMAIN 243 320 RRM 2. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
MOD_RES 2 2 Phosphoserine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 3 3 Phosphoserine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 206 206 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 458 458 Phosphothreonine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 462 462 Phosphoserine.
{ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
HELIX 157 159 {ECO:0000244|PDB:2CJK}.
STRAND 160 163 {ECO:0000244|PDB:2CJK}.
HELIX 172 179 {ECO:0000244|PDB:2CJK}.
TURN 180 182 {ECO:0000244|PDB:2CJK}.
STRAND 185 189 {ECO:0000244|PDB:2CJK}.
TURN 194 196 {ECO:0000244|PDB:2CJK}.
STRAND 203 209 {ECO:0000244|PDB:2CJK}.
HELIX 211 218 {ECO:0000244|PDB:2CJK}.
STRAND 223 226 {ECO:0000244|PDB:2KM8}.
HELIX 236 241 {ECO:0000244|PDB:2CJK}.
STRAND 243 250 {ECO:0000244|PDB:2CJK}.
HELIX 256 264 {ECO:0000244|PDB:2CJK}.
STRAND 265 267 {ECO:0000244|PDB:2KM8}.
STRAND 270 273 {ECO:0000244|PDB:2CJK}.
STRAND 277 281 {ECO:0000244|PDB:2CJK}.
STRAND 284 293 {ECO:0000244|PDB:2CJK}.
HELIX 294 302 {ECO:0000244|PDB:2CJK}.
STRAND 304 306 {ECO:0000244|PDB:2CJK}.
STRAND 308 311 {ECO:0000244|PDB:2CJK}.
STRAND 313 317 {ECO:0000244|PDB:2CJK}.
SEQUENCE 534 AA; 59650 MW; 1B231069437B093D CRC64;
MSSDEEDFND IYGDDKPTTT EEVKKEEEQN KAGSGTSQLD QLAALQALSS SLNKLNNPNS
NNSSSNNSNQ DTSSSKQDGT ANDKEGSNED TKNEKKQESA TSANANANAS SAGPSGLPWE
QLQQTMSQFQ QPSSQSPPQQ QVTQTKEERS KADLSKESCK MFIGGLNWDT TEDNLREYFG
KYGTVTDLKI MKDPATGRSR GFGFLSFEKP SSVDEVVKTQ HILDGKVIDP KRAIPRDEQD
KTGKIFVGGI GPDVRPKEFE EFFSQWGTII DAQLMLDKDT GQSRGFGFVT YDSADAVDRV
CQNKFIDFKD RKIEIKRAEP RHMQQKSSNN GGNNGGNNMN RRGGNFGNQG DFNQMYQNPM
MGGYNPMMNP QAMTDYYQKM QEYYQQMQKQ TGMDYTQMYQ QQMQQMAMMM PGFAMPPNAM
TLNQPQQDSN ATQGSPAPSD SDNNKSNDVQ TIGNTSNTDS GSPPLNLPNG PKGPSQYNDD
HNSGYGYNRD RGDRDRNDRD RDYNHRSGGN HRRNGRGGRG GYNRRNNGYH PYNR


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