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Polyadenylate-binding protein 4 (PABP-4) (Poly(A)-binding protein 4)

 PABP4_ARATH             Reviewed;         662 AA.
O22173; Q9C5J0;
26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
01-JAN-1998, sequence version 1.
25-APR-2018, entry version 136.
RecName: Full=Polyadenylate-binding protein 4;
Short=PABP-4;
Short=Poly(A)-binding protein 4;
Name=PAB4; OrderedLocusNames=At2g23350; ORFNames=T20D16.2;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
GENE FAMILY.
PubMed=12586718;
Belostotsky D.A.;
"Unexpected complexity of poly(A)-binding protein gene families in
flowering plants: three conserved lineages that are at least 200
million years old and possible auto- and cross-regulation.";
Genetics 163:311-319(2003).
[5]
INDUCTION, INTERACTION WITH VIRAL VPG-PRO, AND DISRUPTION PHENOTYPE.
PubMed=18753244; DOI=10.1099/vir.0.2008/002139-0;
Dufresne P.J., Ubalijoro E., Fortin M.G., Laliberte J.F.;
"Arabidopsis thaliana class II poly(A)-binding proteins are required
for efficient multiplication of turnip mosaic virus.";
J. Gen. Virol. 89:2339-2348(2008).
[6]
INTERACTION WITH ERD15/CID1.
PubMed=22118612; DOI=10.1016/j.plantsci.2011.08.009;
Aalto M.K., Helenius E., Kariola T., Pennanen V., Heino P., Horak H.,
Puzorjova I., Kollist H., Palva E.T.;
"ERD15--an attenuator of plant ABA responses and stomatal aperture.";
Plant Sci. 182:19-28(2012).
-!- FUNCTION: Binds the poly(A) tail of mRNA. Appears to be an
important mediator of the multiple roles of the poly(A) tail in
mRNA biogenesis, stability and translation (By similarity). During
infection with potyvirus TuMV, acts as a potential integral
component of the viral replicase complex that could play an
important role in the regulation of potyviral RNA-dependent RNA
polymerase (RdRp) (By similarity). {ECO:0000250}.
-!- SUBUNIT: Interacts with ERD15/CID1. Interacts with Turnip mosaic
virus (TuMV) VPg-Pro. {ECO:0000269|PubMed:18753244,
ECO:0000269|PubMed:22118612}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus
{ECO:0000250}.
-!- INDUCTION: By potyvirus TuMV infection.
{ECO:0000269|PubMed:18753244}.
-!- DISRUPTION PHENOTYPE: Pab2 and pab4 double mutants show
significant growth and development defects and more resistance to
Turnip mosaic virus (TuMV). {ECO:0000269|PubMed:18753244}.
-!- MISCELLANEOUS: A.thaliana contains 8 PABP genes.
-!- SIMILARITY: Belongs to the polyadenylate-binding protein type-1
family. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AC002391; AAB87097.1; -; Genomic_DNA.
EMBL; CP002685; AEC07446.1; -; Genomic_DNA.
EMBL; AF360217; AAK25927.1; -; mRNA.
EMBL; AY050859; AAK92796.1; -; mRNA.
EMBL; AY079389; AAL85120.1; -; mRNA.
PIR; T00497; T00497.
RefSeq; NP_179916.1; NM_127899.4.
UniGene; At.25439; -.
ProteinModelPortal; O22173; -.
SMR; O22173; -.
BioGrid; 2219; 5.
IntAct; O22173; 4.
STRING; 3702.AT2G23350.1; -.
iPTMnet; O22173; -.
PaxDb; O22173; -.
PRIDE; O22173; -.
ProMEX; O22173; -.
EnsemblPlants; AT2G23350.1; AT2G23350.1; AT2G23350.
GeneID; 816867; -.
Gramene; AT2G23350.1; AT2G23350.1; AT2G23350.
KEGG; ath:AT2G23350; -.
Araport; AT2G23350; -.
TAIR; locus:2058573; AT2G23350.
eggNOG; KOG0123; Eukaryota.
eggNOG; ENOG410XR5X; LUCA.
HOGENOM; HOG000217922; -.
InParanoid; O22173; -.
KO; K13126; -.
OMA; MIRITYS; -.
OrthoDB; EOG093606N5; -.
PhylomeDB; O22173; -.
Reactome; R-ATH-156827; L13a-mediated translational silencing of Ceruloplasmin expression.
Reactome; R-ATH-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
Reactome; R-ATH-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
PRO; PR:O22173; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; O22173; baseline and differential.
Genevisible; O22173; AT.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0003729; F:mRNA binding; IDA:TAIR.
GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
GO; GO:0016032; P:viral process; IEA:UniProtKB-KW.
Gene3D; 3.30.70.330; -; 4.
InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
InterPro; IPR036053; PABP-dom.
InterPro; IPR006515; PABP_1234.
InterPro; IPR002004; PABP_HYD.
InterPro; IPR035979; RBD_domain_sf.
InterPro; IPR000504; RRM_dom.
InterPro; IPR003954; RRM_dom_euk.
Pfam; PF00658; PABP; 1.
Pfam; PF00076; RRM_1; 4.
SMART; SM00517; PolyA; 1.
SMART; SM00360; RRM; 4.
SMART; SM00361; RRM_1; 4.
SUPFAM; SSF54928; SSF54928; 3.
SUPFAM; SSF63570; SSF63570; 1.
TIGRFAMs; TIGR01628; PABP-1234; 1.
PROSITE; PS51309; PABC; 1.
PROSITE; PS50102; RRM; 4.
1: Evidence at protein level;
Complete proteome; Cytoplasm; Host-virus interaction; Nucleus;
Reference proteome; Repeat; RNA-binding; Translation regulation.
CHAIN 1 662 Polyadenylate-binding protein 4.
/FTId=PRO_0000422643.
DOMAIN 46 124 RRM 1. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
DOMAIN 134 211 RRM 2. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
DOMAIN 225 302 RRM 3. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
DOMAIN 328 405 RRM 4. {ECO:0000255|PROSITE-
ProRule:PRU00176}.
DOMAIN 558 635 PABC. {ECO:0000255|PROSITE-
ProRule:PRU00641}.
COMPBIAS 12 15 Poly-Pro.
COMPBIAS 30 39 Poly-Gly.
CONFLICT 642 642 E -> D (in Ref. 3; AAK25927).
{ECO:0000305}.
SEQUENCE 662 AA; 71653 MW; 448481E183DF339E CRC64;
MAQVQAPSSH SPPPPAVVND GAATASATPG IGVGGGGDGV THGALCSLYV GDLDFNVTDS
QLYDYFTEVC QVVSVRVCRD AATNTSLGYG YVNYSNTDDA EKAMQKLNYS YLNGKMIRIT
YSSRDSSARR SGVGNLFVKN LDKSVDNKTL HEAFSGCGTI VSCKVATDHM GQSRGYGFVQ
FDTEDSAKNA IEKLNGKVLN DKQIFVGPFL RKEERESAAD KMKFTNVYVK NLSEATTDDE
LKTTFGQYGS ISSAVVMRDG DGKSRCFGFV NFENPEDAAR AVEALNGKKF DDKEWYVGKA
QKKSERELEL SRRYEQGSSD GGNKFDGLNL YVKNLDDTVT DEKLRELFAE FGTITSCKVM
RDPSGTSKGS GFVAFSAASE ASRVLNEMNG KMVGGKPLYV ALAQRKEERR AKLQAQFSQM
RPAFIPGVGP RMPIFTGGAP GLGQQIFYGQ GPPPIIPHQP GFGYQPQLVP GMRPAFFGGP
MMQPGQQGPR PGGRRSGDGP MRHQHQQPMP YMQPQMMPRG RGYRYPSGGR NMPDGPMPGG
MVPVAYDMNV MPYSQPMSAG QLATSLANAT PAQQRTLLGE SLYPLVDQIE SEHAAKVTGM
LLEMDQTEVL HLLESPEALN AKVSEALDVL RNVNQPSSQG SEGNKSGSPS DLLASLSIND
HL


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