PUB1_YEAST
ID PUB1_YEAST Reviewed; 453 AA.
AC P32588; D6W1G2;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 05-OCT-2010, sequence version 4.
DT 03-AUG-2022, entry version 192.
DE RecName: Full=Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 {ECO:0000305};
DE AltName: Full=ARS consensus-binding protein ACBP-60;
DE AltName: Full=Poly uridylate-binding protein {ECO:0000303|PubMed:8413213};
DE Short=Poly(U)-binding protein;
GN Name=PUB1 {ECO:0000303|PubMed:8413213}; Synonyms=RNP1;
GN OrderedLocusNames=YNL016W; ORFNames=N2842;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE, AND SUBCELLULAR LOCATION.
RX PubMed=8413212; DOI=10.1128/mcb.13.10.6102-6113.1993;
RA Anderson J.T., Paddy M.R., Swanson M.S.;
RT "PUB1 is a major nuclear and cytoplasmic polyadenylated RNA-binding protein
RT in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 13:6102-6113(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE, AND SUBCELLULAR LOCATION.
RX PubMed=8413213; DOI=10.1128/mcb.13.10.6114-6123.1993;
RA Matunis M.J., Matunis E.L., Dreyfuss G.;
RT "PUB1: a major yeast poly(A)+ RNA-binding protein.";
RL Mol. Cell. Biol. 13:6114-6123(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE.
RX PubMed=8341595; DOI=10.1093/nar/21.14.3211;
RA Ripmaster T.L., Woolford J.L. Jr.;
RT "A protein containing conserved RNA-recognition motifs is associated with
RT ribosomal subunits in Saccharomyces cerevisiae.";
RL Nucleic Acids Res. 21:3211-3216(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [6]
RP CHARACTERIZATION, AND PARTIAL PROTEIN SEQUENCE.
RX PubMed=8127652; DOI=10.1093/nar/22.1.32;
RA Cockell M., Frutiger S., Hughes G.J., Gasser S.M.;
RT "The yeast protein encoded by PUB1 binds T-rich single stranded DNA.";
RL Nucleic Acids Res. 22:32-40(1994).
RN [7]
RP ACETYLATION AT SER-2.
RX PubMed=9298649; DOI=10.1002/elps.1150180810;
RA Garrels J.I., McLaughlin C.S., Warner J.R., Futcher B., Latter G.I.,
RA Kobayashi R., Schwender B., Volpe T., Anderson D.S., Mesquita-Fuentes R.,
RA Payne W.E.;
RT "Proteome studies of Saccharomyces cerevisiae: identification and
RT characterization of abundant proteins.";
RL Electrophoresis 18:1347-1360(1997).
RN [8]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [9]
RP SUBCELLULAR LOCATION.
RX PubMed=23222640; DOI=10.1038/nsmb.2468;
RA Mitchell S.F., Jain S., She M., Parker R.;
RT "Global analysis of yeast mRNPs.";
RL Nat. Struct. Mol. Biol. 20:127-133(2013).
RN [10]
RP METHYLATION AT ARG-260.
RX PubMed=33856219; DOI=10.1021/acs.jproteome.0c00927;
RA Hamey J.J., Nguyen A., Wilkins M.R.;
RT "Discovery of arginine methylation, phosphorylation, and their co-
RT occurrence in condensate-associated proteins in Saccharomyces cerevisiae.";
RL J. Proteome Res. 20:2420-2434(2021).
RN [11] {ECO:0007744|PDB:3MD3}
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) OF 75-240.
RA Li H., Shi H., Zhu Z., Wang H., Niu L., Teng M.;
RT "Crystal structure of the first two RRM domains of yeast poly(U) binding
RT protein (Pub1).";
RL Submitted (MAR-2010) to the PDB data bank.
RN [12] {ECO:0007744|PDB:2LA4}
RP STRUCTURE BY NMR OF 315-414.
RX PubMed=21931728; DOI=10.1371/journal.pone.0024481;
RA Santiveri C.M., Mirassou Y., Rico-Lastres P., Martinez-Lumbreras S.,
RA Perez-Canadillas J.M.;
RT "Pub1p C-terminal RRM domain interacts with Tif4631p through a conserved
RT region neighbouring the Pab1p binding site.";
RL PLoS ONE 6:e24481-e24481(2011).
CC -!- FUNCTION: May be associated with hnRNA within the nucleus and remains
CC associated during nucleocytoplasmic mRNA transport, once the proteins
CC are in the cytoplasm, disassembly of PUB1-RNA complexes may occur prior
CC to PAB1 binding and formation of a translationally competent RNP
CC complex. Binds to polyadenylated RNA; prefers to bind poly(rU); binds
CC to T-rich single-stranded DNA.
CC -!- INTERACTION:
CC P32588; P40561: SGN1; NbExp=3; IntAct=EBI-14231, EBI-25362;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:23222640,
CC ECO:0000269|PubMed:8413212}. Nucleus {ECO:0000269|PubMed:8413212,
CC ECO:0000269|PubMed:8413213}. Cytoplasm, P-body
CC {ECO:0000269|PubMed:23222640}. Cytoplasm, Stress granule
CC {ECO:0000269|PubMed:23222640}.
CC -!- MISCELLANEOUS: Present with 49600 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA02808.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; L13725; AAC37348.1; -; Unassigned_DNA.
DR EMBL; L20767; AAC37364.1; -; Unassigned_DNA.
DR EMBL; L01797; AAA02808.1; ALT_FRAME; Unassigned_DNA.
DR EMBL; Z71292; CAA95877.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10528.1; -; Genomic_DNA.
DR PIR; S62928; S62928.
DR RefSeq; NP_014382.1; NM_001182855.1.
DR PDB; 2LA4; NMR; -; A=315-414.
DR PDB; 3MD1; X-ray; 1.60 A; A/B=161-240.
DR PDB; 3MD3; X-ray; 2.70 A; A=75-240.
DR PDB; 6Z29; NMR; -; A=316-414.
DR PDBsum; 2LA4; -.
DR PDBsum; 3MD1; -.
DR PDBsum; 3MD3; -.
DR PDBsum; 6Z29; -.
DR AlphaFoldDB; P32588; -.
DR BMRB; P32588; -.
DR SMR; P32588; -.
DR BioGRID; 35810; 699.
DR DIP; DIP-5480N; -.
DR IntAct; P32588; 44.
DR MINT; P32588; -.
DR STRING; 4932.YNL016W; -.
DR iPTMnet; P32588; -.
DR MaxQB; P32588; -.
DR PaxDb; P32588; -.
DR PRIDE; P32588; -.
DR EnsemblFungi; YNL016W_mRNA; YNL016W; YNL016W.
DR GeneID; 855716; -.
DR KEGG; sce:YNL016W; -.
DR SGD; S000004961; PUB1.
DR VEuPathDB; FungiDB:YNL016W; -.
DR eggNOG; KOG0118; Eukaryota.
DR HOGENOM; CLU_025000_4_0_1; -.
DR InParanoid; P32588; -.
DR OMA; RINWASK; -.
DR BioCyc; YEAST:G3O-33055-MON; -.
DR EvolutionaryTrace; P32588; -.
DR PRO; PR:P32588; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P32588; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0010494; C:cytoplasmic stress granule; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0000932; C:P-body; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; IDA:SGD.
DR GO; GO:0008266; F:poly(U) RNA binding; IDA:SGD.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IDA:SGD.
DR GO; GO:0043488; P:regulation of mRNA stability; IMP:SGD.
DR GO; GO:0034063; P:stress granule assembly; IMP:SGD.
DR CDD; cd12614; RRM1_PUB1; 1.
DR CDD; cd12622; RRM3_PUB1; 1.
DR Gene3D; 3.30.70.330; -; 3.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR034509; PUB1_RRM1.
DR InterPro; IPR034639; PUB1_RRM3.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR003954; RRM_dom_euk.
DR Pfam; PF00076; RRM_1; 3.
DR SMART; SM00360; RRM; 3.
DR SMART; SM00361; RRM_1; 2.
DR SUPFAM; SSF54928; SSF54928; 2.
DR PROSITE; PS50102; RRM; 3.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Direct protein sequencing;
KW Methylation; Nucleus; Reference proteome; Repeat; RNA-binding.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298649"
FT CHAIN 2..453
FT /note="Nuclear and cytoplasmic polyadenylated RNA-binding
FT protein PUB1"
FT /id="PRO_0000081745"
FT DOMAIN 75..152
FT /note="RRM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 162..240
FT /note="RRM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT DOMAIN 341..413
FT /note="RRM 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 241..262
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 260..264
FT /note="RNA-binding RGG-box"
FT /evidence="ECO:0000250"
FT REGION 419..453
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..21
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 29..60
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000269|PubMed:9298649"
FT MOD_RES 260
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000269|PubMed:33856219"
FT CONFLICT 268
FT /note="S -> N (in Ref. 1; AAC37348 and 2; AAC37364)"
FT /evidence="ECO:0000305"
FT STRAND 76..83
FT /evidence="ECO:0007829|PDB:3MD3"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:3MD3"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:3MD3"
FT STRAND 101..107
FT /evidence="ECO:0007829|PDB:3MD3"
FT STRAND 115..124
FT /evidence="ECO:0007829|PDB:3MD3"
FT HELIX 125..135
FT /evidence="ECO:0007829|PDB:3MD3"
FT STRAND 146..149
FT /evidence="ECO:0007829|PDB:3MD3"
FT STRAND 162..167
FT /evidence="ECO:0007829|PDB:3MD1"
FT HELIX 175..182
FT /evidence="ECO:0007829|PDB:3MD1"
FT STRAND 188..195
FT /evidence="ECO:0007829|PDB:3MD1"
FT TURN 197..199
FT /evidence="ECO:0007829|PDB:3MD1"
FT STRAND 202..211
FT /evidence="ECO:0007829|PDB:3MD1"
FT HELIX 213..223
FT /evidence="ECO:0007829|PDB:3MD1"
FT STRAND 234..237
FT /evidence="ECO:0007829|PDB:3MD1"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:2LA4"
FT HELIX 326..333
FT /evidence="ECO:0007829|PDB:2LA4"
FT STRAND 342..347
FT /evidence="ECO:0007829|PDB:2LA4"
FT HELIX 354..362
FT /evidence="ECO:0007829|PDB:2LA4"
FT STRAND 368..373
FT /evidence="ECO:0007829|PDB:2LA4"
FT TURN 374..377
FT /evidence="ECO:0007829|PDB:2LA4"
FT STRAND 378..382
FT /evidence="ECO:0007829|PDB:2LA4"
FT HELIX 386..396
FT /evidence="ECO:0007829|PDB:2LA4"
FT STRAND 400..405
FT /evidence="ECO:0007829|PDB:6Z29"
SQ SEQUENCE 453 AA; 50763 MW; 3B81A7735505D3CA CRC64;
MSENNEEQHQ QQQQQQPVAV ETPSAVEAPA SADPSSEQSV AVEGNSEQAE DNQGENDPSV
VPANAITGGR ETSDRVLYVG NLDKAITEDI LKQYFQVGGP IANIKIMIDK NNKNVNYAFV
EYHQSHDANI ALQTLNGKQI ENNIVKINWA FQSQQSSSDD TFNLFVGDLN VNVDDETLRN
AFKDFPSYLS GHVMWDMQTG SSRGYGFVSF TSQDDAQNAM DSMQGQDLNG RPLRINWAAK
RDNNNNNNYQ QRRNYGNNNR GGFRQYNSNN NNNMNMGMNM NMNMNMNNSR GMPPSSMGMP
IGAMPLPSQG QPQQSQTIGL PPQVNPQAVD HIIRSAPPRV TTAYIGNIPH FATEADLIPL
FQNFGFILDF KHYPEKGCCF IKYDTHEQAA VCIVALANFP FQGRNLRTGW GKERSNFMPQ
QQQQGGQPLI MNDQQQPVMS EQQQQQQQQQ QQQ
