NAB3_YEAST
ID NAB3_YEAST Reviewed; 802 AA.
AC P38996; D6W3H8; Q07034;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=Nuclear polyadenylated RNA-binding protein 3;
GN Name=NAB3; Synonyms=HMD1; OrderedLocusNames=YPL190C;
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 [GENOMIC DNA], SUBCELLULAR LOCATION, AND BINDING TO
RP POLYADENYLATED RNA.
RX PubMed=7962083; DOI=10.1083/jcb.127.5.1173;
RA Wilson S.M., Datar K.V., Paddy M.R., Swedlow J.R., Swanson M.S.;
RT "Characterization of nuclear polyadenylated RNA-binding proteins in
RT Saccharomyces cerevisiae.";
RL J. Cell Biol. 127:1173-1184(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX PubMed=7476874; DOI=10.1007/bf02191711;
RA Sugimoto K., Matsumoto K., Kornberg R.D., Reed S.I., Wittenberg C.;
RT "Dosage suppressors of the dominant G1 cyclin mutant CLN3-2: identification
RT of a yeast gene encoding a putative RNA/ssDNA binding protein.";
RL Mol. Gen. Genet. 248:712-718(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [4]
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 [5]
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 [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-86 AND THR-451, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-86 AND THR-451, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: May be required for packaging pre-mRNAs into
CC ribonucleoprotein structures amenable to efficient nuclear RNA
CC processing. Binds to poly(A)+ RNA. Appears to act in the maintenance of
CC CLN3 mRNA levels. {ECO:0000269|PubMed:7476874}.
CC -!- INTERACTION:
CC P38996; P53617: NRD1; NbExp=7; IntAct=EBI-11776, EBI-12228;
CC P38996; Q00416: SEN1; NbExp=5; IntAct=EBI-11776, EBI-16945;
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:7962083}.
CC -!- MISCELLANEOUS: Present with 5830 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
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DR EMBL; U05314; AAA81910.1; -; Genomic_DNA.
DR EMBL; D37935; BAA07154.1; -; Genomic_DNA.
DR EMBL; Z73546; CAA97903.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11244.1; -; Genomic_DNA.
DR PIR; S48529; S48529.
DR RefSeq; NP_015134.1; NM_001184004.1.
DR PDB; 2KVI; NMR; -; A=321-415.
DR PDB; 2L41; NMR; -; A=328-404.
DR PDB; 2XNQ; X-ray; 1.30 A; A=329-404.
DR PDB; 2XNR; X-ray; 1.60 A; A=329-404.
DR PDBsum; 2KVI; -.
DR PDBsum; 2L41; -.
DR PDBsum; 2XNQ; -.
DR PDBsum; 2XNR; -.
DR AlphaFoldDB; P38996; -.
DR BMRB; P38996; -.
DR SMR; P38996; -.
DR BioGRID; 35993; 617.
DR ComplexPortal; CPX-1316; NRD1 snoRNA termination complex.
DR DIP; DIP-3980N; -.
DR IntAct; P38996; 22.
DR MINT; P38996; -.
DR STRING; 4932.YPL190C; -.
DR iPTMnet; P38996; -.
DR MaxQB; P38996; -.
DR PaxDb; P38996; -.
DR PRIDE; P38996; -.
DR EnsemblFungi; YPL190C_mRNA; YPL190C; YPL190C.
DR GeneID; 855911; -.
DR KEGG; sce:YPL190C; -.
DR SGD; S000006111; NAB3.
DR VEuPathDB; FungiDB:YPL190C; -.
DR eggNOG; KOG0118; Eukaryota.
DR HOGENOM; CLU_016358_0_0_1; -.
DR InParanoid; P38996; -.
DR OMA; HGDHGTN; -.
DR BioCyc; YEAST:G3O-34083-MON; -.
DR Reactome; R-SCE-4570464; SUMOylation of RNA binding proteins.
DR EvolutionaryTrace; P38996; -.
DR PRO; PR:P38996; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; P38996; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0035649; C:Nrd1 complex; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR GO; GO:0003723; F:RNA binding; IDA:SGD.
DR GO; GO:0001068; F:transcription regulatory region RNA binding; IDA:SGD.
DR GO; GO:0071041; P:antisense RNA transcript catabolic process; IDA:SGD.
DR GO; GO:0071034; P:CUT catabolic process; IMP:SGD.
DR GO; GO:0031124; P:mRNA 3'-end processing; IMP:SGD.
DR GO; GO:0071028; P:nuclear mRNA surveillance; IMP:SGD.
DR GO; GO:0031126; P:sno(s)RNA 3'-end processing; IMP:SGD.
DR GO; GO:0034472; P:snRNA 3'-end processing; IMP:SGD.
DR GO; GO:0030847; P:termination of RNA polymerase II transcription, exosome-dependent; IDA:SGD.
DR GO; GO:0042780; P:tRNA 3'-end processing; IMP:SGD.
DR CDD; cd12342; RRM_Nab3p; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR Gene3D; 3.40.50.800; -; 1.
DR InterPro; IPR036621; Anticodon-bd_dom_sf.
DR InterPro; IPR034167; Nab3_RRM.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR000504; RRM_dom.
DR Pfam; PF00076; RRM_1; 1.
DR SMART; SM00360; RRM; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS50102; RRM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Phosphoprotein; Reference proteome; RNA-binding.
FT CHAIN 1..802
FT /note="Nuclear polyadenylated RNA-binding protein 3"
FT /id="PRO_0000081657"
FT DOMAIN 330..401
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..174
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 252..293
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 571..675
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 717..802
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 7..34
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 39..141
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 155..174
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 252..281
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 591..613
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 626..640
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 717..758
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 768..802
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 86
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT MOD_RES 451
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT CONFLICT 341
FT /note="N -> I (in Ref. 2; BAA07154)"
FT /evidence="ECO:0000305"
FT STRAND 331..336
FT /evidence="ECO:0007829|PDB:2XNQ"
FT STRAND 339..341
FT /evidence="ECO:0007829|PDB:2XNR"
FT HELIX 344..351
FT /evidence="ECO:0007829|PDB:2XNQ"
FT HELIX 352..354
FT /evidence="ECO:0007829|PDB:2XNQ"
FT STRAND 357..362
FT /evidence="ECO:0007829|PDB:2XNQ"
FT STRAND 364..373
FT /evidence="ECO:0007829|PDB:2XNQ"
FT HELIX 374..384
FT /evidence="ECO:0007829|PDB:2XNQ"
FT STRAND 387..389
FT /evidence="ECO:0007829|PDB:2XNQ"
FT TURN 391..393
FT /evidence="ECO:0007829|PDB:2KVI"
FT STRAND 395..398
FT /evidence="ECO:0007829|PDB:2XNQ"
SQ SEQUENCE 802 AA; 90439 MW; CD6D2C7F24A44993 CRC64;
MSDENHNSDV QDIPSPELSV DSNSNENELM NNSSADDGIE FDAPEEEREA EREEENEEQH
ELEDVNDEEE EDKEEKGEEN GEVINTEEEE EEEHQQKGGN DDDDDDNEEE EEEEEDDDDD
DDDDDDDEEE EEEEEEEGND NSSVGSDSAA EDGEDEEDKK DKTKDKEVEL RRETLEKEQK
DVDEAIKKIT REENDNTHFP TNMENVNYDL LQKQVKYIMD SNMLNLPQFQ HLPQEEKMSA
ILAMLNSNSD TALSVPPHDS TISTTASASA TSGARSNDQR KPPLSDAQRR MRFPRADLSK
PITEEEHDRY AAYLHGENKI TEMHNIPPKS RLFIGNLPLK NVSKEDLFRI FSPYGHIMQI
NIKNAFGFIQ FDNPQSVRDA IECESQEMNF GKKLILEVSS SNARPQFDHG DHGTNSSSTF
ISSAKRPFQT ESGDMYNDDN GAGYKKSRRH TVSCNIFVKR TADRTYAIEV FNRFRDGTGL
ETDMIFLKPR MELGKLINDA AYNGVWGVVL VNKTHNVDVQ TFYKGSQGET KFDEYISISA
DDAVAIFNNI KNNRNNSRPT DYRAMSHQQN IYGAPPLPVP NGPAVGPPPQ TNYYQGYSMP
PPQQQQQQPY GNYGMPPPSH DQGYGSQPPI PMNQSYGRYQ TSIPPPPPQQ QIPQGYGRYQ
AGPPPQPPSQ TPMDQQQLLS AIQNLPPNVV SNLLSMAQQQ QQQPHAQQQL VGLIQSMQGQ
APQQQQQQLG GYSSMNSSSP PPMSTNYNGQ NISAKPSAPP MSHQPPPPQQ QQQQQQQQQQ
QQQQPAGNNV QSLLDSLAKL QK
