USB1_YEAST
ID USB1_YEAST Reviewed; 290 AA.
AC Q12208; D6VYC7;
DT 28-NOV-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=U6 snRNA phosphodiesterase 1 {ECO:0000305};
DE AltName: Full=3'-5' RNA exonuclease USB1 {ECO:0000305|PubMed:28887445};
DE EC=4.6.1.- {ECO:0000269|PubMed:28887445};
DE AltName: Full=Cyclic phosphodiesterase USB1 {ECO:0000305|PubMed:28887445};
DE EC=3.1.4.- {ECO:0000269|PubMed:28887445};
DE AltName: Full=U six biogenesis protein 1;
GN Name=USB1 {ECO:0000255|HAMAP-Rule:MF_03040}; OrderedLocusNames=YLR132C;
GN ORFNames=L3127;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [2]
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 [3]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION
RP [LARGE SCALE ANALYSIS].
RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT "Assigning function to yeast proteins by integration of technologies.";
RL Mol. Cell 12:1353-1365(2003).
RN [4]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [7]
RP SUBCELLULAR LOCATION, FUNCTION, SUBUNIT, AND MUTAGENESIS OF HIS-133 AND
RP HIS-231.
RX PubMed=22899009; DOI=10.1101/gad.193169.112;
RA Mroczek S., Krwawicz J., Kutner J., Lazniewski M., Kucinski I.,
RA Ginalski K., Dziembowski A.;
RT "C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a
RT putative phosphodiesterase responsible for the U6 snRNA 3' end
RT modification.";
RL Genes Dev. 26:1911-1925(2012).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF HIS-133 AND HIS-231.
RX PubMed=23190533; DOI=10.1182/blood-2012-10-461491;
RA Hilcenko C., Simpson P.J., Finch A.J., Bowler F.R., Churcher M.J., Jin L.,
RA Packman L.C., Shlien A., Campbell P., Kirwan M., Dokal I., Warren A.J.;
RT "Aberrant 3' oligoadenylation of spliceosomal U6 small nuclear RNA in
RT poikiloderma with neutropenia.";
RL Blood 121:1028-1038(2013).
RN [9] {ECO:0007744|PDB:5UQJ}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 71-290, CATALYTIC ACTIVITY,
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF PHE-78.
RX PubMed=28887445; DOI=10.1038/s41467-017-00484-w;
RA Didychuk A.L., Montemayor E.J., Carrocci T.J., DeLaitsch A.T.,
RA Lucarelli S.E., Westler W.M., Brow D.A., Hoskins A.A., Butcher S.E.;
RT "Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic
RT phosphodiesterase activities.";
RL Nat. Commun. 8:497-497(2017).
CC -!- FUNCTION: 3'-5' RNA exonuclease that trims the 3' end of oligo(U)
CC tracts of the pre-U6 small nuclear RNA (snRNA) molecule, leading to the
CC formation of a U6 snRNA 3' end-terminated with a 2',3'-cyclic phosphate
CC (PubMed:28887445). In a second step acts as a cyclic phosphodiesterase
CC that hydrolyzes a U6 snRNA 3' end-terminated with a 2',3'-cyclic
CC phosphate to a U6 snRNA 3'-end-terminated with a 3' phosphate
CC (PubMed:28887445, PubMed:22899009). Participates in the U6 snRNA 3' end
CC processing that prevents U6 snRNA degradation (PubMed:28887445,
CC PubMed:23190533, PubMed:22899009). Could be involved in aerobic
CC respiration (PubMed:14690591). {ECO:0000269|PubMed:14690591,
CC ECO:0000269|PubMed:22899009, ECO:0000269|PubMed:23190533,
CC ECO:0000269|PubMed:28887445}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end uridylyl-uridine-RNA = a 3'-end 2',3'-cyclophospho-
CC uridine-RNA + uridine; Xref=Rhea:RHEA:46052, Rhea:RHEA-COMP:17384,
CC Rhea:RHEA-COMP:17385, ChEBI:CHEBI:16704, ChEBI:CHEBI:85643,
CC ChEBI:CHEBI:85644; Evidence={ECO:0000269|PubMed:28887445};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:46053;
CC Evidence={ECO:0000305|PubMed:28887445};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.5. {ECO:0000269|PubMed:28887445};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:22899009}.
CC -!- INTERACTION:
CC Q12208; P32523: PRP19; NbExp=3; IntAct=EBI-31589, EBI-493;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03040,
CC ECO:0000269|PubMed:14690591}. Mitochondrion
CC {ECO:0000269|PubMed:14690591}.
CC -!- DISRUPTION PHENOTYPE: Lethal. {ECO:0000269|PubMed:23190533}.
CC -!- MISCELLANEOUS: Present with 486 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the 2H phosphoesterase superfamily. USB1 family.
CC {ECO:0000255|HAMAP-Rule:MF_03040}.
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DR EMBL; U53881; AAB82399.1; -; Genomic_DNA.
DR EMBL; X91258; CAA62645.1; -; Genomic_DNA.
DR EMBL; Z73304; CAA97703.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09443.1; -; Genomic_DNA.
DR PIR; S59322; S59322.
DR RefSeq; NP_013233.1; NM_001182019.1.
DR PDB; 5UQJ; X-ray; 1.80 A; A=71-290.
DR PDBsum; 5UQJ; -.
DR AlphaFoldDB; Q12208; -.
DR SMR; Q12208; -.
DR BioGRID; 31401; 29.
DR DIP; DIP-2147N; -.
DR IntAct; Q12208; 13.
DR MINT; Q12208; -.
DR STRING; 4932.YLR132C; -.
DR iPTMnet; Q12208; -.
DR MaxQB; Q12208; -.
DR PaxDb; Q12208; -.
DR PRIDE; Q12208; -.
DR EnsemblFungi; YLR132C_mRNA; YLR132C; YLR132C.
DR GeneID; 850823; -.
DR KEGG; sce:YLR132C; -.
DR SGD; S000004122; USB1.
DR VEuPathDB; FungiDB:YLR132C; -.
DR eggNOG; ENOG502S533; Eukaryota.
DR HOGENOM; CLU_083705_0_0_1; -.
DR InParanoid; Q12208; -.
DR OMA; HEPTERD; -.
DR BioCyc; YEAST:G3O-32274-MON; -.
DR PRO; PR:Q12208; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q12208; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0008663; F:2',3'-cyclic-nucleotide 2'-phosphodiesterase activity; IDA:UniProtKB.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; IBA:GO_Central.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:1990838; F:poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends; IDA:UniProtKB.
DR GO; GO:0034477; P:U6 snRNA 3'-end processing; IMP:UniProtKB.
DR HAMAP; MF_03040; USB1; 1.
DR InterPro; IPR027521; Usb1.
DR PANTHER; PTHR13522; PTHR13522; 1.
DR Pfam; PF09749; HVSL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Lyase; Mitochondrion; Nuclease; Nucleus;
KW Reference proteome.
FT CHAIN 1..290
FT /note="U6 snRNA phosphodiesterase 1"
FT /id="PRO_0000262872"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 7..26
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 133
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03040"
FT ACT_SITE 231
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03040"
FT BINDING 133..135
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT BINDING 223..233
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT BINDING 229..233
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT MUTAGEN 78
FT /note="F->A: Slows growth phenotype."
FT /evidence="ECO:0000269|PubMed:28887445"
FT MUTAGEN 78
FT /note="F->H: Does not affect growth phenotype.
FT Significantly decreases in vitro processing."
FT /evidence="ECO:0000269|PubMed:28887445"
FT MUTAGEN 133
FT /note="H->A: Cannot restore cell growth in USB1 depleted
FT cells."
FT /evidence="ECO:0000269|PubMed:22899009,
FT ECO:0000269|PubMed:23190533"
FT MUTAGEN 231
FT /note="H->A: Cannot restore cell growth in USB1 depleted
FT cells."
FT /evidence="ECO:0000269|PubMed:22899009,
FT ECO:0000269|PubMed:23190533"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:5UQJ"
FT HELIX 87..105
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 117..120
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 132..137
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 140..144
FT /evidence="ECO:0007829|PDB:5UQJ"
FT HELIX 145..161
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 167..171
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 176..179
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 186..192
FT /evidence="ECO:0007829|PDB:5UQJ"
FT HELIX 194..214
FT /evidence="ECO:0007829|PDB:5UQJ"
FT TURN 221..223
FT /evidence="ECO:0007829|PDB:5UQJ"
FT HELIX 227..229
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 231..239
FT /evidence="ECO:0007829|PDB:5UQJ"
FT HELIX 242..246
FT /evidence="ECO:0007829|PDB:5UQJ"
FT HELIX 248..262
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 269..273
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 275..278
FT /evidence="ECO:0007829|PDB:5UQJ"
FT STRAND 285..288
FT /evidence="ECO:0007829|PDB:5UQJ"
SQ SEQUENCE 290 AA; 33694 MW; 63BCE8C433136FB5 CRC64;
MEFISADYSS SDGSDTESES SNKSEVQIEY TEKTCIQKAD STDLPAIPDS IILKYHIPPN
LQKYEHQDMN MSRFWRSFTY FEWRPTPAIH RQLQKIICKY KETFMKQEYT NPYQLVDFDP
LFISHLGAPK PLHVSLTRSL LFETEEQRHV FIQEMRNGLR NNEITPFKLQ ICSYPKLYIS
ERANTLYLGL PVSECPNKAQ ISPFKTIIAE ALQKSGISNY QDLIVSRQNL HVSIAIASNP
SKATLKRYQQ LNETMGALLL LNNDFAYKLE FLVNSIYCDE NRHSIRIPFN
