USB1_MOUSE
ID USB1_MOUSE Reviewed; 267 AA.
AC Q91W78; Q3TU91;
DT 06-FEB-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=U6 snRNA phosphodiesterase 1 {ECO:0000305};
DE AltName: Full=3'-5' RNA exonuclease USB1 {ECO:0000250|UniProtKB:Q9BQ65};
DE EC=4.6.1.- {ECO:0000250|UniProtKB:Q9BQ65};
GN Name=Usb1 {ECO:0000255|HAMAP-Rule:MF_03040, ECO:0000312|MGI:MGI:2142454};
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J;
RC TISSUE=Extraembryonic tissue, Liver, Muellerian duct, and Placenta;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=FVB/N; TISSUE=Colon;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
CC -!- FUNCTION: 3'-5' RNA exonuclease that trims the 3' end of oligo(U) and
CC oligo(A) tracts of the pre-U6 small nuclear RNA (snRNA) molecule,
CC leading to the formation of a mature U6 snRNA 3' end-terminated with a
CC 2',3'-cyclic phosphate. Participates in the U6 snRNA 3' end processing
CC that prevents U6 snRNA degradation. In addition also removes uridines
CC from the 3' end of U6atac snRNA and possibly the vault RNA VTRNA1-1.
CC {ECO:0000250|UniProtKB:Q9BQ65}.
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:0000250|UniProtKB:Q9BQ65};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:46053;
CC Evidence={ECO:0000250|UniProtKB:Q9BQ65};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 3'-end uridylyl-adenosine-RNA = a 3'-end 2',3'-cyclophospho-
CC uridine-RNA + adenosine; Xref=Rhea:RHEA:67896, Rhea:RHEA-COMP:17385,
CC Rhea:RHEA-COMP:17386, ChEBI:CHEBI:16335, ChEBI:CHEBI:85644,
CC ChEBI:CHEBI:176518; Evidence={ECO:0000250|UniProtKB:Q9BQ65};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67897;
CC Evidence={ECO:0000250|UniProtKB:Q9BQ65};
CC -!- SUBUNIT: Interacts with PLRG1, CDC5L AND PRPF19.
CC {ECO:0000250|UniProtKB:Q9BQ65}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|HAMAP-Rule:MF_03040}.
CC -!- SIMILARITY: Belongs to the 2H phosphoesterase superfamily. USB1 family.
CC {ECO:0000255|HAMAP-Rule:MF_03040}.
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DR EMBL; AK135527; BAE22567.1; -; mRNA.
DR EMBL; AK160901; BAE36080.1; -; mRNA.
DR EMBL; AK168683; BAE40531.1; -; mRNA.
DR EMBL; BC016418; AAH16418.1; -; mRNA.
DR CCDS; CCDS22560.1; -.
DR RefSeq; NP_598715.2; NM_133954.2.
DR RefSeq; XP_017167985.1; XM_017312496.1.
DR AlphaFoldDB; Q91W78; -.
DR SMR; Q91W78; -.
DR STRING; 10090.ENSMUSP00000034245; -.
DR iPTMnet; Q91W78; -.
DR PhosphoSitePlus; Q91W78; -.
DR EPD; Q91W78; -.
DR MaxQB; Q91W78; -.
DR PaxDb; Q91W78; -.
DR PRIDE; Q91W78; -.
DR ProteomicsDB; 275397; -.
DR GeneID; 101985; -.
DR KEGG; mmu:101985; -.
DR UCSC; uc009myg.2; mouse.
DR CTD; 79650; -.
DR MGI; MGI:2142454; Usb1.
DR eggNOG; KOG3102; Eukaryota.
DR InParanoid; Q91W78; -.
DR OrthoDB; 1507496at2759; -.
DR PhylomeDB; Q91W78; -.
DR TreeFam; TF324364; -.
DR BioGRID-ORCS; 101985; 5 hits in 74 CRISPR screens.
DR PRO; PR:Q91W78; -.
DR Proteomes; UP000000589; Unplaced.
DR RNAct; Q91W78; protein.
DR GO; GO:0045171; C:intercellular bridge; ISO:MGI.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0000175; F:3'-5'-exoribonuclease activity; ISS:UniProtKB.
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; ISS:UniProtKB.
DR GO; GO:0008380; P:RNA splicing; ISS:UniProtKB.
DR GO; GO:0034472; P:snRNA 3'-end processing; ISS:UniProtKB.
DR GO; GO:0034477; P:U6 snRNA 3'-end processing; ISS:UniProtKB.
DR HAMAP; MF_03040; USB1; 1.
DR InterPro; IPR009097; Cyclic_Pdiesterase.
DR InterPro; IPR027521; Usb1.
DR PANTHER; PTHR13522; PTHR13522; 1.
DR Pfam; PF09749; HVSL; 1.
DR SUPFAM; SSF55144; SSF55144; 1.
PE 2: Evidence at transcript level;
KW Hydrolase; Lyase; Nuclease; Nucleus; Reference proteome.
FT CHAIN 1..267
FT /note="U6 snRNA phosphodiesterase 1"
FT /id="PRO_0000274392"
FT REGION 1..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 122
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03040"
FT ACT_SITE 210
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03040"
FT BINDING 122..124
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT BINDING 166
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT BINDING 204
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT BINDING 204
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT BINDING 206..212
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT BINDING 208..212
FT /ligand="UMP"
FT /ligand_id="ChEBI:CHEBI:57865"
FT /evidence="ECO:0000250|UniProtKB:Q9BQ65"
FT CONFLICT 211
FT /note="I -> V (in Ref. 1; BAE22567/BAE40531/BAE36080)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 267 AA; 30250 MW; 632DB96BD5BA2395 CRC64;
MSSAPLVGYS SSGSEDEAEA VAAGRSKPGT GFHRCGQNPV PSEKLPVPDS VLSMFPSTEE
GPEDDSAKHG GRIRTFPHER GNWATHIYIP YEAKEDFRDL LDALLPRAQM FVPRLVLMEE
FHVSLSQSVV LRHHWILPFV QVLKDRMASF QRFFFTANRV KIYTNQEKTR TFIGLEVSSG
HAQFLDLVSE VDRAMKEFDL TTFYQDPSFH ISLAWCVGDA SLQLEGQCLQ ELQEIVDEFE
DSEMLLRVLA NQVRCKSGNK FFSMPLK
