DUS3_YEAST
ID DUS3_YEAST Reviewed; 668 AA.
AC Q06053; D6VZ35; P39519;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 29-APR-2008, sequence version 2.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=tRNA-dihydrouridine(47) synthase [NAD(P)(+)];
DE EC=1.3.1.89 {ECO:0000269|PubMed:12003496};
DE AltName: Full=mRNA-dihydrouridine synthase DUS3 {ECO:0000305};
DE EC=1.3.1.- {ECO:0000250|UniProtKB:Q9UTH9};
DE AltName: Full=tRNA-dihydrouridine synthase 3;
GN Name=DUS3; OrderedLocusNames=YLR401C; ORFNames=L8084.19;
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 504-668.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7816623; DOI=10.1093/nar/22.24.5332;
RA Lygerou Z., Conesa C., Lesage P., Swanson R.N., Ruet A., Carlson M.,
RA Sentenac A., Seraphin B.;
RT "The yeast BDF1 gene encodes a transcription factor involved in the
RT expression of a broad class of genes including snRNAs.";
RL Nucleic Acids Res. 22:5332-5340(1994).
RN [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12003496; DOI=10.1017/s1355838202029825;
RA Xing F., Martzen M.R., Phizicky E.M.;
RT "A conserved family of Saccharomyces cerevisiae synthases effects
RT dihydrouridine modification of tRNA.";
RL RNA 8:370-381(2002).
RN [5]
RP IDENTIFICATION OF FRAMESHIFT.
RX PubMed=12844361; DOI=10.1186/gb-2003-4-7-r45;
RA Brachat S., Dietrich F.S., Voegeli S., Zhang Z., Stuart L., Lerch A.,
RA Gates K., Gaffney T.D., Philippsen P.;
RT "Reinvestigation of the Saccharomyces cerevisiae genome annotation by
RT comparison to the genome of a related fungus: Ashbya gossypii.";
RL Genome Biol. 4:R45.1-R45.13(2003).
RN [6]
RP IDENTIFICATION OF FRAMESHIFT.
RX PubMed=12748633; DOI=10.1038/nature01644;
RA Kellis M., Patterson N., Endrizzi M., Birren B.W., Lander E.S.;
RT "Sequencing and comparison of yeast species to identify genes and
RT regulatory elements.";
RL Nature 423:241-254(2003).
RN [7]
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 [8]
RP FUNCTION.
RX PubMed=14970222; DOI=10.1074/jbc.m401221200;
RA Xing F., Hiley S.L., Hughes T.R., Phizicky E.M.;
RT "The specificities of four yeast dihydrouridine synthases for cytoplasmic
RT tRNAs.";
RL J. Biol. Chem. 279:17850-17860(2004).
RN [9]
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 [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: Catalyzes the synthesis of dihydrouridine, a modified base
CC found in the D-loop of most tRNAs (PubMed:12003496, PubMed:14970222).
CC Specifically modifies U47 in cytoplasmic tRNAs (PubMed:14970222).
CC Catalyzes the synthesis of dihydrouridine in some mRNAs, thereby
CC affecting their translation (By similarity).
CC {ECO:0000250|UniProtKB:Q9UTH9, ECO:0000269|PubMed:12003496,
CC ECO:0000269|PubMed:14970222}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(47) in tRNA + NAD(+) = H(+) + NADH +
CC uridine(47) in tRNA; Xref=Rhea:RHEA:53364, Rhea:RHEA-COMP:13539,
CC Rhea:RHEA-COMP:13540, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443; EC=1.3.1.89;
CC Evidence={ECO:0000269|PubMed:12003496};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:53366;
CC Evidence={ECO:0000269|PubMed:12003496};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(47) in tRNA + NADP(+) = H(+) + NADPH +
CC uridine(47) in tRNA; Xref=Rhea:RHEA:53360, Rhea:RHEA-COMP:13539,
CC Rhea:RHEA-COMP:13540, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443; EC=1.3.1.89;
CC Evidence={ECO:0000269|PubMed:12003496};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:53362;
CC Evidence={ECO:0000269|PubMed:12003496};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5,6-dihydrouridine in mRNA + NAD(+) = a uridine in mRNA +
CC H(+) + NADH; Xref=Rhea:RHEA:69851, Rhea:RHEA-COMP:14658, Rhea:RHEA-
CC COMP:17789, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000250|UniProtKB:Q9UTH9};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:69853;
CC Evidence={ECO:0000250|UniProtKB:Q9UTH9};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5,6-dihydrouridine in mRNA + NADP(+) = a uridine in mRNA +
CC H(+) + NADPH; Xref=Rhea:RHEA:69855, Rhea:RHEA-COMP:14658, Rhea:RHEA-
CC COMP:17789, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000250|UniProtKB:Q9UTH9};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:69857;
CC Evidence={ECO:0000250|UniProtKB:Q9UTH9};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000250|UniProtKB:Q5SMC7};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- SIMILARITY: Belongs to the Dus family. Dus3 subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB82358.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA79376.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U19729; AAB82358.1; ALT_FRAME; Genomic_DNA.
DR EMBL; Z18944; CAA79376.1; ALT_FRAME; Genomic_DNA.
DR EMBL; BK006945; DAA09701.1; -; Genomic_DNA.
DR PIR; S55957; S55957.
DR RefSeq; NP_013505.4; NM_001182289.3.
DR AlphaFoldDB; Q06053; -.
DR SMR; Q06053; -.
DR BioGRID; 31659; 111.
DR DIP; DIP-4469N; -.
DR MINT; Q06053; -.
DR STRING; 4932.YLR401C; -.
DR iPTMnet; Q06053; -.
DR MaxQB; Q06053; -.
DR PaxDb; Q06053; -.
DR PRIDE; Q06053; -.
DR EnsemblFungi; YLR401C_mRNA; YLR401C; YLR401C.
DR GeneID; 851117; -.
DR KEGG; sce:YLR401C; -.
DR SGD; S000004393; DUS3.
DR VEuPathDB; FungiDB:YLR401C; -.
DR eggNOG; KOG2333; Eukaryota.
DR GeneTree; ENSGT00550000075134; -.
DR HOGENOM; CLU_013299_7_0_1; -.
DR InParanoid; Q06053; -.
DR OMA; IAANKPW; -.
DR BioCyc; MetaCyc:G3O-32464-MON; -.
DR BioCyc; YEAST:G3O-32464-MON; -.
DR BRENDA; 1.3.1.89; 984.
DR PRO; PR:Q06053; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; Q06053; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0034399; C:nuclear periphery; IDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR GO; GO:0017150; F:tRNA dihydrouridine synthase activity; IMP:SGD.
DR GO; GO:0102265; F:tRNA-dihydrouridine47 synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0006400; P:tRNA modification; IMP:SGD.
DR CDD; cd02801; DUS_like_FMN; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR035587; DUS-like_FMN-bd.
DR InterPro; IPR018517; tRNA_hU_synthase_CS.
DR InterPro; IPR000571; Znf_CCCH.
DR Pfam; PF01207; Dus; 1.
DR PROSITE; PS01136; UPF0034; 1.
DR PROSITE; PS50103; ZF_C3H1; 2.
PE 1: Evidence at protein level;
KW Cytoplasm; Flavoprotein; FMN; Metal-binding; mRNA processing; NAD; NADP;
KW Nucleus; Oxidoreductase; Reference proteome; Repeat; tRNA processing; Zinc;
KW Zinc-finger.
FT CHAIN 1..668
FT /note="tRNA-dihydrouridine(47) synthase [NAD(P)(+)]"
FT /id="PRO_0000162155"
FT ZN_FING 92..122
FT /note="C3H1-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT ZN_FING 134..164
FT /note="C3H1-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00723"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 59..92
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 227..264
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 227..242
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 386
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7"
FT BINDING 299..301
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7"
FT BINDING 354
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7"
FT BINDING 426
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7"
FT BINDING 457
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7"
FT BINDING 509..511
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7"
FT BINDING 534..535
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7"
SQ SEQUENCE 668 AA; 76596 MW; 0DA116A41699E9C9 CRC64;
MEQNAEKRSI VGDDNSTVKR QDTSPSKGIA HIKPEYIVPL KQNENQKVAI YDEEMSSDRM
TNEFAGGTNK KNKNGRGKKR GQNKNRDNRQ VKEQNVLCPR LIHGDISKCS FGDNCRFVHD
INLYLSTKKP EVESNIFPSC PVFNSLGFCP MGFKCRFLSS HLNKEDNILI SKKEIDPDAQ
TIWSVKGEVN HISPERKLDL IKRRFPFTKS NEILEIIDSF QQECRDSMKP EEEVESTPQL
KKQDPDVEQP VAPQVEQRNK ELSEHRMKQR EVYLKYKDTR YFAQEKKPLD LYHKKIVSPL
TTVGNLPYRR LMRKLGADVT YSEMALAVPL IQGTNSEWAL PKAHTSEFPG FGVQVACSKA
WQAAKAAEAL ANSVSEISEI NLNSGCPIDL LYRQGSGSAL LDNPARMIRC LNAMNYVSKD
IPITVKIRTG TKEGHPIAEG LVKRLVNETD VAAITLHGRS RQQRYTKSAD WDYVSQVADT
LRSAEADFIE TEQGKEGRDS KNRIQFVGNG DVNNFEDWYR YLNGNENIDS VMVARGALIK
PWIFEEVESQ QYLDKTSTER LDILRDYAQF SMEHWGTDEY GISQCRRFFC EFMSFFHRYV
PMGICERYPV KLNERPPNWC GRDELETLMG STDVNDWIKL SDLFFGKTDE NFVFVPKHKS
SSYANRDS
