DUSA_ECOLI
ID DUSA_ECOLI Reviewed; 345 AA.
AC P32695; P76786; Q2M6Q5;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 19-MAR-2014, sequence version 4.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=tRNA-dihydrouridine(20/20a) synthase {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000305|PubMed:22123979};
DE EC=1.3.1.- {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000305|PubMed:22123979};
DE EC=1.3.1.91 {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000305|PubMed:11983710, ECO:0000305|PubMed:22123979};
DE AltName: Full=U20-specific dihydrouridine synthase {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000303|PubMed:25902496};
DE Short=U20-specific Dus {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000303|PubMed:25902496};
DE AltName: Full=tRNA-dihydrouridine synthase A {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000303|PubMed:11983710};
GN Name=dusA {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000303|PubMed:11983710};
GN Synonyms=yjbN; OrderedLocusNames=b4049, JW5950;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 10-19.
RC STRAIN=K12 / BW25113;
RX PubMed=23908556; DOI=10.1074/mcp.m113.029165;
RA Krug K., Carpy A., Behrends G., Matic K., Soares N.C., Macek B.;
RT "Deep coverage of the Escherichia coli proteome enables the assessment of
RT false discovery rates in simple proteogenomic experiments.";
RL Mol. Cell. Proteomics 12:3420-3430(2013).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=11983710; DOI=10.1074/jbc.m203208200;
RA Bishop A.C., Xu J., Johnson R.C., Schimmel P., de Crecy-Lagard V.;
RT "Identification of the tRNA-dihydrouridine synthase family.";
RL J. Biol. Chem. 277:25090-25095(2002).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF CYS-114 AND LYS-153.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=22123979; DOI=10.1073/pnas.1112352108;
RA Yu F., Tanaka Y., Yamashita K., Suzuki T., Nakamura A., Hirano N.,
RA Suzuki T., Yao M., Tanaka I.;
RT "Molecular basis of dihydrouridine formation on tRNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:19593-19598(2011).
RN [7]
RP DUSA SUBFAMILY SPECIFICITY.
RX PubMed=25902496; DOI=10.1073/pnas.1500161112;
RA Byrne R.T., Jenkins H.T., Peters D.T., Whelan F., Stowell J., Aziz N.,
RA Kasatsky P., Rodnina M.V., Koonin E.V., Konevega A.L., Antson A.A.;
RT "Major reorientation of tRNA substrates defines specificity of
RT dihydrouridine synthases.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:6033-6037(2015).
CC -!- FUNCTION: Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified
CC base found in the D-loop of most tRNAs, via the reduction of the C5-C6
CC double bond in target uridines. Specifically modifies U20 and U20a in
CC tRNAs. {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000269|PubMed:11983710,
CC ECO:0000269|PubMed:22123979, ECO:0000305|PubMed:25902496}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(20) in tRNA + NADP(+) = H(+) + NADPH +
CC uridine(20) in tRNA; Xref=Rhea:RHEA:53336, Rhea:RHEA-COMP:13533,
CC Rhea:RHEA-COMP:13534, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443; EC=1.3.1.91;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02041,
CC ECO:0000305|PubMed:11983710, ECO:0000305|PubMed:22123979};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(20) in tRNA + NAD(+) = H(+) + NADH +
CC uridine(20) in tRNA; Xref=Rhea:RHEA:53340, Rhea:RHEA-COMP:13533,
CC Rhea:RHEA-COMP:13534, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443; EC=1.3.1.91;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02041,
CC ECO:0000305|PubMed:11983710, ECO:0000305|PubMed:22123979};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(20a) in tRNA + NADP(+) = H(+) + NADPH +
CC uridine(20a) in tRNA; Xref=Rhea:RHEA:53344, Rhea:RHEA-COMP:13535,
CC Rhea:RHEA-COMP:13536, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02041,
CC ECO:0000305|PubMed:22123979};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(20a) in tRNA + NAD(+) = H(+) + NADH +
CC uridine(20a) in tRNA; Xref=Rhea:RHEA:53348, Rhea:RHEA-COMP:13535,
CC Rhea:RHEA-COMP:13536, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02041,
CC ECO:0000305|PubMed:22123979};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02041};
CC -!- DISRUPTION PHENOTYPE: A dusA dusB dusC triple mutant exhibits a
CC complete lack of 5,6-dihydrouridine modification in cellular tRNA,
CC whereas each single mutant exhibits a partial reduction, compared to
CC wild type (PubMed:11983710). Cells lacking this gene can introduce D
CC modification at neither 20 or 20a in tRNA (PubMed:22123979).
CC {ECO:0000269|PubMed:11983710, ECO:0000269|PubMed:22123979}.
CC -!- MISCELLANEOUS: DusB and DusC together account for about half of the
CC 5,6-dihydrouridine modification observed in wild-type cellular tRNA,
CC and DusA accounts for the other half. These three enzymes seem to act
CC site-specifically on the tRNA D-loop and contain nonredundant catalytic
CC functions in vivo. {ECO:0000269|PubMed:11983710}.
CC -!- SIMILARITY: Belongs to the Dus family. DusA subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_02041}.
CC -!- CAUTION: The U21 position mentioned in PubMed:11983710 corresponds in
CC fact to U20 with the conventional numbering. {ECO:0000305}.
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DR EMBL; U00006; AAC43143.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77019.3; -; Genomic_DNA.
DR EMBL; AP009048; BAE78051.1; -; Genomic_DNA.
DR RefSeq; NP_418473.3; NC_000913.3.
DR RefSeq; WP_001298868.1; NZ_STEB01000022.1.
DR AlphaFoldDB; P32695; -.
DR SMR; P32695; -.
DR BioGRID; 4259608; 5.
DR STRING; 511145.b4049; -.
DR jPOST; P32695; -.
DR PaxDb; P32695; -.
DR PRIDE; P32695; -.
DR EnsemblBacteria; AAC77019; AAC77019; b4049.
DR EnsemblBacteria; BAE78051; BAE78051; BAE78051.
DR GeneID; 66672037; -.
DR GeneID; 948558; -.
DR KEGG; ecj:JW5950; -.
DR KEGG; eco:b4049; -.
DR PATRIC; fig|511145.12.peg.4167; -.
DR EchoBASE; EB1876; -.
DR eggNOG; COG0042; Bacteria.
DR HOGENOM; CLU_013299_2_1_6; -.
DR InParanoid; P32695; -.
DR OMA; LIYPYVD; -.
DR BioCyc; EcoCyc:EG11932-MON; -.
DR BioCyc; MetaCyc:EG11932-MON; -.
DR PRO; PR:P32695; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0010181; F:FMN binding; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0017150; F:tRNA dihydrouridine synthase activity; IMP:EcoCyc.
DR GO; GO:0102264; F:tRNA-dihydrouridine20 synthase activity; IEA:UniProtKB-EC.
DR CDD; cd02801; DUS_like_FMN; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_02041; DusA_subfam; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR035587; DUS-like_FMN-bd.
DR InterPro; IPR001269; DUS_fam.
DR InterPro; IPR004653; DusA.
DR InterPro; IPR018517; tRNA_hU_synthase_CS.
DR PANTHER; PTHR42907; PTHR42907; 1.
DR Pfam; PF01207; Dus; 1.
DR PIRSF; PIRSF006621; Dus; 1.
DR TIGRFAMs; TIGR00742; yjbN; 1.
DR PROSITE; PS01136; UPF0034; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; Flavoprotein; FMN; NADP; Oxidoreductase;
KW Reference proteome; RNA-binding; tRNA processing; tRNA-binding.
FT CHAIN 1..345
FT /note="tRNA-dihydrouridine(20/20a) synthase"
FT /id="PRO_0000162063"
FT ACT_SITE 114
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT BINDING 32..34
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT BINDING 84
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT BINDING 153
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT BINDING 186
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT BINDING 226..228
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT BINDING 248..249
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT SITE 111
FT /note="Interacts with tRNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT SITE 198
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT SITE 201
FT /note="Interacts with tRNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT SITE 314
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT SITE 317
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02041"
FT MUTAGEN 114
FT /note="C->A: Loss of enzymatic activity; when associated
FT with Ala-153."
FT /evidence="ECO:0000269|PubMed:22123979"
FT MUTAGEN 153
FT /note="K->A: Loss of the ability to bind FMN. Loss of
FT enzymatic activity; when associated with Ala-114."
FT /evidence="ECO:0000269|PubMed:22123979"
SQ SEQUENCE 345 AA; 38468 MW; 1FD687C1D0B764D3 CRC64;
MHGNSEMQKI NQTSAMPEKT DVHWSGRFSV APMLDWTDRH CRYFLRLLSR NTLLYTEMVT
TGAIIHGKGD YLAYSEEEHP VALQLGGSDP AALAQCAKLA EARGYDEINL NVGCPSDRVQ
NGMFGACLMG NAQLVADCVK AMRDVVSIPV TVKTRIGIDD QDSYEFLCDF INTVSGKGEC
EMFIIHARKA WLSGLSPKEN REIPPLDYPR VYQLKRDFPH LTMSINGGIK SLEEAKAHLQ
HMDGVMVGRE AYQNPGILAA VDREIFGSSD TDADPVAVVR AMYPYIEREL SQGTYLGHIT
RHMLGLFQGI PGARQWRRYL SENAHKAGAD INVLEHALKL VADKR
