DUSB_ECOLI
ID DUSB_ECOLI Reviewed; 321 AA.
AC P0ABT5; P25717; Q2M8V5;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=tRNA-dihydrouridine synthase B {ECO:0000255|HAMAP-Rule:MF_02042, ECO:0000303|PubMed:11983710};
DE EC=1.3.1.- {ECO:0000255|HAMAP-Rule:MF_02042, ECO:0000305};
GN Name=dusB {ECO:0000255|HAMAP-Rule:MF_02042, ECO:0000303|PubMed:11983710};
GN Synonyms=yhdG; OrderedLocusNames=b3260, JW3228;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=CSH50;
RX PubMed=1547773; DOI=10.1002/j.1460-2075.1992.tb05146.x;
RA Ninnemann O., Koch C., Kahmann R.;
RT "The E.coli fis promoter is subject to stringent control and
RT autoregulation.";
RL EMBO J. 11:1075-1083(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1459953; DOI=10.1128/jb.174.24.8043-8056.1992;
RA Ball C.A., Osuna R., Ferguson K.C., Johnson R.C.;
RT "Dramatic changes in Fis levels upon nutrient upshift in Escherichia
RT coli.";
RL J. Bacteriol. 174:8043-8056(1992).
RN [3]
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 [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-25.
RX PubMed=8226664; DOI=10.1128/jb.175.22.7178-7188.1993;
RA Vanet A., Plumbridge J.A., Alix J.-H.;
RT "Cotranscription of two genes necessary for ribosomal protein L11
RT methylation (prmA) and pantothenate transport (panF) in Escherichia coli K-
RT 12.";
RL J. Bacteriol. 175:7178-7188(1993).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 276-321.
RX PubMed=2837762; DOI=10.1073/pnas.85.12.4237;
RA Koch C., Vanderkerckhove J., Kahmann R.;
RT "Escherichia coli host factor for site-specific DNA inversion: cloning and
RT characterization of the fis gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 85:4237-4241(1988).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 312-321.
RC STRAIN=K12;
RX PubMed=2835774; DOI=10.1073/pnas.85.10.3484;
RA Johnson R.C., Ball C.A., Pfeffer D., Simon M.I.;
RT "Isolation of the gene encoding the Hin recombinational enhancer binding
RT protein.";
RL Proc. Natl. Acad. Sci. U.S.A. 85:3484-3488(1988).
RN [8]
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).
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. {ECO:0000255|HAMAP-Rule:MF_02042,
CC ECO:0000269|PubMed:11983710}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5,6-dihydrouridine in tRNA + NAD(+) = a uridine in tRNA +
CC H(+) + NADH; Xref=Rhea:RHEA:54452, Rhea:RHEA-COMP:13339, Rhea:RHEA-
CC COMP:13887, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000250|UniProtKB:P33371, ECO:0000255|HAMAP-
CC Rule:MF_02042};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5,6-dihydrouridine in tRNA + NADP(+) = a uridine in tRNA +
CC H(+) + NADPH; Xref=Rhea:RHEA:23624, Rhea:RHEA-COMP:13339, Rhea:RHEA-
CC COMP:13887, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000250|UniProtKB:P33371, ECO:0000255|HAMAP-
CC Rule:MF_02042};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000250|UniProtKB:P33371,
CC ECO:0000255|HAMAP-Rule:MF_02042};
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. {ECO:0000269|PubMed:11983710}.
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. DusB subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_02042, ECO:0000305}.
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DR EMBL; X62399; CAA44270.1; -; Genomic_DNA.
DR EMBL; M95784; AAA23782.1; -; Genomic_DNA.
DR EMBL; U18997; AAA58064.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76292.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77301.1; -; Genomic_DNA.
DR EMBL; S67010; AAB28770.2; -; Genomic_DNA.
DR EMBL; J03816; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; J03245; AAA83855.1; -; Genomic_DNA.
DR PIR; B47043; B47043.
DR RefSeq; NP_417726.1; NC_000913.3.
DR RefSeq; WP_001219652.1; NZ_STEB01000012.1.
DR PDB; 6EI9; X-ray; 2.55 A; A/B=1-321.
DR PDBsum; 6EI9; -.
DR AlphaFoldDB; P0ABT5; -.
DR SMR; P0ABT5; -.
DR BioGRID; 4261865; 16.
DR DIP; DIP-48240N; -.
DR IntAct; P0ABT5; 4.
DR STRING; 511145.b3260; -.
DR jPOST; P0ABT5; -.
DR PaxDb; P0ABT5; -.
DR PRIDE; P0ABT5; -.
DR EnsemblBacteria; AAC76292; AAC76292; b3260.
DR EnsemblBacteria; BAE77301; BAE77301; BAE77301.
DR GeneID; 67415907; -.
DR GeneID; 947707; -.
DR KEGG; ecj:JW3228; -.
DR KEGG; eco:b3260; -.
DR PATRIC; fig|1411691.4.peg.3468; -.
DR EchoBASE; EB1287; -.
DR eggNOG; COG0042; Bacteria.
DR HOGENOM; CLU_013299_0_1_6; -.
DR InParanoid; P0ABT5; -.
DR OMA; RPWLFAD; -.
DR PhylomeDB; P0ABT5; -.
DR BioCyc; EcoCyc:EG11311-MON; -.
DR BioCyc; MetaCyc:EG11311-MON; -.
DR PRO; PR:P0ABT5; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
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:0009314; P:response to radiation; IMP:EcoCyc.
DR CDD; cd02801; DUS_like_FMN; 1.
DR Gene3D; 1.10.1200.80; -; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_02042; DusB_subfam; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR035587; DUS-like_FMN-bd.
DR InterPro; IPR001269; DUS_fam.
DR InterPro; IPR032887; DusB.
DR InterPro; IPR024036; tRNA-dHydroUridine_Synthase_C.
DR InterPro; IPR004652; tRNA_dU_NifR3.
DR InterPro; IPR018517; tRNA_hU_synthase_CS.
DR Pfam; PF01207; Dus; 1.
DR PIRSF; PIRSF006621; Dus; 1.
DR TIGRFAMs; TIGR00737; nifR3_yhdG; 1.
DR PROSITE; PS01136; UPF0034; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Flavoprotein; FMN; NADP; Oxidoreductase; Reference proteome;
KW RNA-binding; tRNA processing; tRNA-binding.
FT CHAIN 1..321
FT /note="tRNA-dihydrouridine synthase B"
FT /id="PRO_0000162084"
FT ACT_SITE 100
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7, ECO:0000255|HAMAP-
FT Rule:MF_02042"
FT BINDING 16..18
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P33371, ECO:0000255|HAMAP-
FT Rule:MF_02042"
FT BINDING 70
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P33371, ECO:0000255|HAMAP-
FT Rule:MF_02042"
FT BINDING 139
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P33371, ECO:0000255|HAMAP-
FT Rule:MF_02042"
FT BINDING 200..202
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P33371, ECO:0000255|HAMAP-
FT Rule:MF_02042"
FT BINDING 224..225
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P33371, ECO:0000255|HAMAP-
FT Rule:MF_02042"
FT CONFLICT 131
FT /note="A -> R (in Ref. 1; CAA44270)"
FT /evidence="ECO:0000305"
FT CONFLICT 267
FT /note="H -> D (in Ref. 1; CAA44270)"
FT /evidence="ECO:0000305"
FT STRAND 1..3
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 6..14
FT /evidence="ECO:0007829|PDB:6EI9"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 23..31
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 35..40
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 76..88
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 92..98
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 108..110
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 111..116
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 118..129
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 136..145
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 151..161
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 166..171
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 184..192
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 206..216
FT /evidence="ECO:0007829|PDB:6EI9"
FT STRAND 219..223
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 225..227
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 233..243
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 252..268
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 271..290
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 295..302
FT /evidence="ECO:0007829|PDB:6EI9"
FT HELIX 306..317
FT /evidence="ECO:0007829|PDB:6EI9"
FT TURN 318..320
FT /evidence="ECO:0007829|PDB:6EI9"
SQ SEQUENCE 321 AA; 35866 MW; B9A31AB459825DE5 CRC64;
MRIGQYQLRN RLIAAPMAGI TDRPFRTLCY EMGAGLTVSE MMSSNPQVWE SDKSRLRMVH
IDEPGIRTVQ IAGSDPKEMA DAARINVESG AQIIDINMGC PAKKVNRKLA GSALLQYPDV
VKSILTEVVN AVDVPVTLKI RTGWAPEHRN CEEIAQLAED CGIQALTIHG RTRACLFNGE
AEYDSIRAVK QKVSIPVIAN GDITDPLKAR AVLDYTGADA LMIGRAAQGR PWIFREIQHY
LDTGELLPPL PLAEVKRLLC AHVRELHDFY GPAKGYRIAR KHVSWYLQEH APNDQFRRTF
NAIEDASEQL EALEAYFENF A
