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tRNA-dihydrouridine(20/20a) synthase (EC 1.3.1.-) (EC 1.3.1.91) (U20-specific dihydrouridine synthase) (U20-specific Dus) (tRNA-dihydrouridine synthase A)

 DUSA_ECOLI              Reviewed;         345 AA.
P32695; P76786; Q2M6Q5;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
19-MAR-2014, sequence version 4.
25-OCT-2017, entry version 129.
RecName: Full=tRNA-dihydrouridine(20/20a) synthase {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000305|PubMed:22123979};
EC=1.3.1.- {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000305|PubMed:22123979};
EC=1.3.1.91 {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000305|PubMed:11983710, ECO:0000305|PubMed:22123979};
AltName: Full=U20-specific dihydrouridine synthase {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000303|PubMed:25902496};
Short=U20-specific Dus {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000303|PubMed:25902496};
AltName: Full=tRNA-dihydrouridine synthase A {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000303|PubMed:11983710};
Name=dusA {ECO:0000255|HAMAP-Rule:MF_02041,
ECO:0000303|PubMed:11983710}; Synonyms=yjbN;
OrderedLocusNames=b4049, JW5950;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=8265357; DOI=10.1093/nar/21.23.5408;
Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J.,
Daniels D.L.;
"Analysis of the Escherichia coli genome. IV. DNA sequence of the
region from 89.2 to 92.8 minutes.";
Nucleic Acids Res. 21:5408-5417(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
PROTEIN SEQUENCE OF 10-19.
STRAIN=K12 / BW25113;
PubMed=23908556; DOI=10.1074/mcp.M113.029165;
Krug K., Carpy A., Behrends G., Matic K., Soares N.C., Macek B.;
"Deep coverage of the Escherichia coli proteome enables the assessment
of false discovery rates in simple proteogenomic experiments.";
Mol. Cell. Proteomics 12:3420-3430(2013).
[5]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=K12;
PubMed=11983710; DOI=10.1074/jbc.M203208200;
Bishop A.C., Xu J., Johnson R.C., Schimmel P., de Crecy-Lagard V.;
"Identification of the tRNA-dihydrouridine synthase family.";
J. Biol. Chem. 277:25090-25095(2002).
[6]
FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF CYS-114 AND
LYS-153.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=22123979; DOI=10.1073/pnas.1112352108;
Yu F., Tanaka Y., Yamashita K., Suzuki T., Nakamura A., Hirano N.,
Suzuki T., Yao M., Tanaka I.;
"Molecular basis of dihydrouridine formation on tRNA.";
Proc. Natl. Acad. Sci. U.S.A. 108:19593-19598(2011).
[7]
DUSA SUBFAMILY SPECIFICITY.
PubMed=25902496; DOI=10.1073/pnas.1500161112;
Byrne R.T., Jenkins H.T., Peters D.T., Whelan F., Stowell J., Aziz N.,
Kasatsky P., Rodnina M.V., Koonin E.V., Konevega A.L., Antson A.A.;
"Major reorientation of tRNA substrates defines specificity of
dihydrouridine synthases.";
Proc. Natl. Acad. Sci. U.S.A. 112:6033-6037(2015).
-!- FUNCTION: Catalyzes the synthesis of 5,6-dihydrouridine (D), a
modified base found in the D-loop of most tRNAs, via the reduction
of the C5-C6 double bond in target uridines. Specifically modifies
U20 and U20a in tRNAs. {ECO:0000255|HAMAP-Rule:MF_02041,
ECO:0000269|PubMed:11983710, ECO:0000269|PubMed:22123979,
ECO:0000305|PubMed:25902496}.
-!- CATALYTIC ACTIVITY: 5,6-dihydrouracil(20) in tRNA + NAD(P)(+) =
uracil(20) in tRNA + NAD(P)H. {ECO:0000255|HAMAP-Rule:MF_02041,
ECO:0000305|PubMed:11983710, ECO:0000305|PubMed:22123979}.
-!- CATALYTIC ACTIVITY: 5,6-dihydrouracil(20a) in tRNA + NAD(P)(+) =
uracil(20a) in tRNA + NAD(P)H. {ECO:0000255|HAMAP-Rule:MF_02041,
ECO:0000305|PubMed:22123979}.
-!- COFACTOR:
Name=FMN; Xref=ChEBI:CHEBI:58210;
Evidence={ECO:0000255|HAMAP-Rule:MF_02041};
-!- DISRUPTION PHENOTYPE: A dusA dusB dusC triple mutant exhibits a
complete lack of 5,6-dihydrouridine modification in cellular tRNA,
whereas each single mutant exhibits a partial reduction, compared
to wild type (PubMed:11983710). Cells lacking this gene can
introduce D modification at neither 20 or 20a in tRNA
(PubMed:22123979). {ECO:0000269|PubMed:11983710,
ECO:0000269|PubMed:22123979}.
-!- MISCELLANEOUS: DusB and DusC together account for about half of
the 5,6-dihydrouridine modification observed in wild-type cellular
tRNA, and DusA accounts for the other half. These three enzymes
seem to act site-specifically on the tRNA D-loop and contain
nonredundant catalytic functions in vivo.
{ECO:0000269|PubMed:11983710}.
-!- SIMILARITY: Belongs to the Dus family. DusA subfamily.
{ECO:0000255|HAMAP-Rule:MF_02041}.
-!- CAUTION: The U21 position mentioned in PubMed:11983710 corresponds
in fact to U20 with the conventional numbering. {ECO:0000305}.
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EMBL; U00006; AAC43143.1; -; Genomic_DNA.
EMBL; U00096; AAC77019.3; -; Genomic_DNA.
EMBL; AP009048; BAE78051.1; -; Genomic_DNA.
RefSeq; NP_418473.3; NC_000913.3.
RefSeq; WP_001298868.1; NZ_LN832404.1.
ProteinModelPortal; P32695; -.
SMR; P32695; -.
BioGrid; 4259608; 5.
STRING; 316385.ECDH10B_4238; -.
PaxDb; P32695; -.
PRIDE; P32695; -.
EnsemblBacteria; AAC77019; AAC77019; b4049.
EnsemblBacteria; BAE78051; BAE78051; BAE78051.
GeneID; 948558; -.
KEGG; ecj:JW5950; -.
KEGG; eco:b4049; -.
PATRIC; fig|511145.12.peg.4167; -.
EchoBASE; EB1876; -.
EcoGene; EG11932; dusA.
eggNOG; ENOG4105CEH; Bacteria.
eggNOG; COG0042; LUCA.
HOGENOM; HOG000259834; -.
InParanoid; P32695; -.
KO; K05539; -.
BioCyc; EcoCyc:EG11932-MONOMER; -.
BioCyc; MetaCyc:EG11932-MONOMER; -.
PRO; PR:P32695; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
GO; GO:0017150; F:tRNA dihydrouridine synthase activity; IMP:EcoCyc.
GO; GO:0102264; F:tRNA-dihydrouridine20 synthase activity; IEA:UniProtKB-EC.
CDD; cd02801; DUS_like_FMN; 1.
Gene3D; 3.20.20.70; -; 1.
HAMAP; MF_02041; DusA_subfam; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR035587; DUS-like_FMN-bd.
InterPro; IPR004653; DusA.
InterPro; IPR001269; tRNA_hU_synthase.
InterPro; IPR018517; tRNA_hU_synthase_CS.
PANTHER; PTHR42907; PTHR42907; 1.
Pfam; PF01207; Dus; 1.
PIRSF; PIRSF006621; Dus; 1.
TIGRFAMs; TIGR00742; yjbN; 1.
PROSITE; PS01136; UPF0034; 1.
1: Evidence at protein level;
Complete proteome; Direct protein sequencing; Flavoprotein; FMN; NADP;
Oxidoreductase; Reference proteome; RNA-binding; tRNA processing;
tRNA-binding.
CHAIN 1 345 tRNA-dihydrouridine(20/20a) synthase.
/FTId=PRO_0000162063.
NP_BIND 32 34 FMN. {ECO:0000255|HAMAP-Rule:MF_02041}.
NP_BIND 226 228 FMN. {ECO:0000255|HAMAP-Rule:MF_02041}.
NP_BIND 248 249 FMN. {ECO:0000255|HAMAP-Rule:MF_02041}.
ACT_SITE 114 114 Proton donor. {ECO:0000255|HAMAP-
Rule:MF_02041}.
BINDING 84 84 FMN. {ECO:0000255|HAMAP-Rule:MF_02041}.
BINDING 153 153 FMN. {ECO:0000255|HAMAP-Rule:MF_02041}.
BINDING 186 186 FMN. {ECO:0000255|HAMAP-Rule:MF_02041}.
SITE 111 111 Interacts with tRNA. {ECO:0000255|HAMAP-
Rule:MF_02041}.
SITE 198 198 Interacts with tRNA; defines subfamily-
specific binding signature.
{ECO:0000255|HAMAP-Rule:MF_02041}.
SITE 201 201 Interacts with tRNA. {ECO:0000255|HAMAP-
Rule:MF_02041}.
SITE 314 314 Interacts with tRNA; defines subfamily-
specific binding signature.
{ECO:0000255|HAMAP-Rule:MF_02041}.
SITE 317 317 Interacts with tRNA; defines subfamily-
specific binding signature.
{ECO:0000255|HAMAP-Rule:MF_02041}.
MUTAGEN 114 114 C->A: Loss of enzymatic activity; when
associated with Ala-153.
{ECO:0000269|PubMed:22123979}.
MUTAGEN 153 153 K->A: Loss of the ability to bind FMN.
Loss of enzymatic activity; when
associated with Ala-114.
{ECO:0000269|PubMed:22123979}.
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


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