DUSC_ECOLI
ID DUSC_ECOLI Reviewed; 315 AA.
AC P33371; Q2MAT9;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=tRNA-dihydrouridine(16) synthase {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000305|PubMed:25902496};
DE EC=1.3.1.- {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000269|PubMed:25902496};
DE AltName: Full=U16-specific dihydrouridine synthase {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000303|PubMed:25902496};
DE Short=U16-specific Dus {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000303|PubMed:25902496};
DE AltName: Full=tRNA-dihydrouridine synthase C {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000303|PubMed:11983710};
GN Name=dusC {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000303|PubMed:11983710};
GN Synonyms=yohI; OrderedLocusNames=b2140, JW2128;
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 / BHB2600;
RA Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
RA Church G.M.;
RT "Automated multiplex sequencing of the E.coli genome.";
RL Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
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 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 [5]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH FMN, AND DOMAIN.
RX PubMed=23908023; DOI=10.1107/s1744309113019489;
RA Chen M., Yu J., Tanaka Y., Tanaka M., Tanaka I., Yao M.;
RT "Structure of dihydrouridine synthase C (DusC) from Escherichia coli.";
RL Acta Crystallogr. F 69:834-838(2013).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-98 IN
RP COMPLEXES WITH FMN AND TWO SUBSTRATE TRNAS, FUNCTION, CATALYTIC ACTIVITY,
RP COFACTOR, DOMAIN, ACTIVE SITE, AND MUTAGENESIS OF CYS-98.
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. DusC specifically modifies U16 in
CC tRNAs. {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000269|PubMed:11983710,
CC ECO:0000269|PubMed:25902496}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(16) in tRNA + NADP(+) = H(+) + NADPH +
CC uridine(16) in tRNA; Xref=Rhea:RHEA:53376, Rhea:RHEA-COMP:13543,
CC Rhea:RHEA-COMP:13544, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02043,
CC ECO:0000269|PubMed:25902496};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouridine(16) in tRNA + NAD(+) = H(+) + NADH +
CC uridine(16) in tRNA; Xref=Rhea:RHEA:53380, Rhea:RHEA-COMP:13543,
CC Rhea:RHEA-COMP:13544, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:65315, ChEBI:CHEBI:74443;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02043,
CC ECO:0000269|PubMed:25902496};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02043,
CC ECO:0000305|PubMed:23908023, ECO:0000305|PubMed:25902496};
CC -!- DOMAIN: Is composed of two domains: an N-terminal catalytic domain
CC (residues 1-242) and a C-terminal tRNA recognition domain (residues
CC 245-309). {ECO:0000305|PubMed:23908023, ECO:0000305|PubMed:25902496}.
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. DusC subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_02043, ECO:0000305}.
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DR EMBL; U00007; AAA60503.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75201.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76617.1; -; Genomic_DNA.
DR PIR; C64982; C64982.
DR RefSeq; NP_416645.1; NC_000913.3.
DR RefSeq; WP_001264861.1; NZ_SSZK01000011.1.
DR PDB; 3W9Z; X-ray; 2.10 A; A=1-315.
DR PDB; 4BF9; X-ray; 2.60 A; A=1-315.
DR PDB; 4BFA; X-ray; 1.65 A; A/B=1-315.
DR PDB; 4YCO; X-ray; 2.10 A; A/B/C=1-315.
DR PDB; 4YCP; X-ray; 2.55 A; A=1-315.
DR PDBsum; 3W9Z; -.
DR PDBsum; 4BF9; -.
DR PDBsum; 4BFA; -.
DR PDBsum; 4YCO; -.
DR PDBsum; 4YCP; -.
DR AlphaFoldDB; P33371; -.
DR SMR; P33371; -.
DR BioGRID; 4260457; 10.
DR DIP; DIP-12808N; -.
DR IntAct; P33371; 24.
DR STRING; 511145.b2140; -.
DR jPOST; P33371; -.
DR PaxDb; P33371; -.
DR PRIDE; P33371; -.
DR EnsemblBacteria; AAC75201; AAC75201; b2140.
DR EnsemblBacteria; BAE76617; BAE76617; BAE76617.
DR GeneID; 945458; -.
DR KEGG; ecj:JW2128; -.
DR KEGG; eco:b2140; -.
DR PATRIC; fig|1411691.4.peg.102; -.
DR EchoBASE; EB1957; -.
DR eggNOG; COG0042; Bacteria.
DR HOGENOM; CLU_013299_0_4_6; -.
DR InParanoid; P33371; -.
DR OMA; YRPPAHW; -.
DR PhylomeDB; P33371; -.
DR BioCyc; EcoCyc:EG12022-MON; -.
DR BioCyc; MetaCyc:EG12022-MON; -.
DR BRENDA; 1.3.1.91; 2026.
DR PRO; PR:P33371; -.
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; IDA:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; IDA:UniProtKB.
DR GO; GO:0017150; F:tRNA dihydrouridine synthase activity; IDA:UniProtKB.
DR GO; GO:0002943; P:tRNA dihydrouridine synthesis; IDA:UniProtKB.
DR CDD; cd02801; DUS_like_FMN; 1.
DR Gene3D; 1.20.225.30; -; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_02043; DusC_subfam; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR035587; DUS-like_FMN-bd.
DR InterPro; IPR001269; DUS_fam.
DR InterPro; IPR032886; DusC.
DR InterPro; IPR042270; DusC_C.
DR InterPro; IPR018517; tRNA_hU_synthase_CS.
DR PANTHER; PTHR11082:SF26; PTHR11082:SF26; 1.
DR Pfam; PF01207; Dus; 1.
DR PIRSF; PIRSF006621; Dus; 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..315
FT /note="tRNA-dihydrouridine(16) synthase"
FT /id="PRO_0000162109"
FT ACT_SITE 98
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q5SMC7,
FT ECO:0000305|PubMed:25902496"
FT BINDING 7..9
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:23908023,
FT ECO:0000269|PubMed:25902496, ECO:0007744|PDB:3W9Z,
FT ECO:0007744|PDB:4BF9, ECO:0007744|PDB:4BFA"
FT BINDING 68
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:23908023,
FT ECO:0000269|PubMed:25902496, ECO:0007744|PDB:3W9Z,
FT ECO:0007744|PDB:4BF9, ECO:0007744|PDB:4BFA"
FT BINDING 139
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:23908023,
FT ECO:0000269|PubMed:25902496, ECO:0007744|PDB:3W9Z,
FT ECO:0007744|PDB:4BF9, ECO:0007744|PDB:4BFA"
FT BINDING 200..202
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:23908023,
FT ECO:0000269|PubMed:25902496, ECO:0007744|PDB:3W9Z,
FT ECO:0007744|PDB:4BF9, ECO:0007744|PDB:4BFA"
FT BINDING 224..225
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:23908023,
FT ECO:0000269|PubMed:25902496, ECO:0007744|PDB:3W9Z,
FT ECO:0007744|PDB:4BF9, ECO:0007744|PDB:4BFA"
FT SITE 35
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:25902496"
FT SITE 95
FT /note="Interacts with tRNA"
FT /evidence="ECO:0000269|PubMed:25902496"
FT SITE 176
FT /note="Interacts with tRNA"
FT /evidence="ECO:0000269|PubMed:25902496"
FT SITE 272
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:25902496"
FT SITE 274
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:25902496"
FT SITE 279
FT /note="Interacts with tRNA"
FT /evidence="ECO:0000269|PubMed:25902496"
FT SITE 295
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:25902496"
FT MUTAGEN 98
FT /note="C->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:25902496"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:4BFA"
FT TURN 9..11
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 14..22
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 27..35
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 51..55
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 64..70
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 74..86
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 90..98
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 109..114
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 116..129
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 136..142
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 144..147
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 150..159
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 163..170
FT /evidence="ECO:0007829|PDB:4BFA"
FT TURN 173..176
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 178..180
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 183..192
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 206..216
FT /evidence="ECO:0007829|PDB:4BFA"
FT STRAND 219..224
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 225..229
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 233..239
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 246..258
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 268..280
FT /evidence="ECO:0007829|PDB:4BFA"
FT TURN 281..283
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 285..294
FT /evidence="ECO:0007829|PDB:4BFA"
FT HELIX 300..309
FT /evidence="ECO:0007829|PDB:4BFA"
FT TURN 312..314
FT /evidence="ECO:0007829|PDB:4BFA"
SQ SEQUENCE 315 AA; 35199 MW; 83B33E5034E53565 CRC64;
MRVLLAPMEG VLDSLVRELL TEVNDYDLCI TEFVRVVDQL LPVKVFHRIC PELQNASRTP
SGTLVRVQLL GQFPQWLAEN AARAVELGSW GVDLNCGCPS KTVNGSGGGA TLLKDPELIY
QGAKAMREAV PAHLPVSVKV RLGWDSGEKK FEIADAVQQA GATELVVHGR TKEQGYRAEH
IDWQAIGDIR QRLNIPVIAN GEIWDWQSAQ QCMAISGCDA VMIGRGALNI PNLSRVVKYN
EPRMPWPEVV ALLQKYTRLE KQGDTGLYHV ARIKQWLSYL RKEYDEATEL FQHVRVLNNS
PDIARAIQAI DIEKL
