DUSAL_THET8
ID DUSAL_THET8 Reviewed; 342 AA.
AC Q5SMC7;
DT 22-JUL-2015, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=tRNA-dihydrouridine(20/20a) synthase {ECO:0000255|HAMAP-Rule:MF_02041, ECO:0000305|PubMed:22123979};
DE EC=1.3.1.- {ECO:0000250|UniProtKB:P32695, ECO:0000255|HAMAP-Rule:MF_02041};
DE EC=1.3.1.91 {ECO:0000250|UniProtKB:P32695, ECO:0000255|HAMAP-Rule:MF_02041};
DE AltName: Full=DusA-like 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};
GN Name=dus; OrderedLocusNames=TTHA0016 {ECO:0000312|EMBL:BAD69839.1};
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, AND SUBFAMILY-SPECIFIC TRNA BINDING SIGNATURE.
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).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH FMN AND TRNAS,
RP FUNCTION, COFACTOR, MUTAGENESIS STUDIES, REACTION MECHANISM, AND ACTIVE
RP SITE.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
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).
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:0000305|PubMed:22123979,
CC 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 -!- 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 -!- 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 -!- 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 -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02041,
CC ECO:0000305|PubMed:22123979};
CC -!- SIMILARITY: Belongs to the Dus family. DusA subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_02041}.
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DR EMBL; AP008226; BAD69839.1; -; Genomic_DNA.
DR RefSeq; WP_011227643.1; NC_006461.1.
DR RefSeq; YP_143282.1; NC_006461.1.
DR PDB; 3B0P; X-ray; 1.70 A; A/B=1-342.
DR PDB; 3B0U; X-ray; 1.95 A; X/Y=1-342.
DR PDB; 3B0V; X-ray; 3.51 A; C/D=1-342.
DR PDBsum; 3B0P; -.
DR PDBsum; 3B0U; -.
DR PDBsum; 3B0V; -.
DR AlphaFoldDB; Q5SMC7; -.
DR SMR; Q5SMC7; -.
DR STRING; 300852.55771398; -.
DR EnsemblBacteria; BAD69839; BAD69839; BAD69839.
DR GeneID; 3168530; -.
DR KEGG; ttj:TTHA0016; -.
DR eggNOG; COG0042; Bacteria.
DR HOGENOM; CLU_013299_2_1_0; -.
DR OMA; LIYPYVD; -.
DR PhylomeDB; Q5SMC7; -.
DR Proteomes; UP000000532; 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; NAS:UniProtKB.
DR GO; GO:0102264; F:tRNA-dihydrouridine20 synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0002943; P:tRNA dihydrouridine synthesis; NAS:UniProtKB.
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 PROSITE; PS01136; UPF0034; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Flavoprotein; FMN; NADP; Nucleotide-binding; Oxidoreductase;
KW Reference proteome; RNA-binding; tRNA processing; tRNA-binding.
FT CHAIN 1..342
FT /note="tRNA-dihydrouridine(20/20a) synthase"
FT /id="PRO_0000433569"
FT REGION 313..342
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 313..329
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 93
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:22123979"
FT BINDING 10..12
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0007744|PDB:3B0P, ECO:0007744|PDB:3B0U,
FT ECO:0007744|PDB:3B0V"
FT BINDING 63
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0007744|PDB:3B0P, ECO:0007744|PDB:3B0U,
FT ECO:0007744|PDB:3B0V"
FT BINDING 132
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0007744|PDB:3B0P, ECO:0007744|PDB:3B0U,
FT ECO:0007744|PDB:3B0V"
FT BINDING 164
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0007744|PDB:3B0P, ECO:0007744|PDB:3B0U,
FT ECO:0007744|PDB:3B0V"
FT BINDING 203..205
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0007744|PDB:3B0P, ECO:0007744|PDB:3B0U,
FT ECO:0007744|PDB:3B0V"
FT BINDING 225..226
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0007744|PDB:3B0P, ECO:0007744|PDB:3B0U,
FT ECO:0007744|PDB:3B0V"
FT SITE 90
FT /note="Interacts with tRNA"
FT /evidence="ECO:0000269|PubMed:22123979"
FT SITE 97
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0000305|PubMed:25902496"
FT SITE 175
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0000305|PubMed:25902496"
FT SITE 178
FT /note="Interacts with tRNA"
FT /evidence="ECO:0000269|PubMed:22123979"
FT SITE 290
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0000305|PubMed:25902496"
FT SITE 293
FT /note="Interacts with tRNA; defines subfamily-specific
FT binding signature"
FT /evidence="ECO:0000269|PubMed:22123979,
FT ECO:0000305|PubMed:25902496"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:3B0P"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 17..26
FT /evidence="ECO:0007829|PDB:3B0P"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 39..44
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 47..51
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:3B0P"
FT STRAND 59..65
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 69..81
FT /evidence="ECO:0007829|PDB:3B0P"
FT STRAND 85..91
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 96..100
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 104..109
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 111..124
FT /evidence="ECO:0007829|PDB:3B0P"
FT STRAND 129..135
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 143..155
FT /evidence="ECO:0007829|PDB:3B0P"
FT STRAND 160..164
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 176..178
FT /evidence="ECO:0007829|PDB:3B0U"
FT HELIX 185..194
FT /evidence="ECO:0007829|PDB:3B0P"
FT STRAND 198..205
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 209..216
FT /evidence="ECO:0007829|PDB:3B0P"
FT STRAND 219..224
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 226..230
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 232..235
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 238..241
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 251..268
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 272..276
FT /evidence="ECO:0007829|PDB:3B0P"
FT TURN 280..285
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 289..299
FT /evidence="ECO:0007829|PDB:3B0P"
FT HELIX 302..316
FT /evidence="ECO:0007829|PDB:3B0P"
SQ SEQUENCE 342 AA; 38474 MW; 19DB0828A4C994E0 CRC64;
MLDPRLSVAP MVDRTDRHFR FLVRQVSLGV RLYTEMTVDQ AVLRGNRERL LAFRPEEHPI
ALQLAGSDPK SLAEAARIGE AFGYDEINLN LGCPSEKAQE GGYGACLLLD LARVREILKA
MGEAVRVPVT VKMRLGLEGK ETYRGLAQSV EAMAEAGVKV FVVHARSALL ALSTKANREI
PPLRHDWVHR LKGDFPQLTF VTNGGIRSLE EALFHLKRVD GVMLGRAVYE DPFVLEEADR
RVFGLPRRPS RLEVARRMRA YLEEEVLKGT PPWAVLRHML NLFRGRPKGR LWRRLLSEGR
SLQALDRALR LMEEEVGEEG EKEKPGPRGQ REAAPGPARE GV
