ID H8YYG8_9GAMM Unreviewed; 352 AA.
AC H8YYG8;
DT 16-MAY-2012, integrated into UniProtKB/TrEMBL.
DT 16-MAY-2012, sequence version 1.
DT 24-JAN-2024, entry version 51.
DE RecName: Full=tRNA-dihydrouridine synthase B {ECO:0000256|HAMAP-Rule:MF_02042};
DE EC=1.3.1.- {ECO:0000256|HAMAP-Rule:MF_02042};
GN Name=dusB {ECO:0000256|HAMAP-Rule:MF_02042};
GN ORFNames=Thi970DRAFT_01165 {ECO:0000313|EMBL:EIC23494.1};
OS Thiorhodovibrio frisius.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae;
OC Thiorhodovibrio.
OX NCBI_TaxID=631362 {ECO:0000313|EMBL:EIC23494.1, ECO:0000313|Proteomes:UP000002964};
RN [1] {ECO:0000313|Proteomes:UP000002964}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=970 {ECO:0000313|Proteomes:UP000002964};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S.,
RA Peters L., Land M.L., Hauser L., Vogl K., Liu Z., Overmann J.,
RA Frigaard N.-U., Bryant D.A., Woyke T.J.;
RL Submitted (JUN-2011) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:EIC23494.1, ECO:0000313|Proteomes:UP000002964}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=970 {ECO:0000313|EMBL:EIC23494.1,
RC ECO:0000313|Proteomes:UP000002964};
RG US DOE Joint Genome Institute;
RA Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S.,
RA Peters L., Ovchinnikova G., Zhang X., Detter J.C., Han C., Tapia R.,
RA Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Vogl K., Liu Z.,
RA Overmann J., Frigaard N.-U., Bryant D., Woyke T.;
RL Submitted (NOV-2011) to the EMBL/GenBank/DDBJ databases.
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:0000256|ARBA:ARBA00002790,
CC ECO:0000256|HAMAP-Rule:MF_02042, ECO:0000256|PIRNR:PIRNR006621}.
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:0000256|ARBA:ARBA00001387, ECO:0000256|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:0000256|ARBA:ARBA00001183, ECO:0000256|HAMAP-
CC Rule:MF_02042};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210;
CC Evidence={ECO:0000256|ARBA:ARBA00001917,
CC ECO:0000256|HAMAP-Rule:MF_02042, ECO:0000256|PIRNR:PIRNR006621};
CC -!- SIMILARITY: Belongs to the Dus family. DusB subfamily.
CC {ECO:0000256|HAMAP-Rule:MF_02042}.
CC -!- SIMILARITY: Belongs to the dus family. {ECO:0000256|PIRNR:PIRNR006621}.
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DR EMBL; JH603168; EIC23494.1; -; Genomic_DNA.
DR RefSeq; WP_009147577.1; NZ_JH603168.1.
DR AlphaFoldDB; H8YYG8; -.
DR STRING; 631362.Thi970DRAFT_01165; -.
DR eggNOG; COG0042; Bacteria.
DR HOGENOM; CLU_013299_0_1_6; -.
DR Proteomes; UP000002964; Unassembled WGS sequence.
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; IEA:UniProtKB-UniRule.
DR CDD; cd02801; DUS_like_FMN; 1.
DR Gene3D; 3.20.20.70; Aldolase class I; 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; IPR004652; DusB-like.
DR InterPro; IPR024036; tRNA-dHydroUridine_Synthase_C.
DR InterPro; IPR018517; tRNA_hU_synthase_CS.
DR NCBIfam; TIGR00737; nifR3_yhdG; 1.
DR PANTHER; PTHR45846; TRNA-DIHYDROURIDINE(47) SYNTHASE [NAD(P)(+)]-LIKE; 1.
DR PANTHER; PTHR45846:SF1; TRNA-DIHYDROURIDINE(47) SYNTHASE [NAD(P)(+)]-LIKE; 1.
DR Pfam; PF01207; Dus; 1.
DR PIRSF; PIRSF006621; Dus; 1.
DR SUPFAM; SSF51395; FMN-linked oxidoreductases; 1.
DR PROSITE; PS01136; UPF0034; 1.
PE 3: Inferred from homology;
KW Flavoprotein {ECO:0000256|ARBA:ARBA00022630, ECO:0000256|HAMAP-
KW Rule:MF_02042};
KW FMN {ECO:0000256|ARBA:ARBA00022643, ECO:0000256|HAMAP-Rule:MF_02042};
KW NADP {ECO:0000256|ARBA:ARBA00022857, ECO:0000256|HAMAP-Rule:MF_02042};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002, ECO:0000256|HAMAP-
KW Rule:MF_02042}; Reference proteome {ECO:0000313|Proteomes:UP000002964};
KW RNA-binding {ECO:0000256|ARBA:ARBA00022884, ECO:0000256|HAMAP-
KW Rule:MF_02042};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_02042}; tRNA-binding {ECO:0000256|HAMAP-Rule:MF_02042}.
FT DOMAIN 31..318
FT /note="DUS-like FMN-binding"
FT /evidence="ECO:0000259|Pfam:PF01207"
FT ACT_SITE 117
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042,
FT ECO:0000256|PIRSR:PIRSR006621-1"
FT BINDING 33..35
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 87
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 156
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 217..219
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 241..242
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
SQ SEQUENCE 352 AA; 38314 MW; 3354C697ADFE7206 CRC64;
MPESVPMSSV ANRLKLPLRI GSLELPSRVF LAPMASITDR PFRRLCREFG AGLAFSEMLS
ANPALRHTRT SAERLDHQGE PRPFAVQIAG ANPEDMADFA RHAVDQGADL IDINLGCPAK
KVCRQAAGSA LLRDEPLVAR IMEQVVRAVN VPVSVKTRTG WSPQEKNLAQ IAQIAQNSGI
AMLTVHGRTR ACGYNGQAEH NSLSALREQI TIPLVANGDI DTAETAHKVL EQTGADAVMI
GRAALGKPWI FARIERFLAT GEQTGPPDPA VNPERNPDQI RDILLSHLAA LHDFYGEARG
LRVARKHIIW YCQDLPGFKQ ASGALLMATS AAIQHRLVQS YFANLMTGET DT
//
