ID Q2YCT1_NITMU Unreviewed; 337 AA.
AC Q2YCT1;
DT 20-DEC-2005, integrated into UniProtKB/TrEMBL.
DT 20-DEC-2005, sequence version 1.
DT 27-MAR-2024, entry version 113.
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 OrderedLocusNames=Nmul_A0131 {ECO:0000313|EMBL:ABB73440.1};
GN ORFNames=SAMN05216403_1327 {ECO:0000313|EMBL:SEG11685.1};
OS Nitrosospira multiformis (strain ATCC 25196 / NCIMB 11849 / C 71).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales;
OC Nitrosomonadaceae; Nitrosospira.
OX NCBI_TaxID=323848 {ECO:0000313|EMBL:ABB73440.1, ECO:0000313|Proteomes:UP000002718};
RN [1] {ECO:0000313|EMBL:ABB73440.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=ATCC 25196 {ECO:0000313|EMBL:ABB73440.1};
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Lykidis A., Richardson P.;
RT "Complete sequence of Chromosome 1 of Nitrosospira multiformis ATCC
RT 25196.";
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Proteomes:UP000002718}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25196 / NCIMB 11849 / C 71
RC {ECO:0000313|Proteomes:UP000002718};
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Lykidis A., Richardson P.;
RT "Complete sequence of chromosome 1 of Nitrosospira multiformis ATCC
RT 25196.";
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:ABB73440.1, ECO:0000313|Proteomes:UP000002718}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25196 {ECO:0000313|EMBL:ABB73440.1}, and ATCC 25196 /
RC NCIMB 11849 / C 71 {ECO:0000313|Proteomes:UP000002718};
RX PubMed=18390676; DOI=10.1128/AEM.02722-07;
RA Norton J.M., Klotz M.G., Stein L.Y., Arp D.J., Bottomley P.J., Chain P.S.,
RA Hauser L.J., Land M.L., Larimer F.W., Shin M.W., Starkenburg S.R.;
RT "Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing
RT bacterium from the soil environment.";
RL Appl. Environ. Microbiol. 74:3559-3572(2008).
RN [4] {ECO:0000313|EMBL:SEG11685.1, ECO:0000313|Proteomes:UP000236751}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Nl13 {ECO:0000313|EMBL:SEG11685.1,
RC ECO:0000313|Proteomes:UP000236751};
RA de Groot N.N.;
RL Submitted (OCT-2016) 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; CP000103; ABB73440.1; -; Genomic_DNA.
DR EMBL; FNVK01000032; SEG11685.1; -; Genomic_DNA.
DR RefSeq; WP_011379495.1; NZ_FNVK01000032.1.
DR AlphaFoldDB; Q2YCT1; -.
DR STRING; 323848.Nmul_A0131; -.
DR KEGG; nmu:Nmul_A0131; -.
DR eggNOG; COG0042; Bacteria.
DR HOGENOM; CLU_013299_0_1_4; -.
DR OrthoDB; 9764501at2; -.
DR Proteomes; UP000002718; Chromosome.
DR Proteomes; UP000236751; 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:UP000002718};
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 13..319
FT /note="DUS-like FMN-binding"
FT /evidence="ECO:0000259|Pfam:PF01207"
FT ACT_SITE 100
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042,
FT ECO:0000256|PIRSR:PIRSR006621-1"
FT BINDING 16..18
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 70
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 139
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 200..202
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
FT BINDING 224..225
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02042"
SQ SEQUENCE 337 AA; 36546 MW; 413BAC1693D0216B CRC64;
MKIGSHTLKN NLIVAPMAGV TDRPFRQLCK SMGAGMAVSE MVSSNSLLWG SEKTRRRANH
EGEVDPISVQ IAGADPAMMA EAARYNVAQG AQIIDINMGC PAKKICNVMA GSALLQDPPL
VGRILDAVIG AVRVPVTLKI RTGWDTQHKN ALSIARIAEN AGIQALAIHG RTRACAYTGH
AEYDTIAAVK AEVRIPVVAN GDITTPEKAK HVLDYTGADA VMIGRAAQGR PWIFREIDHY
LATGSHLPLP EVAEIHRVLV AHLHDLYSFY GEYSGVRIAR KHISWYTKGL VGSAGFRHAM
NQLQSTDQQL SAVNDFFSEL AGYGRRLTYV EAEELVA
//
