ID   MNMA_NITWN              Reviewed;         400 AA.
AC   Q3SV21;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2005, sequence version 1.
DT   03-AUG-2022, entry version 108.
DE   RecName: Full=tRNA-specific 2-thiouridylase MnmA {ECO:0000255|HAMAP-Rule:MF_00144};
DE            EC=2.8.1.13 {ECO:0000255|HAMAP-Rule:MF_00144};
GN   Name=mnmA {ECO:0000255|HAMAP-Rule:MF_00144}; OrderedLocusNames=Nwi_0603;
OS   Nitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 /
OS   NCIMB 11846 / Nb-255).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Bradyrhizobiaceae; Nitrobacter.
OX   NCBI_TaxID=323098;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255;
RX   PubMed=16517654; DOI=10.1128/aem.72.3.2050-2063.2006;
RA   Starkenburg S.R., Chain P.S.G., Sayavedra-Soto L.A., Hauser L., Land M.L.,
RA   Larimer F.W., Malfatti S.A., Klotz M.G., Bottomley P.J., Arp D.J.,
RA   Hickey W.J.;
RT   "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium
RT   Nitrobacter winogradskyi Nb-255.";
RL   Appl. Environ. Microbiol. 72:2050-2063(2006).
CC   -!- FUNCTION: Catalyzes the 2-thiolation of uridine at the wobble position
CC       (U34) of tRNA, leading to the formation of s(2)U34. {ECO:0000255|HAMAP-
CC       Rule:MF_00144}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=AH2 + ATP + S-sulfanyl-L-cysteinyl-[protein] + uridine(34) in
CC         tRNA = 2-thiouridine(34) in tRNA + A + AMP + diphosphate + H(+) + L-
CC         cysteinyl-[protein]; Xref=Rhea:RHEA:47032, Rhea:RHEA-COMP:10131,
CC         Rhea:RHEA-COMP:11726, Rhea:RHEA-COMP:11727, Rhea:RHEA-COMP:11728,
CC         ChEBI:CHEBI:13193, ChEBI:CHEBI:15378, ChEBI:CHEBI:17499,
CC         ChEBI:CHEBI:29950, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC         ChEBI:CHEBI:61963, ChEBI:CHEBI:65315, ChEBI:CHEBI:87170,
CC         ChEBI:CHEBI:456215; EC=2.8.1.13; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00144};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00144}.
CC   -!- SIMILARITY: Belongs to the MnmA/TRMU family. {ECO:0000255|HAMAP-
CC       Rule:MF_00144}.
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DR   EMBL; CP000115; ABA03870.1; -; Genomic_DNA.
DR   RefSeq; WP_011313930.1; NC_007406.1.
DR   AlphaFoldDB; Q3SV21; -.
DR   SMR; Q3SV21; -.
DR   STRING; 323098.Nwi_0603; -.
DR   EnsemblBacteria; ABA03870; ABA03870; Nwi_0603.
DR   KEGG; nwi:Nwi_0603; -.
DR   eggNOG; COG0482; Bacteria.
DR   HOGENOM; CLU_035188_0_1_5; -.
DR   OMA; AVCTGHY; -.
DR   OrthoDB; 1054741at2; -.
DR   Proteomes; UP000002531; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0016783; F:sulfurtransferase activity; IEA:InterPro.
DR   GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0006400; P:tRNA modification; IEA:UniProtKB-UniRule.
DR   CDD; cd01998; tRNA_Me_trans; 1.
DR   Gene3D; 2.30.30.280; -; 1.
DR   Gene3D; 3.40.50.620; -; 1.
DR   HAMAP; MF_00144; tRNA_thiouridyl_MnmA; 1.
DR   InterPro; IPR023382; Adenine_a_hdrlase_dom.
DR   InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR   InterPro; IPR004506; tRNA-specific_2-thiouridylase.
DR   TIGRFAMs; TIGR00420; trmU; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Cytoplasm; Disulfide bond; Nucleotide-binding;
KW   Reference proteome; RNA-binding; Transferase; tRNA processing;
KW   tRNA-binding.
FT   CHAIN           1..400
FT                   /note="tRNA-specific 2-thiouridylase MnmA"
FT                   /id="PRO_0000349716"
FT   REGION          160..162
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        113
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        210
FT                   /note="Cysteine persulfide intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         19..26
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         45
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         137
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            138
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            352
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   DISULFID        113..210
FT                   /note="Alternate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
SQ   SEQUENCE   400 AA;  43383 MW;  1E84C4D279A41390 CRC64;
     MLNSLDLEGR PQDTRVVVAM SGGVDSSVTA ALLKSEGYDV VGITLQLYDH GAATHRKGAC
     CAGQDIHDAR NVAARLGVPH YVLDYESRFR ETVIENFADS YASGETPVPC IECNRQVKFR
     DLLATARELG AAALATGHYV SSRRLADGSR ALLCAADTDR DQSYFLFATT REQLDFLRFP
     LGDMTKQQTR ELARRFGLSV ADKHDSQDIC FVPTGRYTDI ISRLKPNAMV SGDIVDLDGH
     VIGHHEGIVH FTVGQRRGLG IASGAPLYVL SLDAANRRVV VGPREALKMH RIVLRDVNWI
     GDGALDRAIG AGLELFVRVR STRRPQPAWL RVVDGRYEVE LVAGEEGVSP GQACVFYDGA
     EGQSRVLGGG FIARAMAQRA NEAAAQSGTL AQSFAAELRG