ID   MNMA_PARDP              Reviewed;         389 AA.
AC   A1B9H0;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 1.
DT   03-AUG-2022, entry version 87.
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=Pden_4098;
OS   Paracoccus denitrificans (strain Pd 1222).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC   Rhodobacteraceae; Paracoccus.
OX   NCBI_TaxID=318586;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Pd 1222;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S.,
RA   Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M.,
RA   Richardson P.;
RT   "Complete sequence of chromosome 2 of Paracoccus denitrificans PD1222.";
RL   Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
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; CP000490; ABL72164.1; -; Genomic_DNA.
DR   RefSeq; WP_011750332.1; NC_008687.1.
DR   AlphaFoldDB; A1B9H0; -.
DR   SMR; A1B9H0; -.
DR   STRING; 318586.Pden_4098; -.
DR   PRIDE; A1B9H0; -.
DR   EnsemblBacteria; ABL72164; ABL72164; Pden_4098.
DR   KEGG; pde:Pden_4098; -.
DR   eggNOG; COG0482; Bacteria.
DR   HOGENOM; CLU_035188_0_1_5; -.
DR   OMA; AVCTGHY; -.
DR   Proteomes; UP000000361; Chromosome 2.
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..389
FT                   /note="tRNA-specific 2-thiouridylase MnmA"
FT                   /id="PRO_0000349728"
FT   REGION          174..176
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        128
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        225
FT                   /note="Cysteine persulfide intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         34..41
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         60
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         152
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            153
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            365
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   DISULFID        128..225
FT                   /note="Alternate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
SQ   SEQUENCE   389 AA;  42019 MW;  FDFF9D26B5ACDD7B CRC64;
     MTAPSLSLRH AAPYSTVNSL GFPKPPAQTR VVVAMSGGVD SSVVAAMLAA QGYDVIGVTL
     QLYDHGAALA KKGACCAGQD IHDARRVAER IGFPHYVLDY ENKFRESVIE EFADAYLAGA
     TPVPCIRCNE RVKFRDLLQT ARELDADCMA TGHYIRRLMG PKGAELHMAA DPARDQSYFL
     FSTTQEQLDF LRFPLGGLAS KAETRALAAQ YGLAVADKPD SQDICFVPNG DYASVIEKLR
     PGAADPGEIV DMDGNVLGSH RGVIHYTIGQ RRGLGIGGLG DPLYVVRLEP DTRRVVVGPK
     QALATKIVPV TEVNWLGDEP FEDEIAVTAR IRSTRPPRPA ILRVTGKHRA EIELLDPEEG
     VSPGQACVFY ATEGSRVLGG GWISHRRGG