ID   MNMA_RHIWR              Reviewed;         378 AA.
AC   A5VFM2;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   02-SEP-2008, sequence version 2.
DT   03-AUG-2022, entry version 79.
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=Swit_4751;
OS   Rhizorhabdus wittichii (strain DSM 6014 / CCUG 31198 / JCM 15750 / NBRC
OS   105917 / EY 4224 / RW1) (Sphingomonas wittichii).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC   Sphingomonadaceae; Rhizorhabdus.
OX   NCBI_TaxID=392499;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 6014 / CCUG 31198 / JCM 15750 / NBRC 105917 / EY 4224 / RW1;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA   Tice H., Pitluck S., Saunders E., Brettin T., Bruce D., Detter J.C.,
RA   Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M., Hauser L.,
RA   Kyrpides N., Kim E., Halden R.U., Miller T.R., Salzberg S.L., Eisen J.A.,
RA   Richardson P.;
RT   "Complete sequence of chromosome of Sphingomonas wittichii RW1.";
RL   Submitted (MAY-2007) 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}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ABQ71088.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; CP000699; ABQ71088.1; ALT_INIT; Genomic_DNA.
DR   AlphaFoldDB; A5VFM2; -.
DR   SMR; A5VFM2; -.
DR   STRING; 392499.Swit_4751; -.
DR   EnsemblBacteria; ABQ71088; ABQ71088; Swit_4751.
DR   KEGG; swi:Swit_4751; -.
DR   eggNOG; COG0482; Bacteria.
DR   HOGENOM; CLU_035188_0_1_5; -.
DR   Proteomes; UP000001989; 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..378
FT                   /note="tRNA-specific 2-thiouridylase MnmA"
FT                   /id="PRO_0000349804"
FT   REGION          168..170
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        121
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        218
FT                   /note="Cysteine persulfide intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         27..34
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         53
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         145
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            146
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            350
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   DISULFID        121..218
FT                   /note="Alternate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
SQ   SEQUENCE   378 AA;  40098 MW;  A7EA14EB60D0EEF0 CRC64;
     MGAPMNPEFQ LEGRAPGSLA GARIVVAMSG GVDSSVVAAL AAASGAETIG VTLQLYDHGA
     AVGRTGSCCA GQDIRDARAV ADRLGIAHYV FDYESRFRDS VIADFADEYA AGRTPIPCVR
     CNQGVKFTDL FGIARDLGAD CLATGHYVRR VVGAGGRAEL HRAADPARDQ SYFLFATTRD
     QLDYLRFPLG AMPKPRVREI AAELGLGVAA KPDSQDICFV PDGDYASIVK RLRPEAAEEG
     EIVGLDGRVL GRHRGLIHFT VGQRRGIEIG GSPEPLYVVR LEPETKRLVV GPRRALAVSA
     AMLDDVNWIG EGYEGPLTAK VRSLAKPVPA RFEDGAVRFD QPEYGVAPGQ AAVLYAGDRV
     LGGGWIRATV PAELAVAA