ID   MNMA_PARPJ              Reviewed;         383 AA.
AC   B2SX74;
DT   24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-2008, sequence version 1.
DT   03-AUG-2022, entry version 74.
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=Bphyt_0689;
OS   Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)
OS   (Burkholderia phytofirmans).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Paraburkholderia.
OX   NCBI_TaxID=398527;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 17436 / LMG 22146 / PsJN;
RX   PubMed=21551308; DOI=10.1128/jb.05055-11;
RA   Weilharter A., Mitter B., Shin M.V., Chain P.S., Nowak J., Sessitsch A.;
RT   "Complete genome sequence of the plant growth-promoting endophyte
RT   Burkholderia phytofirmans strain PsJN.";
RL   J. Bacteriol. 193:3383-3384(2011).
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; CP001052; ACD15113.1; -; Genomic_DNA.
DR   RefSeq; WP_012431750.1; NC_010681.1.
DR   AlphaFoldDB; B2SX74; -.
DR   SMR; B2SX74; -.
DR   STRING; 398527.Bphyt_0689; -.
DR   EnsemblBacteria; ACD15113; ACD15113; Bphyt_0689.
DR   KEGG; bpy:Bphyt_0689; -.
DR   eggNOG; COG0482; Bacteria.
DR   HOGENOM; CLU_035188_1_0_4; -.
DR   OMA; AVCTGHY; -.
DR   OrthoDB; 1054741at2; -.
DR   Proteomes; UP000001739; Chromosome 1.
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; RNA-binding;
KW   Transferase; tRNA processing; tRNA-binding.
FT   CHAIN           1..383
FT                   /note="tRNA-specific 2-thiouridylase MnmA"
FT                   /id="PRO_1000096288"
FT   REGION          95..97
FT                   /note="Interaction with target base in tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   REGION          148..150
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   REGION          310..311
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        100
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   ACT_SITE        198
FT                   /note="Cysteine persulfide intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         9..16
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         35
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   BINDING         124
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            125
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   SITE            345
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
FT   DISULFID        100..198
FT                   /note="Alternate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00144"
SQ   SEQUENCE   383 AA;  41796 MW;  11A2C04FCBC10162 CRC64;
     MSKQKVVVGM SGGVDSSVTA WLLKEQGYDV VGLFMKNWED DDDSEYCSTR QDWIDVVSVA
     DLIGIDVEAV NFAAEYKDRV FAEFLREYSA GRTPNPDVLC NAEIKFKAFL DHAMSLGAET
     IATGHYARVR QNERNGRFEL LKAFDHTKDQ SYFLHRLNQA QLSKTLFPLG EIPKTKVREI
     AEQIALPNAK KKDSTGICFI GERPFRDFLN RYLPTKPGPM KTTDGKVVGE HIGLAFYTFG
     QRKGIGLGGS KDGSGEPWFV AGKDIASNTL YVAQGHDHAW LLSHTLSAGN TSWVAGEPPA
     DGFACGAKTR YRQADAPCTF SSAGSGEGLF ELNFDAAQWA VTPGQSAVLY DGDVCLGGGI
     IEHAVTGQPV AREPQKAALL NAR