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Database: UniProt
Entry: A0A258YYU9_9PROT
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ID   A0A258YYU9_9PROT        Unreviewed;       358 AA.
AC   A0A258YYU9;
DT   20-DEC-2017, integrated into UniProtKB/TrEMBL.
DT   20-DEC-2017, sequence version 1.
DT   24-JAN-2024, entry version 17.
DE   RecName: Full=tRNA-specific 2-thiouridylase MnmA {ECO:0000256|HAMAP-Rule:MF_00144};
DE            EC=2.8.1.13 {ECO:0000256|HAMAP-Rule:MF_00144};
GN   Name=mnmA {ECO:0000256|HAMAP-Rule:MF_00144};
GN   ORFNames=B7Y21_05715 {ECO:0000313|EMBL:OYZ57877.1};
OS   Hydrogenophilales bacterium 16-61-112.
OC   Bacteria; Pseudomonadota; Hydrogenophilia; Hydrogenophilales.
OX   NCBI_TaxID=1970519 {ECO:0000313|EMBL:OYZ57877.1, ECO:0000313|Proteomes:UP000216368};
RN   [1] {ECO:0000313|EMBL:OYZ57877.1, ECO:0000313|Proteomes:UP000216368}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=16-61-112 {ECO:0000313|EMBL:OYZ57877.1};
RA   Kantor R.S., Colenbrander Nelson T., Marshall S., Bennett D., Apte S.,
RA   Camacho D., Thomas B.C., Warren L.A., Banfield J.F.;
RT   "Lifting the veil on microbial sulfur biogeochemistry in mining
RT   wastewaters.";
RL   Submitted (MAR-2017) 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:0000256|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;
CC         Evidence={ECO:0000256|ARBA:ARBA00001042, ECO:0000256|HAMAP-
CC         Rule:MF_00144};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00144}.
CC   -!- SIMILARITY: Belongs to the MnmA/TRMU family. {ECO:0000256|HAMAP-
CC       Rule:MF_00144}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:OYZ57877.1}.
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DR   EMBL; NCHD01000023; OYZ57877.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A258YYU9; -.
DR   Proteomes; UP000216368; Unassembled WGS sequence.
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; Adenine nucleotide alpha hydrolases-like domains; 1.
DR   Gene3D; 3.40.50.620; HUPs; 1.
DR   Gene3D; 2.40.30.10; Translation factors; 1.
DR   HAMAP; MF_00144; tRNA_thiouridyl_MnmA; 1.
DR   InterPro; IPR046885; MnmA-like_C.
DR   InterPro; IPR046884; MnmA-like_central.
DR   InterPro; IPR023382; MnmA-like_central_sf.
DR   InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR   InterPro; IPR004506; tRNA-specific_2-thiouridylase.
DR   NCBIfam; TIGR00420; trmU; 1.
DR   PANTHER; PTHR11933:SF5; MITOCHONDRIAL TRNA-SPECIFIC 2-THIOURIDYLASE 1; 1.
DR   PANTHER; PTHR11933; TRNA 5-METHYLAMINOMETHYL-2-THIOURIDYLATE -METHYLTRANSFERASE; 1.
DR   Pfam; PF03054; tRNA_Me_trans; 1.
DR   Pfam; PF20258; tRNA_Me_trans_C; 1.
DR   Pfam; PF20259; tRNA_Me_trans_M; 1.
DR   SUPFAM; SSF52402; Adenine nucleotide alpha hydrolases-like; 1.
PE   3: Inferred from homology;
KW   ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW   Rule:MF_00144}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00144};
KW   Disulfide bond {ECO:0000256|ARBA:ARBA00023157, ECO:0000256|HAMAP-
KW   Rule:MF_00144};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW   Rule:MF_00144};
KW   RNA-binding {ECO:0000256|ARBA:ARBA00022884, ECO:0000256|HAMAP-
KW   Rule:MF_00144};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW   Rule:MF_00144};
KW   tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW   Rule:MF_00144};
KW   tRNA-binding {ECO:0000256|ARBA:ARBA00022555, ECO:0000256|HAMAP-
KW   Rule:MF_00144}.
FT   DOMAIN          205..272
FT                   /note="tRNA-specific 2-thiouridylase MnmA-like central"
FT                   /evidence="ECO:0000259|Pfam:PF20259"
FT   DOMAIN          283..357
FT                   /note="tRNA-specific 2-thiouridylase MnmA-like C-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF20258"
FT   REGION          94..96
FT                   /note="Interaction with target base in tRNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   REGION          146..148
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   REGION          308..309
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   ACT_SITE        99
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   ACT_SITE        196
FT                   /note="Cysteine persulfide intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   BINDING         8..15
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   BINDING         34
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   BINDING         123
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   SITE            124
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   SITE            341
FT                   /note="Interaction with tRNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT   DISULFID        99..196
FT                   /note="Alternate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
SQ   SEQUENCE   358 AA;  39228 MW;  C9EE9FB9AAC368C1 CRC64;
     MSTRVVVGMS GGVDSAVAAY LLKQQGYDVL GVFMKNWDDD DNTEHCTARE DFLDVLAVAD
     VLGIEVEAVN FAAEYKERVF SYFLAEYQAG RTPNPDVLCN AEIKFKAFLD DAIARGAEFI
     ATGHYVGKGA DEYGRATLLR AADANKDQSY FLYRLSQAQV QPALFPLAPL PKPEVRQIAK
     KIGLPNAAKK DSTGICFIGE RNFRGFLERY LPRDPGDMRT PEGKCVGQHQ GLMYYTLGQR
     QGLGIGGQKD GNDDPWFVAA KDMASNTLIV VQGHEHPLLL RSSLGAGQLN WISGEAPDPE
     RPYTAKTRYR QTDAACRITT LADDTLELVF DTPQWAVTPG QSVVLYEGKV CLGGGIIS
//
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