ID A0A139JQD4_9MOLU Unreviewed; 382 AA.
AC A0A139JQD4;
DT 08-JUN-2016, integrated into UniProtKB/TrEMBL.
DT 08-JUN-2016, sequence version 1.
DT 27-MAR-2024, entry version 25.
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=AXA84_0275 {ECO:0000313|EMBL:KXT29203.1}, AXA84_0289
GN {ECO:0000313|EMBL:KXT29187.1}, DH96_01375
GN {ECO:0000313|EMBL:RAM57738.1};
OS Candidatus Phytoplasma oryzae.
OC Bacteria; Mycoplasmatota; Mollicutes; Acholeplasmatales;
OC Acholeplasmataceae; Phytoplasma; 16SrXI (Rice yellow dwarf group).
OX NCBI_TaxID=203274 {ECO:0000313|EMBL:KXT29187.1, ECO:0000313|Proteomes:UP000070069};
RN [1] {ECO:0000313|EMBL:RAM57738.1, ECO:0000313|Proteomes:UP000249343}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NGS-S10 {ECO:0000313|EMBL:RAM57738.1,
RC ECO:0000313|Proteomes:UP000249343};
RA Kawicha P., Dickinson M., Hodgetts J.;
RT "Genome study of Napier grass stunt phytoplasma.";
RL Submitted (APR-2014) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KXT29187.1, ECO:0000313|Proteomes:UP000070069}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Mbita1 {ECO:0000313|EMBL:KXT29187.1};
RA Fischer A., Santa-Cruz I., Wambua L., Olds C., Midega C., Dickinson M.,
RA Kawicha P., Khan Z., Masiga D., Jores J., Bernd S.;
RT "A draft genome sequence of Candidatus Phytoplasma oryzae strain Mbita1,
RT the causative agent of Napier Grass stunt disease in Kenya.";
RL Submitted (FEB-2016) 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: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-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:KXT29187.1}.
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DR EMBL; LTBM01000008; KXT29187.1; -; Genomic_DNA.
DR EMBL; LTBM01000007; KXT29203.1; -; Genomic_DNA.
DR EMBL; JHUK01000003; RAM57738.1; -; Genomic_DNA.
DR RefSeq; WP_066540390.1; NZ_LTBM01000008.1.
DR AlphaFoldDB; A0A139JQD4; -.
DR PATRIC; fig|203274.3.peg.431; -.
DR OrthoDB; 9800696at2; -.
DR Proteomes; UP000070069; Unassembled WGS sequence.
DR Proteomes; UP000249343; 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:0008168; F:methyltransferase activity; 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:0032259; P:methylation; 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};
KW Methyltransferase {ECO:0000313|EMBL:KXT29187.1};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00144}; Reference proteome {ECO:0000313|Proteomes:UP000249343};
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 214..278
FT /note="tRNA-specific 2-thiouridylase MnmA-like central"
FT /evidence="ECO:0000259|Pfam:PF20259"
FT DOMAIN 314..369
FT /note="tRNA-specific 2-thiouridylase MnmA-like C-terminal"
FT /evidence="ECO:0000259|Pfam:PF20258"
FT REGION 104..106
FT /note="Interaction with target base in tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT REGION 155..157
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT REGION 320..321
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT ACT_SITE 109
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT ACT_SITE 205
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 133
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT SITE 134
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT SITE 353
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
SQ SEQUENCE 382 AA; 44550 MW; ABAFC8F5252531C8 CRC64;
MKKKVIIGLS GGVDSSVAAF LLKQKGFEVE GIFMRNWESS LNNDIEGNNF IDNNICPQER
DFQDALKIAK QLGIKCSRVD FIEEYWQKVF SIFLKQIRKN LTPNPDVLCN NQIKFLTFLN
YAKKFKPHYI AMGHYAQIIY KNHQPILTKS VDQNKDQTYF LSQLKKKQLK KIIFPLGKLT
KSEVREIARR EKLANADKKD STGICFIGER KFFNFLNNYL PTQKGPIKDI NGNFLKEHDG
VFKYTIGQRK NLNLKVSKQN SGPWFVVGKD LKNNTLYVDQ NFNSSFLYSD SALIVDVIWR
RYDGIIMSRN VRNKLKAKFR YRQLDQNVEI AWINKTTLKV FYKQKIKSVT PGQICAFYQK
DFCLGAGMIL EVYLRNKKLL YT
//
