ID A0A1A5YKA7_9BACL Unreviewed; 375 AA.
AC A0A1A5YKA7;
DT 05-OCT-2016, integrated into UniProtKB/TrEMBL.
DT 05-OCT-2016, sequence version 1.
DT 24-JAN-2024, entry version 20.
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=A7K91_17480 {ECO:0000313|EMBL:OBR65825.1};
OS Paenibacillus oryzae.
OC Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
OX NCBI_TaxID=1844972 {ECO:0000313|EMBL:OBR65825.1, ECO:0000313|Proteomes:UP000092024};
RN [1] {ECO:0000313|EMBL:OBR65825.1, ECO:0000313|Proteomes:UP000092024}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1DrF-4 {ECO:0000313|EMBL:OBR65825.1,
RC ECO:0000313|Proteomes:UP000092024};
RA Zhang J., Zhang X.;
RT "Paenibacillus oryzae. sp. nov., isolated from the rice root.";
RL Submitted (MAY-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: 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:OBR65825.1}.
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DR EMBL; LYPA01000052; OBR65825.1; -; Genomic_DNA.
DR RefSeq; WP_068682710.1; NZ_LYPA01000052.1.
DR AlphaFoldDB; A0A1A5YKA7; -.
DR STRING; 1844972.A7K91_17480; -.
DR OrthoDB; 9800696at2; -.
DR Proteomes; UP000092024; 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}; Reference proteome {ECO:0000313|Proteomes:UP000092024};
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 209..278
FT /note="tRNA-specific 2-thiouridylase MnmA-like central"
FT /evidence="ECO:0000259|Pfam:PF20259"
FT DOMAIN 287..363
FT /note="tRNA-specific 2-thiouridylase MnmA-like C-terminal"
FT /evidence="ECO:0000259|Pfam:PF20258"
FT REGION 99..101
FT /note="Interaction with target base in tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT REGION 151..153
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT REGION 314..315
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT ACT_SITE 104
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT ACT_SITE 201
FT /note="Cysteine persulfide intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT BINDING 13..20
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT BINDING 39
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT BINDING 128
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT SITE 129
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT SITE 347
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT DISULFID 104..201
FT /note="Alternate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
SQ SEQUENCE 375 AA; 41747 MW; B0B14673DC619A55 CRC64;
MSKSIAETRV VVGMSGGVDS SVAALLLKQQ GYDVIGIFMK NWDDTDEFGH CTAEEDSEDV
RRVCDKIGIP YYTVNFERQY FDKVFTYFLD EYKRGRTPNP DVMCNREIKF GDFLNKALEL
NADYLATGHY ARVERSEDGT VKLLRGVDSG KDQTYFLSAL NQEQLNRAMF PIGHLPKSEV
RRIAEEAGLH TAKKKDSTGV CFIGERNFKQ FLSGYLPAQP GDMIDIATGQ KMGRHDGLMY
YTLGQRQGLG IGGSGTGSGE PWFVADKDLE RNILYVVQGE RHPSLYSHSL TASGMNWIVP
RQDTKSLVCT AKFRYRQPDQ EVEVVMEADG AARVVFANPQ KAITPGQAVV FYNGDECLGG
GTIDIVHKAS AEPVR
//