ID A0A0F7HEM8_SERFO Unreviewed; 367 AA.
AC A0A0F7HEM8;
DT 22-JUL-2015, integrated into UniProtKB/TrEMBL.
DT 22-JUL-2015, sequence version 1.
DT 24-JAN-2024, entry version 52.
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 ECO:0000313|EMBL:AKG71131.1};
GN ORFNames=BSQ40_26825 {ECO:0000313|EMBL:OKP20006.1}, CRN79_25030
GN {ECO:0000313|EMBL:ATM78893.1}, DFO62_102250
GN {ECO:0000313|EMBL:RDL27379.1}, H8I91_02785
GN {ECO:0000313|EMBL:MBC3249180.1}, HZI44_09625
GN {ECO:0000313|EMBL:NYA32963.1}, NCTC13193_02504
GN {ECO:0000313|EMBL:VEI68973.1}, WN53_19490
GN {ECO:0000313|EMBL:AKG71131.1};
OS Serratia fonticola.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Serratia.
OX NCBI_TaxID=47917 {ECO:0000313|EMBL:AKG71131.1, ECO:0000313|Proteomes:UP000034699};
RN [1] {ECO:0000313|EMBL:AKG71131.1, ECO:0000313|Proteomes:UP000034699}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 4576 {ECO:0000313|EMBL:AKG71131.1,
RC ECO:0000313|Proteomes:UP000034699};
RA Chan K.-G., Ee R.;
RT "Complete Genome Sequencing of Serratia Fonticola DSM-4576.";
RL Submitted (APR-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:OKP20006.1, ECO:0000313|Proteomes:UP000186436}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=5l {ECO:0000313|EMBL:OKP20006.1,
RC ECO:0000313|Proteomes:UP000186436};
RA Goncharov A., Grigoriev S., Azarov D., Kolodzhieva V., Tikhonov A.,
RA Akhremenko Y., Tarasova L., Zueva L., Suvorov A.;
RT "Draft genome sequence of Serratia fonticola 5l isolated from intestinal
RT tract content of a 9000-year-old elk (Alces alces) from permafrost on the
RT Omoloy river.";
RL Submitted (NOV-2016) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:ATM78893.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=FDAARGOS_411 {ECO:0000313|EMBL:ATM78893.1};
RA Minogue T., Wolcott M., Wasieloski L., Aguilar W., Moore D., Tallon L.J.,
RA Sadzewicz L., Ott S., Zhao X., Nagaraj S., Vavikolanu K., Aluvathingal J.,
RA Nadendla S., Sichtig H.;
RT "FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
RT Supporting development and validation of Infectious Disease Dx tests.";
RL Submitted (OCT-2017) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|Proteomes:UP000221800}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FDAARGOS_411 {ECO:0000313|Proteomes:UP000221800};
RA Goldberg B., Campos J., Tallon L., Sadzewicz L., Ott S., Zhao X.,
RA Nagaraj S., Vavikolanu K., Aluvathingal J., Nadendla S., Geyer C.,
RA Sichtig H.;
RT "FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
RT Supporting development and validation of Infectious Disease Dx tests.";
RL Submitted (OCT-2017) to the EMBL/GenBank/DDBJ databases.
RN [5] {ECO:0000313|EMBL:RDL27379.1, ECO:0000313|Proteomes:UP000255042}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=E2309 {ECO:0000313|EMBL:RDL27379.1,
RC ECO:0000313|Proteomes:UP000255042};
RA Venturi V.;
RT "Genome sequencing of rice bacterial endophytes.";
RL Submitted (JUL-2018) to the EMBL/GenBank/DDBJ databases.
RN [6] {ECO:0000313|EMBL:VEI68973.1, ECO:0000313|Proteomes:UP000270487}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCTC13193 {ECO:0000313|EMBL:VEI68973.1,
RC ECO:0000313|Proteomes:UP000270487};
RG Pathogen Informatics;
RL Submitted (DEC-2018) to the EMBL/GenBank/DDBJ databases.
RN [7] {ECO:0000313|EMBL:MBC3249180.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=UPMP2128 {ECO:0000313|EMBL:NYA32963.1,
RC ECO:0000313|Proteomes:UP000529380}, and UPMP2131
RC {ECO:0000313|EMBL:MBC3249180.1};
RA Richter L., Du Plessis E.M., Duvenage S., Allam M., Korsten L.;
RT "Food and environmental bacterial isolates.";
RL Submitted (AUG-2020) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the 2-thiolation of uridine at the wobble position
CC (U34) of tRNA(Lys), tRNA(Glu) and tRNA(Gln), leading to the formation
CC of s(2)U34, the first step of tRNA-mnm(5)s(2)U34 synthesis. Sulfur is
CC provided by IscS, via a sulfur-relay system. Binds ATP and its
CC substrate tRNAs. {ECO:0000256|HAMAP-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 -!- SUBUNIT: Interacts with TusE. {ECO:0000256|HAMAP-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}.
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DR EMBL; CP011254; AKG71131.1; -; Genomic_DNA.
DR EMBL; CP023956; ATM78893.1; -; Genomic_DNA.
DR EMBL; JACNYM010000002; MBC3249180.1; -; Genomic_DNA.
DR EMBL; JACBIW010000007; NYA32963.1; -; Genomic_DNA.
DR EMBL; MQRH01000040; OKP20006.1; -; Genomic_DNA.
DR EMBL; QRAU01000002; RDL27379.1; -; Genomic_DNA.
DR EMBL; LR134492; VEI68973.1; -; Genomic_DNA.
DR RefSeq; WP_021178255.1; NZ_SUPV01000002.1.
DR AlphaFoldDB; A0A0F7HEM8; -.
DR STRING; 47917.AV650_14920; -.
DR GeneID; 30322361; -.
DR KEGG; sfw:WN53_19490; -.
DR PATRIC; fig|47917.8.peg.4046; -.
DR OMA; AVCTGHY; -.
DR OrthoDB; 9800696at2; -.
DR Proteomes; UP000034699; Chromosome.
DR Proteomes; UP000186436; Unassembled WGS sequence.
DR Proteomes; UP000221800; Chromosome.
DR Proteomes; UP000255042; Unassembled WGS sequence.
DR Proteomes; UP000270487; Chromosome 1.
DR Proteomes; UP000529380; Unassembled WGS sequence.
DR Proteomes; UP000596701; 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, ECO:0000256|HAMAP-
KW Rule:MF_00144}; Methyltransferase {ECO:0000313|EMBL:MBC3249180.1};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00144}; Reference proteome {ECO:0000313|Proteomes:UP000034699};
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 208..276
FT /note="tRNA-specific 2-thiouridylase MnmA-like central"
FT /evidence="ECO:0000259|Pfam:PF20259"
FT DOMAIN 287..361
FT /note="tRNA-specific 2-thiouridylase MnmA-like C-terminal"
FT /evidence="ECO:0000259|Pfam:PF20258"
FT REGION 98..100
FT /note="Interaction with target base in tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT REGION 150..152
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT REGION 312..313
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT ACT_SITE 103
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT ACT_SITE 200
FT /note="Cysteine persulfide intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT BINDING 12..19
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT BINDING 38
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 345
FT /note="Interaction with tRNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
FT DISULFID 103..200
FT /note="Alternate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00144"
SQ SEQUENCE 367 AA; 41053 MW; B441E5AC445D90B0 CRC64;
MSDNSQKKVI VGMSGGVDSS VTAYLLQQQG YQVAGLFMKN WEEDDDEEYC SAATDLADAQ
AVCDKLGIEL HTVNFAAEYW DNVFELFLEE YKAGRTPNPD ILCNKEIKFK AFLEFAAEDL
GADFIATGHY VRRQDVDGKS RLLRGVDGNK DQSYFLYTLS HEQVAQSLFP VGELEKPEVR
RIAEQLELVT AKKKDSTGIC FIGERKFRDF LGRYLPAQPG PIVSVDGQTI GEHQGLMYHT
LGQRKGLGIG GMKDSSEDPW YVVDKDVANN ILVVAQGHEH PRLMSIGLIA QQLHWVDRLP
LTQPLRCTVK TRYRQQDIPC TVTPLDAERI EVRFDEPVAA VTPGQSAVFY QGDICLGGGI
IEQRIQE
//