MNMA_ECOLI
ID MNMA_ECOLI Reviewed; 368 AA.
AC P25745; P75964;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 4.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=tRNA-specific 2-thiouridylase MnmA;
DE EC=2.8.1.13 {ECO:0000269|PubMed:12549933, ECO:0000269|PubMed:16387657};
GN Name=mnmA; Synonyms=asuE, trmU, ycfB; OrderedLocusNames=b1133, JW1119;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 138-368.
RC STRAIN=K12;
RX PubMed=8969519; DOI=10.1099/13500872-142-11-3219;
RA Green S.M., Malik T., Giles I.G., Drabble W.T.;
RT "The purB gene of Escherichia coli K-12 is located in an operon.";
RL Microbiology 142:3219-3230(1996).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 254-368.
RC STRAIN=K12;
RX PubMed=1729205; DOI=10.1128/jb.174.1.130-136.1992;
RA He B., Smith J.M., Zalkin H.;
RT "Escherichia coli purB gene: cloning, nucleotide sequence, and regulation
RT by purR.";
RL J. Bacteriol. 174:130-136(1992).
RN [6]
RP MUTANT STUDIES.
RC STRAIN=K12;
RX PubMed=3881393; DOI=10.1128/jb.161.1.368-376.1985;
RA Sullivan M.A., Cannon J.F., Webb F.H., Bock R.M.;
RT "Antisuppressor mutation in Escherichia coli defective in biosynthesis of
RT 5-methylaminomethyl-2-thiouridine.";
RL J. Bacteriol. 161:368-376(1985).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, ATP-BINDING, AND TRNA-BINDING.
RC STRAIN=K12 / MC1061 / ATCC 53338 / DSM 7140;
RX PubMed=12549933; DOI=10.1021/bi026536+;
RA Kambampati R., Lauhon C.T.;
RT "MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in
RT Escherichia coli.";
RL Biochemistry 42:1109-1117(2003).
RN [8]
RP CATALYTIC ACTIVITY, AND INTERACTION WITH TUSE.
RX PubMed=16387657; DOI=10.1016/j.molcel.2005.11.001;
RA Ikeuchi Y., Shigi N., Kato J., Nishimura A., Suzuki T.;
RT "Mechanistic insights into sulfur relay by multiple sulfur mediators
RT involved in thiouridine biosynthesis at tRNA wobble positions.";
RL Mol. Cell 21:97-108(2006).
RN [9]
RP CRYSTALLIZATION.
RX PubMed=16582487; DOI=10.1107/s174430910600738x;
RA Numata T., Ikeuchi Y., Fukai S., Adachi H., Matsumura H., Takano K.,
RA Murakami S., Inoue T., Mori Y., Sasaki T., Suzuki T., Nureki O.;
RT "Crystallization and preliminary X-ray analysis of the tRNA thiolation
RT enzyme MnmA from Escherichia coli complexed with tRNA(Glu).";
RL Acta Crystallogr. F 62:368-371(2006).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) IN COMPLEXES WITH AMP AND TRNA, AND
RP MUTAGENESIS OF ASP-17; MET-37; ASN-97; ASP-99; CYS-102; LYS-107; HIS-128;
RP LYS-149; GLN-151; CYS-199; PHE-200; THR-239; ARG-311 AND GLN-344.
RX PubMed=16871210; DOI=10.1038/nature04896;
RA Numata T., Ikeuchi Y., Fukai S., Suzuki T., Nureki O.;
RT "Snapshots of tRNA sulphuration via an adenylated intermediate.";
RL Nature 442:419-424(2006).
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:0000269|PubMed:12549933}.
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:0000269|PubMed:12549933, ECO:0000269|PubMed:16387657};
CC -!- SUBUNIT: Interacts with TusE. {ECO:0000269|PubMed:16387657}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- MISCELLANEOUS: During the reaction, ATP is used to activate the C2 atom
CC of U34 by adenylation. After this, the persulfide sulfur on the
CC catalytic cysteine is transferred to the C2 atom of U34. The reaction
CC probably involves hydrogen sulfide that is generated from the
CC persulfide intermediate and that acts as nucleophile towards the
CC activated C2 atom on U34. Subsequently, Cys-102 acts as nucleophile
CC towards Cys-199, and a transient disulfide bond is formed.
CC -!- SIMILARITY: Belongs to the MnmA/TRMU family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a 5-methylaminomethyl-2-
CC methyltransferase involved in tRNA modification. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA41994.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC74217.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA35955.1; -; Genomic_DNA.
DR EMBL; X59307; CAA41994.1; ALT_FRAME; Genomic_DNA.
DR EMBL; M74924; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; B64858; B64858.
DR RefSeq; NP_415651.4; NC_000913.3.
DR RefSeq; WP_001297484.1; NZ_STEB01000016.1.
DR PDB; 2DER; X-ray; 3.10 A; A/B=1-368.
DR PDB; 2DET; X-ray; 3.40 A; A=1-368.
DR PDB; 2DEU; X-ray; 3.40 A; A/B=1-368.
DR PDBsum; 2DER; -.
DR PDBsum; 2DET; -.
DR PDBsum; 2DEU; -.
DR AlphaFoldDB; P25745; -.
DR SMR; P25745; -.
DR BioGRID; 4263129; 67.
DR BioGRID; 850062; 1.
DR ComplexPortal; CPX-2145; tRNA-specific 2-thiouridylase tusE-mnmA complex.
DR DIP; DIP-11035N; -.
DR IntAct; P25745; 8.
DR STRING; 511145.b1133; -.
DR jPOST; P25745; -.
DR PaxDb; P25745; -.
DR PRIDE; P25745; -.
DR EnsemblBacteria; AAC74217; AAC74217; b1133.
DR EnsemblBacteria; BAA35955; BAA35955; BAA35955.
DR GeneID; 66670600; -.
DR GeneID; 945690; -.
DR KEGG; ecj:JW1119; -.
DR KEGG; eco:b1133; -.
DR PATRIC; fig|1411691.4.peg.1133; -.
DR EchoBASE; EB1320; -.
DR eggNOG; COG0482; Bacteria.
DR HOGENOM; CLU_035188_1_0_6; -.
DR InParanoid; P25745; -.
DR OMA; AVCTGHY; -.
DR PhylomeDB; P25745; -.
DR BioCyc; EcoCyc:EG11344-MON; -.
DR BioCyc; MetaCyc:EG11344-MON; -.
DR BRENDA; 2.8.1.13; 2026.
DR BRENDA; 2.8.1.4; 2026.
DR BRENDA; 2.8.1.7; 2026.
DR EvolutionaryTrace; P25745; -.
DR PRO; PR:P25745; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:1990228; C:sulfurtransferase complex; IPI:ComplexPortal.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016783; F:sulfurtransferase activity; IDA:EcoCyc.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0002143; P:tRNA wobble position uridine thiolation; IDA:EcoCyc.
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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Disulfide bond; Nucleotide-binding;
KW Reference proteome; RNA-binding; Transferase; tRNA processing;
KW tRNA-binding.
FT CHAIN 1..368
FT /note="tRNA-specific 2-thiouridylase MnmA"
FT /id="PRO_0000121588"
FT REGION 97..99
FT /note="Interaction with target base in tRNA"
FT REGION 149..151
FT /note="Interaction with tRNA"
FT REGION 243..252
FT /note="Interaction with tRNA"
FT REGION 311..312
FT /note="Interaction with tRNA"
FT ACT_SITE 102
FT /note="Nucleophile"
FT ACT_SITE 199
FT /note="Cysteine persulfide intermediate"
FT BINDING 11..18
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 37
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 127
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT SITE 128
FT /note="Interaction with tRNA"
FT SITE 344
FT /note="Interaction with tRNA"
FT DISULFID 102..199
FT /note="Alternate"
FT MUTAGEN 17
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 37
FT /note="M->A: Reduces activity by 60%."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 97
FT /note="N->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 99
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 102
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 107
FT /note="K->M: Reduces activity by 75%."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 128
FT /note="H->A: Reduces activity by 90%."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 149
FT /note="K->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 151
FT /note="Q->E: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 199
FT /note="C->A: Abolishes the incorporation of sulfur from the
FT sulfur-relay system; loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 200
FT /note="F->A: Reduces activity by 60%."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 239
FT /note="T->A: Reduces activity by 50%."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 311
FT /note="R->A: Reduces activity by 75%."
FT /evidence="ECO:0000269|PubMed:16871210"
FT MUTAGEN 344
FT /note="Q->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:16871210"
FT STRAND 7..11
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 19..26
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 45..65
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 75..81
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 83..91
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 98..105
FT /evidence="ECO:0007829|PDB:2DER"
FT TURN 106..109
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 110..117
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 122..125
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 131..135
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 138..142
FT /evidence="ECO:0007829|PDB:2DER"
FT TURN 147..149
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 160..165
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 175..184
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 198..204
FT /evidence="ECO:0007829|PDB:2DER"
FT HELIX 206..211
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 220..223
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 224..226
FT /evidence="ECO:0007829|PDB:2DEU"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 259..265
FT /evidence="ECO:0007829|PDB:2DER"
FT TURN 266..269
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 270..276
FT /evidence="ECO:0007829|PDB:2DER"
FT TURN 280..282
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 284..294
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 302..311
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 317..322
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 325..327
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 329..338
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 344..350
FT /evidence="ECO:0007829|PDB:2DER"
FT STRAND 353..365
FT /evidence="ECO:0007829|PDB:2DER"
SQ SEQUENCE 368 AA; 40959 MW; 22CA92676D0805CC CRC64;
MSETAKKVIV GMSGGVDSSV SAWLLQQQGY QVEGLFMKNW EEDDGEEYCT AAADLADAQA
VCDKLGIELH TVNFAAEYWD NVFELFLAEY KAGRTPNPDI LCNKEIKFKA FLEFAAEDLG
ADYIATGHYV RRADVDGKSR LLRGLDSNKD QSYFLYTLSH EQIAQSLFPV GELEKPQVRK
IAEDLGLVTA KKKDSTGICF IGERKFREFL GRYLPAQPGK IITVDGDEIG EHQGLMYHTL
GQRKGLGIGG TKEGTEEPWY VVDKDVENNI LVVAQGHEHP RLMSVGLIAQ QLHWVDREPF
TGTMRCTVKT RYRQTDIPCT VKALDDDRIE VIFDEPVAAV TPGQSAVFYN GEVCLGGGII
EQRLPLPV
