TMCAL_BACSU
ID TMCAL_BACSU Reviewed; 415 AA.
AC O34513; Q797S9;
DT 30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=tRNA(Met) cytidine acetate ligase {ECO:0000255|HAMAP-Rule:MF_01539, ECO:0000303|PubMed:30150682};
DE EC=6.3.4.- {ECO:0000255|HAMAP-Rule:MF_01539, ECO:0000269|PubMed:30150682};
GN Name=tmcAL {ECO:0000255|HAMAP-Rule:MF_01539, ECO:0000303|PubMed:30150682};
GN Synonyms=ylbM; OrderedLocusNames=BSU15060;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RA Bertero M., Presecan E., Glaser P., Richou A., Danchin A.;
RT "Bacillus subtilis chromosomal region downstream nprE.";
RL Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3] {ECO:0007744|PDB:5Y0N, ECO:0007744|PDB:5Y0O, ECO:0007744|PDB:5Y0P, ECO:0007744|PDB:5Y0Q}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEXES WITH ATP AND ATP
RP ANALOGS, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF GLU-9; HIS-14; HIS-17; HIS-20; ARG-44; LYS-129; LYS-133;
RP LYS-134; ASN-162; ARG-187; ILE-188; SER-206; THR-208; ARG-211; TYR-253;
RP TYR-256; ARG-279; LYS-298; LYS-300; ARG-301; ARG-306; ARG-309; LYS-352;
RP LYS-353 AND LYS-362.
RC STRAIN=168;
RX PubMed=30150682; DOI=10.1038/s41589-018-0119-z;
RA Taniguchi T., Miyauchi K., Sakaguchi Y., Yamashita S., Soma A., Tomita K.,
RA Suzuki T.;
RT "Acetate-dependent tRNA acetylation required for decoding fidelity in
RT protein synthesis.";
RL Nat. Chem. Biol. 14:1010-1020(2018).
CC -!- FUNCTION: Catalyzes the formation of N(4)-acetylcytidine (ac(4)C) at
CC the wobble position of elongator tRNA(Met), using acetate and ATP as
CC substrates. First activates an acetate ion to form acetyladenylate (Ac-
CC AMP) and then transfers the acetyl group to tRNA to form ac(4)C34.
CC {ECO:0000255|HAMAP-Rule:MF_01539, ECO:0000269|PubMed:30150682}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=acetate + ATP + cytidine(34) in elongator tRNA(Met) = AMP +
CC diphosphate + N(4)-acetylcytidine(34) in elongator tRNA(Met);
CC Xref=Rhea:RHEA:58144, Rhea:RHEA-COMP:10693, Rhea:RHEA-COMP:10694,
CC ChEBI:CHEBI:30089, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:74900, ChEBI:CHEBI:82748, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01539,
CC ECO:0000269|PubMed:30150682};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:30150682}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01539,
CC ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Deletion mutant lacks the ac(4)C34 modification
CC and displays a cold-sensitive phenotype. {ECO:0000269|PubMed:30150682}.
CC -!- SIMILARITY: Belongs to the TmcAL family. {ECO:0000255|HAMAP-
CC Rule:MF_01539, ECO:0000305}.
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DR EMBL; Z98682; CAB11359.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13379.1; -; Genomic_DNA.
DR PIR; B69875; B69875.
DR RefSeq; NP_389389.1; NC_000964.3.
DR RefSeq; WP_003244707.1; NZ_JNCM01000035.1.
DR PDB; 5Y0N; X-ray; 2.30 A; A/B=1-415.
DR PDB; 5Y0O; X-ray; 2.30 A; A/B=1-415.
DR PDB; 5Y0P; X-ray; 2.30 A; A/B=1-415.
DR PDB; 5Y0Q; X-ray; 2.10 A; A/B=1-415.
DR PDBsum; 5Y0N; -.
DR PDBsum; 5Y0O; -.
DR PDBsum; 5Y0P; -.
DR PDBsum; 5Y0Q; -.
DR AlphaFoldDB; O34513; -.
DR SMR; O34513; -.
DR STRING; 224308.BSU15060; -.
DR PaxDb; O34513; -.
DR EnsemblBacteria; CAB13379; CAB13379; BSU_15060.
DR GeneID; 936548; -.
DR KEGG; bsu:BSU15060; -.
DR PATRIC; fig|224308.179.peg.1641; -.
DR eggNOG; COG1323; Bacteria.
DR InParanoid; O34513; -.
DR OMA; WARTKMA; -.
DR PhylomeDB; O34513; -.
DR BioCyc; BSUB:BSU15060-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016879; F:ligase activity, forming carbon-nitrogen bonds; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006400; P:tRNA modification; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.620; -; 1.
DR HAMAP; MF_01539; TmcAL; 1.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR008513; tRNA(Met)_cyd_acetate_ligase.
DR PANTHER; PTHR37825; PTHR37825; 1.
DR Pfam; PF05636; HIGH_NTase1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Ligase; Nucleotide-binding;
KW Reference proteome; RNA-binding; tRNA processing; tRNA-binding.
FT CHAIN 1..415
FT /note="tRNA(Met) cytidine acetate ligase"
FT /id="PRO_0000147160"
FT BINDING 7..20
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01539,
FT ECO:0000269|PubMed:30150682"
FT BINDING 101
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01539,
FT ECO:0000269|PubMed:30150682"
FT BINDING 162
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01539,
FT ECO:0000269|PubMed:30150682"
FT BINDING 187..188
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01539,
FT ECO:0000269|PubMed:30150682"
FT MUTAGEN 9
FT /note="E->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 14
FT /note="H->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 17
FT /note="H->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 20
FT /note="H->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 44
FT /note="R->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 129
FT /note="K->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 133
FT /note="K->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 134
FT /note="K->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 162
FT /note="N->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 187
FT /note="R->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 188
FT /note="I->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 206
FT /note="S->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 208
FT /note="T->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 211
FT /note="R->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 253
FT /note="Y->E: Cannot form a dimer and has no activity; when
FT associated with Glu-256."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 256
FT /note="Y->E: Cannot form a dimer and has no activity; when
FT associated with Glu-253."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 279
FT /note="R->A: Strong decrease in activity. Decreases tRNA
FT binding."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 298
FT /note="K->A: Strong decrease in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 300
FT /note="K->A: Strong decrease in activity. Decreases tRNA
FT binding."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 301
FT /note="R->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 306
FT /note="R->A: Almost loss of activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 309
FT /note="R->A: Almost loss of activity. Decreases tRNA
FT binding."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 352
FT /note="K->A: Strong decrease in activity. Decreases tRNA
FT binding."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 353
FT /note="K->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:30150682"
FT MUTAGEN 362
FT /note="K->A: Strong decrease in activity. Decreases tRNA
FT binding."
FT /evidence="ECO:0000269|PubMed:30150682"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 15..28
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 52..60
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT TURN 61..63
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 79..92
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 96..103
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 108..133
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 138..150
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 158..160
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 161..176
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 181..186
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 192..195
FT /evidence="ECO:0007829|PDB:5Y0O"
FT HELIX 207..215
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 220..222
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 228..241
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 247..250
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 251..257
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 263..267
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 276..286
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 290..297
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 300..302
FT /evidence="ECO:0007829|PDB:5Y0N"
FT HELIX 304..316
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 320..328
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 329..331
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 335..340
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 342..351
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT TURN 352..354
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 359..362
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 363..365
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 369..381
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT TURN 382..384
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT HELIX 389..399
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT STRAND 403..406
FT /evidence="ECO:0007829|PDB:5Y0Q"
FT TURN 407..410
FT /evidence="ECO:0007829|PDB:5Y0Q"
SQ SEQUENCE 415 AA; 46989 MW; 4776188611CEC2C6 CRC64;
MKAVGLVVEY NPFHNGHLYH AQTAKLQTGC DTAVAVMSGH FLQRGEPAVV SKWARTKMAL
QSGVDLVIEL PYLYAVQKAD IFARGSVSIL NELECEALFF GSENGDIKPF LETAQLIDEH
KHILNDRIKE ELKKGASYPA AAAIAFSSIL HTESALDLSK PNNILGYQYV TSILTGGYPM
KPYTTARISS DYHDADLPEG ENHIASATSI RKAMIGQNLE ACLRFLPAAS ARELAAYRKS
FGLWHTPESY FSYLKYSLST VTARELQQVY EVEEGLEHRI IRSIRKSSSY QEFMELLKTK
RYTWTRLQRM NTHILTRTKK QDMQKLLDND KAPYIRLLGM TKKGQAYLSE KKKALSVPLV
SKLSSFSHPA LDLDVKASRI YSLPIEEPLR TEFDLQEYGH APIRYDEDEQ HFLNV
