TSAD_ECOLI
ID TSAD_ECOLI Reviewed; 337 AA.
AC P05852; Q2M9E1;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 29-AUG-2003, sequence version 2.
DT 03-AUG-2022, entry version 186.
DE RecName: Full=tRNA N6-adenosine threonylcarbamoyltransferase {ECO:0000255|HAMAP-Rule:MF_01445};
DE EC=2.3.1.234 {ECO:0000255|HAMAP-Rule:MF_01445, ECO:0000269|PubMed:22378793};
DE AltName: Full=N6-L-threonylcarbamoyladenine synthase {ECO:0000255|HAMAP-Rule:MF_01445};
DE Short=t(6)A synthase {ECO:0000255|HAMAP-Rule:MF_01445};
DE AltName: Full=t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaD {ECO:0000255|HAMAP-Rule:MF_01445};
DE AltName: Full=tRNA threonylcarbamoyladenosine biosynthesis protein TsaD {ECO:0000255|HAMAP-Rule:MF_01445};
GN Name=tsaD {ECO:0000255|HAMAP-Rule:MF_01445}; Synonyms=gcp, ygjD;
GN OrderedLocusNames=b3064, JW3036;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3297921; DOI=10.1016/0378-1119(87)90303-9;
RA Nesin M., Lupski J.R., Svec P., Godson G.N.;
RT "Possible new genes as revealed by molecular analysis of a 5-kb Escherichia
RT coli chromosomal region 5' to the rpsU-dnaG-rpoD macromolecular-synthesis
RT operon.";
RL Gene 51:149-161(1987).
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 DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9743119; DOI=10.1038/nbt0998-851;
RA Arigoni F., Talabot F., Peitsch M.C., Edgerton M.D., Meldrum E., Allet E.,
RA Fish R., Jamotte T., Curchod M.-L., Loferer H.;
RT "A genome-based approach for the identification of essential bacterial
RT genes.";
RL Nat. Biotechnol. 16:851-856(1998).
RN [5]
RP DISRUPTION PHENOTYPE.
RX PubMed=19578062; DOI=10.1093/nar/gkp557;
RA Oberto J., Breuil N., Hecker A., Farina F., Brochier-Armanet C.,
RA Culetto E., Forterre P.;
RT "Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein,
RT is essential for mitochondrial genome maintenance.";
RL Nucleic Acids Res. 37:5343-5352(2009).
RN [6]
RP DISRUPTION PHENOTYPE, SUBUNIT, INTERACTION WITH TSAB, CLEAVAGE BY TSAB,
RP LACK OF GLYCOPROTEASE ACTIVITY, AND SUBCELLULAR LOCATION.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=19376873; DOI=10.1128/jb.00136-09;
RA Handford J.I., Ize B., Buchanan G., Butland G.P., Greenblatt J., Emili A.,
RA Palmer T.;
RT "Conserved network of proteins essential for bacterial viability.";
RL J. Bacteriol. 191:4732-4749(2009).
RN [7]
RP INTERACTION WITH TSAB.
RC STRAIN=K12;
RX PubMed=20701780; DOI=10.1186/1471-2164-11-470;
RA Rajagopala S.V., Yamamoto N., Zweifel A.E., Nakamichi T., Huang H.K.,
RA Mendez-Rios J.D., Franca-Koh J., Boorgula M.P., Fujita K., Suzuki K.,
RA Hu J.C., Wanner B.L., Mori H., Uetz P.;
RT "The Escherichia coli K-12 ORFeome: a resource for comparative molecular
RT microbiology.";
RL BMC Genomics 11:470-470(2010).
RN [8]
RP FUNCTION IN METABOLISM OF GLYCATED PROTEINS.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=20824107; DOI=10.1128/mbio.00195-10;
RA Katz C., Cohen-Or I., Gophna U., Ron E.Z.;
RT "The ubiquitous conserved glycopeptidase gcp prevents accumulation of toxic
RT glycated proteins.";
RL MBio 1:E195-E195(2010).
RN [9]
RP FUNCTION IN T(6)A37 FORMATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=21183954; DOI=10.1038/emboj.2010.343;
RA Srinivasan M., Mehta P., Yu Y., Prugar E., Koonin E.V., Karzai A.W.,
RA Sternglanz R.;
RT "The highly conserved KEOPS/EKC complex is essential for a universal tRNA
RT modification, t6A.";
RL EMBO J. 30:873-881(2011).
RN [10]
RP PROPOSED FUNCTION AS A LIGASE, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=21285948; DOI=10.1038/emboj.2010.363;
RA El Yacoubi B., Hatin I., Deutsch C., Kahveci T., Rousset J.P.,
RA Iwata-Reuyl D., Murzin A.G., de Crecy-Lagard V.;
RT "A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA
RT modification.";
RL EMBO J. 30:882-893(2011).
RN [11]
RP FUNCTION IN T(6)A37 FORMATION, CATALYTIC ACTIVITY, GENE NAME, AND
RP INTERACTION WITH TSAB AND TSAC.
RC STRAIN=K12;
RX PubMed=22378793; DOI=10.1074/jbc.m112.344028;
RA Deutsch C., El Yacoubi B., de Crecy-Lagard V., Iwata-Reuyl D.;
RT "Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA
RT nucleoside.";
RL J. Biol. Chem. 287:13666-13673(2012).
CC -!- FUNCTION: Required for the formation of a threonylcarbamoyl group on
CC adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning
CC with adenine. Is probably involved in the transfer of the
CC threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6
CC group of A37, together with TsaE and TsaB. TsaD likely plays a direct
CC catalytic role in this reaction. May also be involved in the metabolism
CC of glycated proteins, but does not show sialoglycoprotease activity
CC against glycophorin A. {ECO:0000269|PubMed:20824107,
CC ECO:0000269|PubMed:21183954, ECO:0000269|PubMed:22378793}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(37) in tRNA + L-threonylcarbamoyladenylate = AMP +
CC H(+) + N(6)-L-threonylcarbamoyladenosine(37) in tRNA;
CC Xref=Rhea:RHEA:37059, Rhea:RHEA-COMP:10162, Rhea:RHEA-COMP:10163,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:73682, ChEBI:CHEBI:74411,
CC ChEBI:CHEBI:74418, ChEBI:CHEBI:456215; EC=2.3.1.234;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01445,
CC ECO:0000269|PubMed:22378793};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01445};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01445};
CC -!- SUBUNIT: Homodimer. Interacts with TsaB; may form a heterodimer with
CC TsaB. Also interacts with TsaC. {ECO:0000269|PubMed:19376873,
CC ECO:0000269|PubMed:20701780, ECO:0000269|PubMed:21285948,
CC ECO:0000269|PubMed:22378793}.
CC -!- INTERACTION:
CC P05852; P76256: tsaB; NbExp=8; IntAct=EBI-561994, EBI-560669;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01445,
CC ECO:0000269|PubMed:19376873}.
CC -!- PTM: Can be proteolytically processed in vitro by TsaB.
CC {ECO:0000269|PubMed:19376873}.
CC -!- DISRUPTION PHENOTYPE: Appears essential for growth, since no null
CC mutants can be obtained. Conditional depletion of this gene prevents
CC t(6)A37 modification, and leads to pleiotropic phenotypes including
CC increased or reduced cell size, unusual distribution of DNA around the
CC cell periphery, nucleoid loss, and membrane/cell envelope defects.
CC These phenotypes could be indirect effects of severe translation
CC defects. The TsaD depletion phenotype is suppressed by overexpressing
CC the response regulator RstA. {ECO:0000269|PubMed:19376873,
CC ECO:0000269|PubMed:19578062, ECO:0000269|PubMed:21183954,
CC ECO:0000269|PubMed:9743119}.
CC -!- MISCELLANEOUS: TsaBCDE are necessary and sufficient for tRNA(NNU)
CC t(6)A37 threonylcarbamoyladenosine modification in vitro in E.coli.
CC {ECO:0000305|PubMed:22378793}.
CC -!- SIMILARITY: Belongs to the KAE1 / TsaD family. {ECO:0000255|HAMAP-
CC Rule:MF_01445}.
CC -!- CAUTION: Was proposed to be a ligase for bicarbonate and threonine
CC (PubMed:21285948): in the first step, TsaD would catalyze transfer of a
CC gamma-phosphate group from ATP to bicarbonate, yielding
CC carboxyphosphate and ADP; carboxyphosphate would then react with the
CC threonine amine, producing N-carbamoylthreonine and phosphate. However,
CC the protein ortholog in B.subtilis was shown to be involved in another
CC step of t(6)A37 biosynthesis, i.e. the transfer of the
CC threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6
CC group of A37, together with TsaE and TsaB (PubMed:23072323). The
CC protein ortholog in yeast (QRI7) was also shown to catalyze this step,
CC and does not require the presence of additional proteins
CC (PubMed:23620299). {ECO:0000305|PubMed:21285948}.
CC -!- CAUTION: The well-known t(6)A modification appears to be a hydrolyzed
CC artifact of natural cyclic t(6)A (ct(6)A) that occurs during the
CC preparation and handling of tRNA in E.coli and many other species
CC (PubMed:23242255). In these species, the t(6)A modification is
CC processed further by dehydration into ct(6)A, a reaction catalyzed by
CC TcdA. {ECO:0000305}.
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DR EMBL; M16194; AAA72575.1; -; Genomic_DNA.
DR EMBL; U28379; AAA89144.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76100.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77115.1; -; Genomic_DNA.
DR PIR; F65094; QQECR6.
DR RefSeq; NP_417536.1; NC_000913.3.
DR RefSeq; WP_001264352.1; NZ_STEB01000001.1.
DR PDB; 4WQ4; X-ray; 2.33 A; A/B=1-337.
DR PDB; 4WQ5; X-ray; 2.33 A; A/B=1-337.
DR PDB; 4YDU; X-ray; 2.33 A; A/B=1-337.
DR PDB; 6Z81; X-ray; 2.31 A; A/B=1-337.
DR PDBsum; 4WQ4; -.
DR PDBsum; 4WQ5; -.
DR PDBsum; 4YDU; -.
DR PDBsum; 6Z81; -.
DR AlphaFoldDB; P05852; -.
DR SMR; P05852; -.
DR BioGRID; 4261402; 87.
DR BioGRID; 851894; 3.
DR ComplexPortal; CPX-1094; YgjD-YeaZ-YjeE complex.
DR DIP; DIP-9749N; -.
DR IntAct; P05852; 14.
DR STRING; 511145.b3064; -.
DR jPOST; P05852; -.
DR PaxDb; P05852; -.
DR PRIDE; P05852; -.
DR DNASU; 947578; -.
DR EnsemblBacteria; AAC76100; AAC76100; b3064.
DR EnsemblBacteria; BAE77115; BAE77115; BAE77115.
DR GeneID; 947578; -.
DR KEGG; ecj:JW3036; -.
DR KEGG; eco:b3064; -.
DR PATRIC; fig|1411691.4.peg.3666; -.
DR EchoBASE; EB1158; -.
DR eggNOG; COG0533; Bacteria.
DR HOGENOM; CLU_023208_0_2_6; -.
DR InParanoid; P05852; -.
DR OMA; HLEGHIY; -.
DR PhylomeDB; P05852; -.
DR BioCyc; EcoCyc:EG11171-MON; -.
DR BioCyc; MetaCyc:EG11171-MON; -.
DR BRENDA; 2.3.1.234; 2026.
DR PRO; PR:P05852; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0000408; C:EKC/KEOPS complex; IPI:ComplexPortal.
DR GO; GO:0140032; F:glycosylation-dependent protein binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0005506; F:iron ion binding; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0061711; F:N(6)-L-threonylcarbamoyladenine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:1990145; P:maintenance of translational fidelity; IC:ComplexPortal.
DR GO; GO:0002949; P:tRNA threonylcarbamoyladenosine modification; IDA:ComplexPortal.
DR HAMAP; MF_01445; TsaD; 1.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR000905; Gcp-like_dom.
DR InterPro; IPR017861; KAE1/TsaD.
DR InterPro; IPR017860; Peptidase_M22_CS.
DR InterPro; IPR022450; TsaD.
DR PANTHER; PTHR11735; PTHR11735; 1.
DR PANTHER; PTHR11735:SF6; PTHR11735:SF6; 1.
DR Pfam; PF00814; TsaD; 1.
DR PRINTS; PR00789; OSIALOPTASE.
DR SUPFAM; SSF53067; SSF53067; 1.
DR TIGRFAMs; TIGR00329; gcp_kae1; 1.
DR TIGRFAMs; TIGR03723; T6A_TsaD_YgjD; 1.
DR PROSITE; PS01016; GLYCOPROTEASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acyltransferase; Cytoplasm; Iron; Metal-binding;
KW Reference proteome; Transferase; tRNA processing.
FT CHAIN 1..337
FT /note="tRNA N6-adenosine threonylcarbamoyltransferase"
FT /id="PRO_0000096962"
FT BINDING 111
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01445"
FT BINDING 115
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01445"
FT BINDING 134..138
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01445"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01445"
FT BINDING 180
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01445"
FT BINDING 272
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01445"
FT BINDING 300
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01445"
FT CONFLICT 136
FT /note="S -> C (in Ref. 1; AAA72575)"
FT /evidence="ECO:0000305"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 9..19
FT /evidence="ECO:0007829|PDB:6Z81"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 23..31
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 33..37
FT /evidence="ECO:0007829|PDB:6Z81"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 44..66
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 75..83
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 85..101
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 111..117
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 118..121
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 128..138
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 140..148
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 150..159
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 162..172
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 180..188
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 212..223
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 229..258
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 261..267
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 268..271
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 273..285
FT /evidence="ECO:0007829|PDB:6Z81"
FT STRAND 289..291
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 295..297
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 303..315
FT /evidence="ECO:0007829|PDB:6Z81"
FT HELIX 331..333
FT /evidence="ECO:0007829|PDB:6Z81"
SQ SEQUENCE 337 AA; 36008 MW; AD676E3B635EC637 CRC64;
MRVLGIETSC DETGIAIYDD EKGLLANQLY SQVKLHADYG GVVPELASRD HVRKTVPLIQ
AALKESGLTA KDIDAVAYTA GPGLVGALLV GATVGRSLAF AWDVPAIPVH HMEGHLLAPM
LEDNPPEFPF VALLVSGGHT QLISVTGIGQ YELLGESIDD AAGEAFDKTA KLLGLDYPGG
PLLSKMAAQG TAGRFVFPRP MTDRPGLDFS FSGLKTFAAN TIRDNGTDDQ TRADIARAFE
DAVVDTLMIK CKRALDQTGF KRLVMAGGVS ANRTLRAKLA EMMKKRRGEV FYARPEFCTD
NGAMIAYAGM VRFKAGATAD LGVSVRPRWP LAELPAA
