TCDA_ECOLI
ID TCDA_ECOLI Reviewed; 268 AA.
AC Q46927; Q2MA22;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=tRNA threonylcarbamoyladenosine dehydratase;
DE EC=6.1.-.-;
DE AltName: Full=t(6)A37 dehydratase;
GN Name=tcdA; Synonyms=csdL, ygdL; OrderedLocusNames=b2812, JW2783;
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 / 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 [2]
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 [3]
RP FUNCTION AS A SULFUR ACCEPTOR PROTEIN, INTERACTION WITH CSDE, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=20054882; DOI=10.1111/j.1365-2958.2009.06954.x;
RA Trotter V., Vinella D., Loiseau L., Ollagnier de Choudens S., Fontecave M.,
RA Barras F.;
RT "The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf
RT components and participates in a new sulphur transfer pathway by recruiting
RT CsdL (ex-YgdL), a ubiquitin-modifying-like protein.";
RL Mol. Microbiol. 74:1527-1542(2009).
RN [4]
RP IDENTIFICATION, FUNCTION AS T(6)A DEHYDRATASE, CATALYTIC ACTIVITY, GENE
RP NAME, AND DISRUPTION PHENOTYPE.
RX PubMed=23242255; DOI=10.1038/nchembio.1137;
RA Miyauchi K., Kimura S., Suzuki T.;
RT "A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed
RT tRNA hypermodification.";
RL Nat. Chem. Biol. 9:105-111(2013).
CC -!- FUNCTION: Catalyzes the ATP-dependent dehydration of
CC threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic
CC t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine.
CC TcdA is also part of a sulfur transfer pathway; is able to accept
CC sulfur from CsdA directly in vitro, but CsdE might act as the sulfur
CC donor in vivo. {ECO:0000269|PubMed:20054882,
CC ECO:0000269|PubMed:23242255}.
CC -!- SUBUNIT: Interacts with CsdE. {ECO:0000269|PubMed:20054882}.
CC -!- INTERACTION:
CC Q46927; Q46925: csdA; NbExp=2; IntAct=EBI-1130463, EBI-545660;
CC Q46927; P0AGF2: csdE; NbExp=3; IntAct=EBI-1130463, EBI-1130454;
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene have a normal growth
CC phenotype, but are unable to survive in a competitive growth situation
CC with the wild-type strain. They display only the t(6)A but not the
CC ct(6)A modification in tRNAs, and have lower decoding efficiency than
CC wild-type. They show no defects in motility or antibiotic sensitivity.
CC In growth competition experiments, a tcdA mutant shows reduced fitness
CC compared to wild-type, but outcompetes a csdA mutant.
CC {ECO:0000269|PubMed:20054882, ECO:0000269|PubMed:23242255}.
CC -!- MISCELLANEOUS: ct(6)A is involved in promoting decoding efficiency. It
CC is an unstable modification that can be easily hydrolyzed and converted
CC to t(6)A during nucleoside preparation by conventional methods
CC (PubMed:23242255). This explains why it was described as t(6)A37 in
CC earlier studies. {ECO:0000305|PubMed:23242255}.
CC -!- SIMILARITY: Belongs to the HesA/MoeB/ThiF family. {ECO:0000305}.
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DR EMBL; U29581; AAB40462.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75854.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76884.1; -; Genomic_DNA.
DR PIR; H65063; H65063.
DR RefSeq; NP_417292.1; NC_000913.3.
DR RefSeq; WP_000117728.1; NZ_SSZK01000003.1.
DR PDB; 4D79; X-ray; 1.77 A; A/B/C/D=1-268.
DR PDB; 4D7A; X-ray; 1.80 A; A/B/C/D=1-268.
DR PDB; 4RDH; X-ray; 2.10 A; A/B/C/D=1-268.
DR PDB; 4RDI; X-ray; 1.95 A; A/B/C/D=1-268.
DR PDB; 4YED; X-ray; 1.90 A; A/B/C/D=1-268.
DR PDBsum; 4D79; -.
DR PDBsum; 4D7A; -.
DR PDBsum; 4RDH; -.
DR PDBsum; 4RDI; -.
DR PDBsum; 4YED; -.
DR AlphaFoldDB; Q46927; -.
DR SMR; Q46927; -.
DR BioGRID; 4261127; 834.
DR IntAct; Q46927; 9.
DR STRING; 511145.b2812; -.
DR PaxDb; Q46927; -.
DR PRIDE; Q46927; -.
DR EnsemblBacteria; AAC75854; AAC75854; b2812.
DR EnsemblBacteria; BAE76884; BAE76884; BAE76884.
DR GeneID; 66673321; -.
DR GeneID; 947291; -.
DR KEGG; ecj:JW2783; -.
DR KEGG; eco:b2812; -.
DR PATRIC; fig|511145.12.peg.2912; -.
DR EchoBASE; EB2893; -.
DR eggNOG; COG1179; Bacteria.
DR HOGENOM; CLU_013325_4_0_6; -.
DR InParanoid; Q46927; -.
DR OMA; DMDDICV; -.
DR PhylomeDB; Q46927; -.
DR BioCyc; EcoCyc:G7456-MON; -.
DR BioCyc; MetaCyc:G7456-MON; -.
DR PRO; PR:Q46927; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0030955; F:potassium ion binding; IDA:EcoCyc.
DR GO; GO:0031402; F:sodium ion binding; IDA:EcoCyc.
DR GO; GO:0061503; F:tRNA threonylcarbamoyladenosine dehydratase; IDA:EcoCyc.
DR GO; GO:0008641; F:ubiquitin-like modifier activating enzyme activity; IEA:InterPro.
DR GO; GO:0061504; P:cyclic threonylcarbamoyladenosine biosynthetic process; IMP:EcoCyc.
DR InterPro; IPR045886; ThiF/MoeB/HesA.
DR InterPro; IPR000594; ThiF_NAD_FAD-bd.
DR InterPro; IPR035985; Ubiquitin-activating_enz.
DR PANTHER; PTHR43267; PTHR43267; 1.
DR Pfam; PF00899; ThiF; 1.
DR SUPFAM; SSF69572; SSF69572; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Ligase; Membrane; Nucleotide-binding;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..268
FT /note="tRNA threonylcarbamoyladenosine dehydratase"
FT /id="PRO_0000120579"
FT TRANSMEM 237..257
FT /note="Helical"
FT /evidence="ECO:0000255"
FT HELIX 7..20
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 22..29
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 42..51
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 55..60
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:4D79"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 85..96
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:4D79"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 114..118
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 132..144
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 149..152
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 161..163
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 164..168
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:4D79"
FT HELIX 176..189
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 202..206
FT /evidence="ECO:0007829|PDB:4D79"
FT STRAND 219..222
FT /evidence="ECO:0007829|PDB:4YED"
FT HELIX 242..266
FT /evidence="ECO:0007829|PDB:4D79"
SQ SEQUENCE 268 AA; 28562 MW; D1609BA2224EB300 CRC64;
MSVVISDAWR QRFGGTARLY GEKALQLFAD AHICVVGIGG VGSWAAEALA RTGIGAITLI
DMDDVCVTNT NRQIHALRDN VGLAKAEVMA ERIRQINPEC RVTVVDDFVT PDNVAQYMSV
GYSYVIDAID SVRPKAALIA YCRRNKIPLV TTGGAGGQID PTQIQVTDLA KTIQDPLAAK
LRERLKSDFG VVKNSKGKLG VDCVFSTEAL VYPQSDGTVC AMKATAEGPK RMDCASGFGA
ATMVTATFGF VAVSHALKKM MAKAARQG
