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Protein

tRNA threonylcarbamoyladenosine dehydratase

Gene

tcdA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t6A37) to form cyclic t6A37 (ct6A37) in tRNAs that read codons beginning with adenine. TcdA is also part of a sulfur transfer pathway; is able to accept sulfur from CsdA directly in vitro, but CsdE might act as the sulfur donor in vivo.2 Publications

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • potassium ion binding Source: EcoCyc
  • small protein activating enzyme activity Source: InterPro
  • sodium ion binding Source: EcoCyc
  • tRNA threonylcarbamoyladenosine dehydratase Source: EcoCyc

GO - Biological processi

  • cyclic threonylcarbamoyladenosine biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7456-MONOMER.
ECOL316407:JW2783-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA threonylcarbamoyladenosine dehydratase (EC:6.1.-.-)
Alternative name(s):
t(6)A37 dehydratase
Gene namesi
Name:tcdA
Synonyms:csdL, ygdL
Ordered Locus Names:b2812, JW2783
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13084. tcdA.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei237 – 25721HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene have a normal growth phenotype, but are unable to survive in a competitive growth situation with the wild-type strain. They display only the t6A but not the ct6A modification in tRNAs, and have lower decoding efficiency than wild-type. They show no defects in motility or antibiotic sensitivity. In growth competition experiments, a tcdA mutant shows reduced fitness compared to wild-type, but outcompetes a csdA mutant.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 268268tRNA threonylcarbamoyladenosine dehydratasePRO_0000120579Add
BLAST

Proteomic databases

PaxDbiQ46927.

Interactioni

Subunit structurei

Interacts with CsdE.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
csdEP0AGF23EBI-1130463,EBI-1130454

Protein-protein interaction databases

BioGridi4261127. 823 interactions.
IntActiQ46927. 9 interactions.
STRINGi511145.b2812.

Structurei

Secondary structure

1
268
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 2014Combined sources
Helixi22 – 298Combined sources
Beta strandi32 – 365Combined sources
Helixi42 – 5110Combined sources
Beta strandi55 – 606Combined sources
Helixi67 – 693Combined sources
Turni70 – 723Combined sources
Helixi78 – 803Combined sources
Helixi85 – 9612Combined sources
Beta strandi101 – 1055Combined sources
Turni111 – 1133Combined sources
Helixi114 – 1185Combined sources
Beta strandi123 – 1275Combined sources
Helixi132 – 14413Combined sources
Beta strandi149 – 1524Combined sources
Helixi161 – 1633Combined sources
Beta strandi164 – 1685Combined sources
Helixi169 – 1713Combined sources
Helixi176 – 18914Combined sources
Beta strandi202 – 2065Combined sources
Beta strandi219 – 2224Combined sources
Helixi242 – 26625Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4D79X-ray1.77A/B/C/D1-268[»]
4D7AX-ray1.80A/B/C/D1-268[»]
4RDHX-ray2.10A/B/C/D1-268[»]
4RDIX-ray1.95A/B/C/D1-268[»]
4YEDX-ray1.90A/B/C/D1-268[»]
ProteinModelPortaliQ46927.
SMRiQ46927. Positions 2-268.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the HesA/MoeB/ThiF family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105CUZ. Bacteria.
COG1179. LUCA.
HOGENOMiHOG000263839.
InParanoidiQ46927.
OMAiDMDDICV.
PhylomeDBiQ46927.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR016040. NAD(P)-bd_dom.
IPR000594. ThiF_NAD_FAD-bd.
[Graphical view]
PfamiPF00899. ThiF. 1 hit.
[Graphical view]
SUPFAMiSSF69572. SSF69572. 1 hit.

Sequencei

Sequence statusi: Complete.

Q46927-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVVISDAWR QRFGGTARLY GEKALQLFAD AHICVVGIGG VGSWAAEALA
60 70 80 90 100
RTGIGAITLI DMDDVCVTNT NRQIHALRDN VGLAKAEVMA ERIRQINPEC
110 120 130 140 150
RVTVVDDFVT PDNVAQYMSV GYSYVIDAID SVRPKAALIA YCRRNKIPLV
160 170 180 190 200
TTGGAGGQID PTQIQVTDLA KTIQDPLAAK LRERLKSDFG VVKNSKGKLG
210 220 230 240 250
VDCVFSTEAL VYPQSDGTVC AMKATAEGPK RMDCASGFGA ATMVTATFGF
260
VAVSHALKKM MAKAARQG
Length:268
Mass (Da):28,562
Last modified:November 1, 1996 - v1
Checksum:iD1609BA2224EB300
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29581 Genomic DNA. Translation: AAB40462.1.
U00096 Genomic DNA. Translation: AAC75854.1.
AP009048 Genomic DNA. Translation: BAE76884.1.
PIRiH65063.
RefSeqiNP_417292.1. NC_000913.3.
WP_000117728.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75854; AAC75854; b2812.
BAE76884; BAE76884; BAE76884.
GeneIDi947291.
KEGGiecj:JW2783.
eco:b2812.
PATRICi32121040. VBIEscCol129921_2912.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29581 Genomic DNA. Translation: AAB40462.1.
U00096 Genomic DNA. Translation: AAC75854.1.
AP009048 Genomic DNA. Translation: BAE76884.1.
PIRiH65063.
RefSeqiNP_417292.1. NC_000913.3.
WP_000117728.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4D79X-ray1.77A/B/C/D1-268[»]
4D7AX-ray1.80A/B/C/D1-268[»]
4RDHX-ray2.10A/B/C/D1-268[»]
4RDIX-ray1.95A/B/C/D1-268[»]
4YEDX-ray1.90A/B/C/D1-268[»]
ProteinModelPortaliQ46927.
SMRiQ46927. Positions 2-268.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261127. 823 interactions.
IntActiQ46927. 9 interactions.
STRINGi511145.b2812.

Proteomic databases

PaxDbiQ46927.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75854; AAC75854; b2812.
BAE76884; BAE76884; BAE76884.
GeneIDi947291.
KEGGiecj:JW2783.
eco:b2812.
PATRICi32121040. VBIEscCol129921_2912.

Organism-specific databases

EchoBASEiEB2893.
EcoGeneiEG13084. tcdA.

Phylogenomic databases

eggNOGiENOG4105CUZ. Bacteria.
COG1179. LUCA.
HOGENOMiHOG000263839.
InParanoidiQ46927.
OMAiDMDDICV.
PhylomeDBiQ46927.

Enzyme and pathway databases

BioCyciEcoCyc:G7456-MONOMER.
ECOL316407:JW2783-MONOMER.

Miscellaneous databases

PROiQ46927.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR016040. NAD(P)-bd_dom.
IPR000594. ThiF_NAD_FAD-bd.
[Graphical view]
PfamiPF00899. ThiF. 1 hit.
[Graphical view]
SUPFAMiSSF69572. SSF69572. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiTCDA_ECOLI
AccessioniPrimary (citable) accession number: Q46927
Secondary accession number(s): Q2MA22
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

ct6A is involved in promoting decoding efficiency. It is an unstable modification that can be easily hydrolyzed and converted to t6A during nucleoside preparation by conventional methods (PubMed:23242255). This explains why it was descibed as t6A37 in earlier studies.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.