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Protein

Threonylcarbamoyl-AMP synthase

Gene

tsaC

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

Functioni

Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t6A37) in tRNAs that read codons beginning with adenine. Catalyzes the conversion of L-threonine, bicarbonate/CO2 and ATP to give threonylcarbamoyl-AMP (TC-AMP) as the acyladenylate intermediate, with the release of pyrophosphate. Is also able to catalyze the reverse reaction in vitro, i.e. the formation of ATP from TC-AMP and PPi. Shows higher affinity for the full-length tRNA(Thr) lacking only the t6A37 modification than for its fully modified counterpart. Could also be required for the maturation of 16S rRNA. Binds to double-stranded RNA but does not interact tightly with either of the ribosomal subunits, or the 70S particles.UniRule annotation5 Publications

Catalytic activityi

L-threonine + ATP + bicarbonate = L-threonylcarbamoyladenylate + diphosphate + H2O.UniRule annotation1 Publication

Kineticsi

kcat is 0.10 sec(-1) for ATP-dependent TC-AMP formation and 20 sec(-1) for the reverse reaction.

  1. KM=93 µM for ATP1 Publication
  2. KM=0.68 µM for L-threonylcarbamoyl-AMP1 Publication

    GO - Molecular functioni

    • ATP binding Source: EcoCyc
    • double-stranded RNA binding Source: EcoCyc
    • nucleotidyltransferase activity Source: UniProtKB
    • tRNA binding Source: EcoCyc

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    Ribosome biogenesis, rRNA processing, tRNA processing

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding, RNA-binding, tRNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7698-MONOMER.
    ECOL316407:JW3243-MONOMER.
    BRENDAi2.7.7.87. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Threonylcarbamoyl-AMP synthaseUniRule annotation (EC:2.7.7.87UniRule annotation)
    Short name:
    TC-AMP synthaseUniRule annotation
    Alternative name(s):
    L-threonylcarbamoyladenylate synthaseUniRule annotation
    Ribosome maturation factor TsaC
    t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaCUniRule annotation
    tRNA threonylcarbamoyladenosine biosynthesis protein TsaCUniRule annotation
    Gene namesi
    Name:tsaCUniRule annotation
    Synonyms:rimN, yrdC
    Ordered Locus Names:b3282, JW3243
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12840. tsaC.

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    • cytoplasm Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    The knockdown of this gene results in a loss of t6A37 modification in tRNAs.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi50 – 501K → A: Loss of activity. 1 Publication
    Mutagenesisi52 – 521R → A: Loss of activity. 1 Publication
    Mutagenesisi56 – 561K → A: No change in activity. 1 Publication
    Mutagenesisi110 – 1101R → A: No change in activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 190190Threonylcarbamoyl-AMP synthasePRO_0000202018Add
    BLAST

    Proteomic databases

    PaxDbiP45748.
    PRIDEiP45748.

    Interactioni

    Subunit structurei

    Interacts with TsaB and TsaD.1 Publication

    Protein-protein interaction databases

    DIPiDIP-12916N.
    IntActiP45748. 12 interactions.
    MINTiMINT-1230775.
    STRINGi511145.b3282.

    Structurei

    Secondary structure

    1
    190
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 1815Combined sources
    Beta strandi23 – 264Combined sources
    Beta strandi28 – 358Combined sources
    Helixi40 – 5011Combined sources
    Helixi54 – 563Combined sources
    Beta strandi59 – 646Combined sources
    Helixi65 – 684Combined sources
    Helixi69 – 713Combined sources
    Helixi79 – 868Combined sources
    Beta strandi90 – 989Combined sources
    Helixi105 – 1084Combined sources
    Beta strandi111 – 1188Combined sources
    Helixi122 – 13110Combined sources
    Beta strandi135 – 1406Combined sources
    Helixi151 – 1588Combined sources
    Beta strandi177 – 1804Combined sources
    Turni181 – 1833Combined sources
    Beta strandi184 – 1863Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HRUX-ray2.00A/B1-188[»]
    ProteinModelPortaliP45748.
    SMRiP45748. Positions 3-188.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP45748.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini7 – 190184YrdC-likeUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the SUA5 family. TsaC subfamily.UniRule annotation
    Contains 1 YrdC-like domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0009.
    HOGENOMiHOG000076163.
    InParanoidiP45748.
    KOiK07566.
    OMAiFASWPGP.
    OrthoDBiEOG6C5RT4.
    PhylomeDBiP45748.

    Family and domain databases

    Gene3Di3.90.870.10. 1 hit.
    HAMAPiMF_01852. TsaC.
    InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
    IPR023535. TC-AMP_synthase.
    IPR006070. YrdC-like_dom.
    [Graphical view]
    PfamiPF01300. Sua5_yciO_yrdC. 1 hit.
    [Graphical view]
    SUPFAMiSSF55821. SSF55821. 1 hit.
    PROSITEiPS51163. YRDC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P45748-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNNNLQRDAI AAAIDVLNEE RVIAYPTEAV FGVGCDPDSE TAVMRLLELK
    60 70 80 90 100
    QRPVDKGLIL IAANYEQLKP YIDDTMLTDV QRETIFSRWP GPVTFVFPAP
    110 120 130 140 150
    ATTPRWLTGR FDSLAVRVTD HPLVVALCQA YGKPLVSTSA NLSGLPPCRT
    160 170 180 190
    VDEVRAQFGA AFPVVPGETG GRLNPSEIRD ALTGELFRQG
    Length:190
    Mass (Da):20,768
    Last modified:July 15, 1998 - v2
    Checksum:i4DCAAA8873FAB56F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA58079.1. Frameshift.
    U00096 Genomic DNA. Translation: AAC76307.1.
    AP009048 Genomic DNA. Translation: BAE78009.1.
    PIRiE65120.
    RefSeqiNP_417741.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC76307; AAC76307; b3282.
    BAE78009; BAE78009; BAE78009.
    GeneIDi947783.
    KEGGiecj:Y75_p3894.
    eco:b3282.
    PATRICi32121998. VBIEscCol129921_3376.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA58079.1. Frameshift.
    U00096 Genomic DNA. Translation: AAC76307.1.
    AP009048 Genomic DNA. Translation: BAE78009.1.
    PIRiE65120.
    RefSeqiNP_417741.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HRUX-ray2.00A/B1-188[»]
    ProteinModelPortaliP45748.
    SMRiP45748. Positions 3-188.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-12916N.
    IntActiP45748. 12 interactions.
    MINTiMINT-1230775.
    STRINGi511145.b3282.

    Proteomic databases

    PaxDbiP45748.
    PRIDEiP45748.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76307; AAC76307; b3282.
    BAE78009; BAE78009; BAE78009.
    GeneIDi947783.
    KEGGiecj:Y75_p3894.
    eco:b3282.
    PATRICi32121998. VBIEscCol129921_3376.

    Organism-specific databases

    EchoBASEiEB2689.
    EcoGeneiEG12840. tsaC.

    Phylogenomic databases

    eggNOGiCOG0009.
    HOGENOMiHOG000076163.
    InParanoidiP45748.
    KOiK07566.
    OMAiFASWPGP.
    OrthoDBiEOG6C5RT4.
    PhylomeDBiP45748.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7698-MONOMER.
    ECOL316407:JW3243-MONOMER.
    BRENDAi2.7.7.87. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP45748.
    PROiP45748.

    Family and domain databases

    Gene3Di3.90.870.10. 1 hit.
    HAMAPiMF_01852. TsaC.
    InterProiIPR017945. DHBP_synth_RibB-like_a/b_dom.
    IPR023535. TC-AMP_synthase.
    IPR006070. YrdC-like_dom.
    [Graphical view]
    PfamiPF01300. Sua5_yciO_yrdC. 1 hit.
    [Graphical view]
    SUPFAMiSSF55821. SSF55821. 1 hit.
    PROSITEiPS51163. YRDC. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography."
      Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.
      Electrophoresis 20:2181-2195(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: B / BL21.
    4. "The YrdC protein -- a putative ribosome maturation factor."
      Kaczanowska M., Ryden-Aulin M.
      Biochim. Biophys. Acta 1727:87-96(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN MATURATION OF 16S RRNA.
      Strain: K12 / MG1655 / ATCC 47076.
    5. "The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA."
      El Yacoubi B., Lyons B., Cruz Y., Reddy R., Nordin B., Agnelli F., Williamson J.R., Schimmel P., Swairjo M.A., de Crecy-Lagard V.
      Nucleic Acids Res. 37:2894-2909(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ATP-BINDING, TRNA-BINDING, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-50; ARG-52; LYS-56 AND ARG-110.
      Strain: K12 / MG1655 / ATCC 47076.
    6. "A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification."
      El Yacoubi B., Hatin I., Deutsch C., Kahveci T., Rousset J.P., Iwata-Reuyl D., Murzin A.G., de Crecy-Lagard V.
      EMBO J. 30:882-893(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
      Strain: K12.
    7. "YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase."
      Harris K.A., Jones V., Bilbille Y., Swairjo M.A., Agris P.F.
      RNA 17:1678-1687(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROPOSED FUNCTION AS A THREONYLCARBAMOYLTRANSFERASE, TRNA-BINDING, ATP-BINDING, THREONINE-BINDING.
      Strain: K12 / MG1655 / ATCC 47076.
    8. "Mechanism of N6-threonylcarbamoyladenosine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP."
      Lauhon C.T.
      Biochemistry 51:8950-8963(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A TC-AMP SYNTHASE, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
    9. "Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside."
      Deutsch C., El Yacoubi B., de Crecy-Lagard V., Iwata-Reuyl D.
      J. Biol. Chem. 287:13666-13673(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN T(6)A37 FORMATION, GENE NAME, INTERACTION WITH TSAB AND TSAD.
      Strain: K12.
    10. "The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding."
      Teplova M., Tereshko V., Sanishvili R., Joachimiak A., Bushueva T., Anderson W.F., Egli M.
      Protein Sci. 9:2557-2566(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), RNA-BINDING.

    Entry informationi

    Entry nameiTSAC_ECOLI
    AccessioniPrimary (citable) accession number: P45748
    Secondary accession number(s): Q2M6U7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: July 15, 1998
    Last modified: June 24, 2015
    This is version 121 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    TsaBCDE are necessary and sufficient for tRNA(NNU) t6A37 threonylcarbamoyladenosine modification in vitro in E.coli.1 Publication
    Unlike previously thought, the formation of TC-AMP does not proceed via an ATP-activated bicarbonate intermediate such as carboxy-AMP.1 Publication

    Caution

    Was also proposed to catalyze the transfer of the threonylcarbamoyl moiety of TC-AMP to the N6 group of A37 (PubMed:21285948 and PubMed:21775474). However, it was shown that this reaction is catalyzed in B.subtilis by the TsaEBD proteins (PubMed:23072323).1 Publication
    The well-known t6A modification appears to be a hydrolyzed artifact of natural cyclic t6A (ct6A) that occurs during the preparation and handling of tRNA in E.coli and many other species (PubMed:23242255). In these species, the t6A modification is processed further by dehydration into ct6A, a reaction catalyzed by TcdA.Curated

    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

    External Data

    Dasty 3

    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 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.