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Protein

Phosphopantetheine adenylyltransferase

Gene

coaD

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

Functioni

Reversibly transfers an adenylyl group from ATP to 4'-phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate (PubMed:10480925). The crystal structures in complex with substrates suggest the enyzme stabilizes the transition state without the direct involvement of enzymatic functional groups in the reaction (PubMed:11812124).2 Publications

Catalytic activityi

ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA.UniRule annotation2 Publications

Cofactori

Mg2+1 PublicationNote: Crystallized in the absence of Mg2+, the catalytic metal is not bound by the protein but probably by non-esterified oxygen atoms from ATP and/or ordered H(2)O (PubMed:11812124).1 Publication

Enzyme regulationi

Inhibited by CoA, which competes with ATP, 4'-phosphopantetheine and 3'-dephospho-CoA (PubMed:12837781). Binds 0.5 CoA tightly per monomer in the same position as 3'-dephospho-CoA but in a different fashion (PubMed:12837781, PubMed:17873050). CoA is not a substrate for the enzyme (PubMed:10480925).1 Publication2 Publications

Kineticsi

kcat is 1.37/s (PubMed:17873050) to 3.3/s (PubMed:10480925).2 Publications

Manual assertion based on experiment ini

  1. KM=7.0 µM for 3'-dephospho-CoA1 Publication
  2. KM=17.0 µM for 3'-dephospho-CoA1 Publication
  3. KM=0.22 mM for diphosphate1 Publication
  4. KM=0.23 mM for diphosphate1 Publication
  5. KM=220 µM for ATP1 Publication
  6. KM=4.7 µM for 4'-phosphopantetheine1 Publication

    pH dependencei

    Optimum pH is 6.9.1 Publication

    Pathwayi: coenzyme A biosynthesis

    This protein is involved in step 4 of the subpathway that synthesizes CoA from (R)-pantothenate.UniRule annotation
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. Pantothenate kinase (coaA)
    2. Coenzyme A biosynthesis bifunctional protein CoaBC (coaBC)
    3. Coenzyme A biosynthesis bifunctional protein CoaBC (coaBC)
    4. Phosphopantetheine adenylyltransferase (coaD)
    5. Dephospho-CoA kinase (coaE)
    This subpathway is part of the pathway coenzyme A biosynthesis, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes CoA from (R)-pantothenate, the pathway coenzyme A biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei10Substrate-binding (4'-phosphopantetheine)Combined sources2 Publications1
    Binding sitei18ATPCombined sources1 Publication1
    Binding sitei42Substrate-binding (4'-phosphopantetheine)Combined sources3 Publications1
    Binding sitei74Substrate-binding (4'-phosphopantetheine); via amide nitrogenCombined sources3 Publications1
    Binding sitei88Substrate-binding (4'-phosphopantetheine)Combined sources1 Publication1
    Binding sitei95Product-binding (3'-dephospho-CoA)Combined sources1 Publication1
    Binding sitei99ATPCombined sources1 Publication1
    Binding sitei99Product-binding (3'-dephospho-CoA)Combined sources1 Publication1
    Binding sitei134Substrate-binding (4'-phosphopantetheine)Combined sources3 Publications1
    Binding sitei138Substrate-binding (4'-phosphopantetheine)Combined sources3 Publications1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi7 – 11ATPCombined sources1 Publication5
    Nucleotide bindingi88 – 91ATPCombined sources1 Publication4
    Nucleotide bindingi124 – 130ATPCombined sources1 Publication7

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • pantetheine-phosphate adenylyltransferase activity Source: EcoCyc

    GO - Biological processi

    • coenzyme A biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    Coenzyme A biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:PANTEPADENYLYLTRAN-MONOMER.
    ECOL316407:JW3609-MONOMER.
    MetaCyc:PANTEPADENYLYLTRAN-MONOMER.
    BRENDAi2.7.7.3. 2026.
    SABIO-RKP0A6I6.
    UniPathwayiUPA00241; UER00355.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphopantetheine adenylyltransferaseUniRule annotation (EC:2.7.7.3UniRule annotation2 Publications)
    Alternative name(s):
    Dephospho-CoA pyrophosphorylaseUniRule annotation
    Pantetheine-phosphate adenylyltransferaseUniRule annotation
    Short name:
    PPATUniRule annotation
    Gene namesi
    Name:coaD1 PublicationUniRule annotation
    Synonyms:kdtB1 Publication, yicA
    Ordered Locus Names:b3634, JW3609
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11190. coaD.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001562041 – 159Phosphopantetheine adenylyltransferaseAdd BLAST159

    Proteomic databases

    PaxDbiP0A6I6.
    PRIDEiP0A6I6.

    Interactioni

    Subunit structurei

    Homohexamer, a dimerized trimer with a solvent channel through the middle (PubMed:10480925, PubMed:10205156, PubMed:11812124, PubMed:12837781, PubMed:17873050). In crystals only 1 trimer is seen to bind substrate/product at a time (PubMed:10205156, PubMed:11812124).5 Publications

    Protein-protein interaction databases

    BioGridi4263379. 238 interactors.
    DIPiDIP-35966N.
    IntActiP0A6I6. 10 interactors.
    STRINGi511145.b3634.

    Chemistry databases

    BindingDBiP0A6I6.

    Structurei

    Secondary structure

    1159
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 9Combined sources6
    Helixi16 – 28Combined sources13
    Beta strandi29 – 37Combined sources9
    Helixi40 – 42Combined sources3
    Helixi48 – 58Combined sources11
    Turni59 – 61Combined sources3
    Beta strandi65 – 70Combined sources6
    Helixi74 – 80Combined sources7
    Beta strandi85 – 89Combined sources5
    Helixi96 – 109Combined sources14
    Beta strandi113 – 118Combined sources6
    Helixi122 – 124Combined sources3
    Helixi129 – 137Combined sources9
    Helixi143 – 145Combined sources3
    Helixi148 – 159Combined sources12

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B6TX-ray1.80A/B1-159[»]
    1GN8X-ray1.83A/B1-159[»]
    1H1TX-ray1.78A/B1-159[»]
    1QJCX-ray1.63A/B2-159[»]
    5JBNX-ray1.45A/B1-159[»]
    ProteinModelPortaliP0A6I6.
    SMRiP0A6I6.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6I6.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni7 – 11Product-binding (3'-dephospho-CoA)Combined sources1 Publication5
    Regioni88 – 89Product-binding (3'-dephospho-CoA)Combined sources1 Publication2
    Regioni124 – 127Product-binding (3'-dephospho-CoA)Combined sources1 Publication4

    Sequence similaritiesi

    Belongs to the bacterial CoaD family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4108ZEF. Bacteria.
    COG0669. LUCA.
    HOGENOMiHOG000006518.
    InParanoidiP0A6I6.
    KOiK00954.
    OMAiEFQMALM.
    PhylomeDBiP0A6I6.

    Family and domain databases

    CDDicd02163. PPAT. 1 hit.
    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_00151. PPAT_bact. 1 hit.
    InterProiIPR004821. Cyt_trans-like.
    IPR001980. LPS_biosynth.
    IPR014729. Rossmann-like_a/b/a_fold.
    [Graphical view]
    PfamiPF01467. CTP_transf_like. 1 hit.
    [Graphical view]
    PRINTSiPR01020. LPSBIOSNTHSS.
    TIGRFAMsiTIGR01510. coaD_prev_kdtB. 1 hit.
    TIGR00125. cyt_tran_rel. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0A6I6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQKRAIYPGT FDPITNGHID IVTRATQMFD HVILAIAASP SKKPMFTLEE
    60 70 80 90 100
    RVALAQQATA HLGNVEVVGF SDLMANFARN QHATVLIRGL RAVADFEYEM
    110 120 130 140 150
    QLAHMNRHLM PELESVFLMP SKEWSFISSS LVKEVARHQG DVTHFLPENV

    HQALMAKLA
    Length:159
    Mass (Da):17,837
    Last modified:March 29, 2005 - v1
    Checksum:iC4D7B8715A061B91
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M60670 Genomic DNA. Translation: AAA24044.1.
    M86305 Genomic DNA. Translation: AAA03746.1.
    U00039 Genomic DNA. Translation: AAB18611.1.
    U00096 Genomic DNA. Translation: AAC76658.1.
    AP009048 Genomic DNA. Translation: BAE77658.1.
    PIRiJU0468.
    RefSeqiNP_418091.1. NC_000913.3.
    WP_001171866.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76658; AAC76658; b3634.
    BAE77658; BAE77658; BAE77658.
    GeneIDi947386.
    KEGGiecj:JW3609.
    eco:b3634.
    PATRICi32122755. VBIEscCol129921_3754.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M60670 Genomic DNA. Translation: AAA24044.1.
    M86305 Genomic DNA. Translation: AAA03746.1.
    U00039 Genomic DNA. Translation: AAB18611.1.
    U00096 Genomic DNA. Translation: AAC76658.1.
    AP009048 Genomic DNA. Translation: BAE77658.1.
    PIRiJU0468.
    RefSeqiNP_418091.1. NC_000913.3.
    WP_001171866.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1B6TX-ray1.80A/B1-159[»]
    1GN8X-ray1.83A/B1-159[»]
    1H1TX-ray1.78A/B1-159[»]
    1QJCX-ray1.63A/B2-159[»]
    5JBNX-ray1.45A/B1-159[»]
    ProteinModelPortaliP0A6I6.
    SMRiP0A6I6.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263379. 238 interactors.
    DIPiDIP-35966N.
    IntActiP0A6I6. 10 interactors.
    STRINGi511145.b3634.

    Chemistry databases

    BindingDBiP0A6I6.

    Proteomic databases

    PaxDbiP0A6I6.
    PRIDEiP0A6I6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76658; AAC76658; b3634.
    BAE77658; BAE77658; BAE77658.
    GeneIDi947386.
    KEGGiecj:JW3609.
    eco:b3634.
    PATRICi32122755. VBIEscCol129921_3754.

    Organism-specific databases

    EchoBASEiEB1176.
    EcoGeneiEG11190. coaD.

    Phylogenomic databases

    eggNOGiENOG4108ZEF. Bacteria.
    COG0669. LUCA.
    HOGENOMiHOG000006518.
    InParanoidiP0A6I6.
    KOiK00954.
    OMAiEFQMALM.
    PhylomeDBiP0A6I6.

    Enzyme and pathway databases

    UniPathwayiUPA00241; UER00355.
    BioCyciEcoCyc:PANTEPADENYLYLTRAN-MONOMER.
    ECOL316407:JW3609-MONOMER.
    MetaCyc:PANTEPADENYLYLTRAN-MONOMER.
    BRENDAi2.7.7.3. 2026.
    SABIO-RKP0A6I6.

    Miscellaneous databases

    EvolutionaryTraceiP0A6I6.
    PROiP0A6I6.

    Family and domain databases

    CDDicd02163. PPAT. 1 hit.
    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_00151. PPAT_bact. 1 hit.
    InterProiIPR004821. Cyt_trans-like.
    IPR001980. LPS_biosynth.
    IPR014729. Rossmann-like_a/b/a_fold.
    [Graphical view]
    PfamiPF01467. CTP_transf_like. 1 hit.
    [Graphical view]
    PRINTSiPR01020. LPSBIOSNTHSS.
    TIGRFAMsiTIGR01510. coaD_prev_kdtB. 1 hit.
    TIGR00125. cyt_tran_rel. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiCOAD_ECOLI
    AccessioniPrimary (citable) accession number: P0A6I6
    Secondary accession number(s): P23875, Q2M7U8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 29, 2005
    Last sequence update: March 29, 2005
    Last modified: November 2, 2016
    This is version 104 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally thought to have an essential function in lipopolysaccharide biosynthesis.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.