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Q68WP2

- PPDK_RICTY

UniProt

Q68WP2 - PPDK_RICTY

Protein

Pyruvate, phosphate dikinase

Gene

ppdK

Organism
Rickettsia typhi (strain ATCC VR-144 / Wilmington)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 65 (01 Oct 2014)
      Sequence version 1 (11 Oct 2004)
      Previous versions | rss
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    Functioni

    Catalyzes the reversible phosphorylation of pyruvate and phosphate.By similarity

    Catalytic activityi

    ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate.

    Cofactori

    Magnesium.By similarity

    Enzyme regulationi

    Activated by light-induced dephosphorylation. Inhibited by dark-induced phosphorylation. Both reactions are catalyzed by PDRP1 By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei97 – 971ATPSequence Analysis
    Active sitei460 – 4601Tele-phosphohistidine intermediateBy similarity
    Binding sitei566 – 5661SubstrateBy similarity
    Binding sitei622 – 6221SubstrateBy similarity
    Metal bindingi750 – 7501MagnesiumBy similarity
    Binding sitei750 – 7501SubstrateBy similarity
    Binding sitei771 – 7711Substrate; via carbonyl oxygenBy similarity
    Binding sitei772 – 7721Substrate; via amide nitrogenBy similarity
    Binding sitei773 – 7731SubstrateBy similarity
    Metal bindingi774 – 7741MagnesiumBy similarity
    Binding sitei774 – 7741Substrate; via amide nitrogenBy similarity
    Active sitei836 – 8361Proton donorBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. kinase activity Source: UniProtKB-KW
    3. metal ion binding Source: UniProtKB-KW
    4. pyruvate, phosphate dikinase activity Source: UniProtKB-EC

    GO - Biological processi

    1. pyruvate metabolic process Source: InterPro

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciRTYP257363:GJEQ-501-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyruvate, phosphate dikinase (EC:2.7.9.1)
    Alternative name(s):
    Pyruvate, orthophosphate dikinase
    Gene namesi
    Name:ppdK
    Ordered Locus Names:RT0478
    OrganismiRickettsia typhi (strain ATCC VR-144 / Wilmington)
    Taxonomic identifieri257363 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiatyphus group
    ProteomesiUP000000604: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 880880Pyruvate, phosphate dikinasePRO_0000289279Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei458 – 4581Phosphothreonine; by PDRP1By similarity

    Post-translational modificationi

    Phosphorylation of Thr-458 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme By similarity.By similarity

    Keywords - PTMi

    Phosphoprotein

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Protein-protein interaction databases

    STRINGi257363.RT0478.

    Structurei

    3D structure databases

    ProteinModelPortaliQ68WP2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 348348N-terminalAdd
    BLAST
    Regioni349 – 40557Linker 1Add
    BLAST
    Regioni406 – 50398CentralAdd
    BLAST
    Regioni504 – 53835Linker 2Add
    BLAST
    Regioni539 – 879341C-terminalAdd
    BLAST

    Domaini

    The N-terminal domain contains the ATP/Pi active site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate active site.By similarity

    Sequence similaritiesi

    Belongs to the PEP-utilizing enzyme family.Curated

    Phylogenomic databases

    eggNOGiCOG0574.
    HOGENOMiHOG000039664.
    KOiK01006.
    OMAiAVIYRKI.
    OrthoDBiEOG6N0HGQ.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    3.30.1490.20. 2 hits.
    3.30.470.20. 1 hit.
    3.50.30.10. 1 hit.
    InterProiIPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR008279. PEP-util_enz_mobile_dom.
    IPR018274. PEP_util_AS.
    IPR000121. PEP_util_C.
    IPR023151. PEP_util_CS.
    IPR002192. PPDK_PEP-bd.
    IPR010121. Pyruvate_phosphate_dikinase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PANTHERiPTHR22931:SF9. PTHR22931:SF9. 1 hit.
    PfamiPF00391. PEP-utilizers. 1 hit.
    PF02896. PEP-utilizers_C. 1 hit.
    PF01326. PPDK_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000853. PPDK. 1 hit.
    SUPFAMiSSF51621. SSF51621. 1 hit.
    SSF52009. SSF52009. 1 hit.
    TIGRFAMsiTIGR01828. pyru_phos_dikin. 1 hit.
    PROSITEiPS00742. PEP_ENZYMES_2. 1 hit.
    PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q68WP2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNKLIYYFGN NGSDGNASMK NILGNKGAGL AEMSNLKLPI PNGFTITTEL    50
    CNYFYKHNNN LPKNFQNELQ QAITKLEITT GKIFGSTTSN PLLLSVRSGS 100
    TVSMPGMMDT ILNLGMNNEV CNALADSCGN KLFALDSYRR FLEMYGSTVL 150
    SIPSDLFEQI YEKHKVQADI YKDSDITVEL LEKIIDDFKR LHIKYTKQLI 200
    KDPYEQLESA IKAVLYSWKN NRAIVYRKLN NISEDFGTAI NIQEMVFGNL 250
    GKTSATGVVF TRSPSTGEKK LFGEFLINAQ GEDIVSGTRT PMPIIANDSN 300
    SMQAMMPEVF TKLSQIAKKL EEHYLDMQDI EFTIENNKLY ILQTRTAKRT 350
    AIAAINIAVQ MVEEKLISKE QALMRIDPES LNQLLHTRID YSKKLTAIAE 400
    GLPASPGAAT GIVVFSPYDA EKLSHHHKVI LVRHDTSPED INGMHVASGI 450
    LTIRGGMTSH AAVVARGMGK PCVCGTNNLS IDEQKQILIA GDIVIKQGDI 500
    ITIDGGSGKI FLGEMPLIQP TFSEESTLIL DWADEISSLK VRANAETVND 550
    ALVSIKFGAQ GIGLCRSEHM FFDKNKIPLV REMIIAPDIE RRQCALQKLL 600
    PLQTEDFKAL FRVMKNKPVN IRLLDPPLHE FLPTTDEDKK NLAHSLNLPL 650
    SMIHQRLHAM HEVNPMLGHR GCRLGICLPE IYQMQIEAIL TAIFELHKKE 700
    HIESNLELMI PLISNVAEIK KLKMDIYAVV KKLEQRYSYK FSFTLGTMIE 750
    LPRAALGSKK IAKEVDYFSF GTNDLTQTTY GISRDDIASF LPYYLEEKIF 800
    ESDPFTTLDE EGVGELIKIA IKRGKSSNAN LKLGACGEHA GNPTSIAFFH 850
    KMNLNYVSCS PYRIPIARIA AAQAKIKQGS 880
    Length:880
    Mass (Da):98,165
    Last modified:October 11, 2004 - v1
    Checksum:iFFFE55AEEA138B34
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE017197 Genomic DNA. Translation: AAU03950.1.
    RefSeqiYP_067432.1. NC_006142.1.

    Genome annotation databases

    EnsemblBacteriaiAAU03950; AAU03950; RT0478.
    GeneIDi2959286.
    KEGGirty:RT0478.
    PATRICi17910198. VBIRicTyp34752_0507.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE017197 Genomic DNA. Translation: AAU03950.1 .
    RefSeqi YP_067432.1. NC_006142.1.

    3D structure databases

    ProteinModelPortali Q68WP2.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 257363.RT0478.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAU03950 ; AAU03950 ; RT0478 .
    GeneIDi 2959286.
    KEGGi rty:RT0478.
    PATRICi 17910198. VBIRicTyp34752_0507.

    Phylogenomic databases

    eggNOGi COG0574.
    HOGENOMi HOG000039664.
    KOi K01006.
    OMAi AVIYRKI.
    OrthoDBi EOG6N0HGQ.

    Enzyme and pathway databases

    BioCyci RTYP257363:GJEQ-501-MONOMER.

    Family and domain databases

    Gene3Di 3.20.20.60. 1 hit.
    3.30.1490.20. 2 hits.
    3.30.470.20. 1 hit.
    3.50.30.10. 1 hit.
    InterProi IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR008279. PEP-util_enz_mobile_dom.
    IPR018274. PEP_util_AS.
    IPR000121. PEP_util_C.
    IPR023151. PEP_util_CS.
    IPR002192. PPDK_PEP-bd.
    IPR010121. Pyruvate_phosphate_dikinase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view ]
    PANTHERi PTHR22931:SF9. PTHR22931:SF9. 1 hit.
    Pfami PF00391. PEP-utilizers. 1 hit.
    PF02896. PEP-utilizers_C. 1 hit.
    PF01326. PPDK_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000853. PPDK. 1 hit.
    SUPFAMi SSF51621. SSF51621. 1 hit.
    SSF52009. SSF52009. 1 hit.
    TIGRFAMsi TIGR01828. pyru_phos_dikin. 1 hit.
    PROSITEi PS00742. PEP_ENZYMES_2. 1 hit.
    PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC VR-144 / Wilmington.

    Entry informationi

    Entry nameiPPDK_RICTY
    AccessioniPrimary (citable) accession number: Q68WP2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 29, 2007
    Last sequence update: October 11, 2004
    Last modified: October 1, 2014
    This is version 65 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The reaction takes place in three steps, each mediated by a carrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain.

    Keywords - Technical termi

    Complete proteome

    Documents

    1. Rickettsia typhi
      Rickettsia typhi (strain Wilmington): entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3