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Protein

Propionate kinase

Gene

tdcD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.

Catalytic activityi

ATP + propanoate = ADP + propanoyl phosphate.UniRule annotation

Cofactori

Mg2+UniRule annotation

Kineticsi

  1. KM=112 µM for ATP (at 25 degrees Celsius and pH 7.5)1 Publication
  2. KM=2.3 mM for propionate (at 25 degrees Celsius and pH 7.5)1 Publication
  3. KM=26.9 mM for acetate (at 25 degrees Celsius and pH 7.5)1 Publication

    Pathwayi: L-threonine degradation via propanoate pathway

    This protein is involved in step 4 of the subpathway that synthesizes propanoate from L-threonine.UniRule annotation
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. L-threonine dehydratase catabolic TdcB (tdcB)
    2. no protein annotated in this organism
    3. no protein annotated in this organism
    4. Propionate kinase (tdcD)
    This subpathway is part of the pathway L-threonine degradation via propanoate pathway, which is itself part of Amino-acid degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes propanoate from L-threonine, the pathway L-threonine degradation via propanoate pathway and in Amino-acid degradation.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi11 – 111MagnesiumUniRule annotation
    Binding sitei11 – 111ATP
    Binding sitei18 – 181ATPUniRule annotation
    Binding sitei86 – 861SubstrateUniRule annotation
    Active sitei143 – 1431Proton donor/acceptorUniRule annotation
    Binding sitei175 – 1751ATP
    Sitei175 – 1751Transition state stabilizerUniRule annotation
    Sitei236 – 2361Transition state stabilizerUniRule annotation
    Metal bindingi381 – 3811MagnesiumUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi203 – 2075ATP
    Nucleotide bindingi278 – 2803ATP
    Nucleotide bindingi326 – 3305ATPUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciSENT99287:GCTI-3262-MONOMER.
    BRENDAi2.7.2.15. 5542.
    UniPathwayiUPA00052; UER00510.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Propionate kinaseUniRule annotation (EC:2.7.2.15UniRule annotation)
    Gene namesi
    Name:tdcDUniRule annotation
    Synonyms:oxd-2
    Ordered Locus Names:STM3242
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 402402Propionate kinasePRO_0000107656Add
    BLAST

    Proteomic databases

    PaxDbiO06961.
    PRIDEiO06961.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM3242.

    Structurei

    Secondary structure

    1
    402
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 127Combined sources
    Beta strandi17 – 237Combined sources
    Turni24 – 263Combined sources
    Beta strandi29 – 379Combined sources
    Beta strandi40 – 489Combined sources
    Beta strandi53 – 575Combined sources
    Helixi60 – 7314Combined sources
    Helixi77 – 793Combined sources
    Beta strandi80 – 889Combined sources
    Turni91 – 933Combined sources
    Helixi102 – 11110Combined sources
    Helixi112 – 1143Combined sources
    Helixi116 – 13217Combined sources
    Beta strandi136 – 1427Combined sources
    Helixi145 – 1495Combined sources
    Helixi152 – 1554Combined sources
    Helixi161 – 1677Combined sources
    Helixi176 – 19015Combined sources
    Helixi194 – 1963Combined sources
    Beta strandi198 – 21417Combined sources
    Beta strandi217 – 2226Combined sources
    Beta strandi229 – 2313Combined sources
    Helixi242 – 25211Combined sources
    Helixi256 – 26510Combined sources
    Helixi268 – 2736Combined sources
    Helixi279 – 2879Combined sources
    Helixi291 – 31222Combined sources
    Beta strandi315 – 3173Combined sources
    Beta strandi320 – 3245Combined sources
    Helixi325 – 3306Combined sources
    Helixi332 – 3409Combined sources
    Helixi341 – 3455Combined sources
    Helixi351 – 3555Combined sources
    Helixi358 – 3603Combined sources
    Beta strandi362 – 3643Combined sources
    Beta strandi371 – 3766Combined sources
    Helixi381 – 39212Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1X3MX-ray2.20A2-402[»]
    1X3NX-ray2.30A2-402[»]
    2E1YX-ray2.60A2-402[»]
    2E1ZX-ray1.98A2-402[»]
    2E20X-ray2.40A2-402[»]
    4FWKX-ray2.80A2-402[»]
    4FWLX-ray2.40A2-397[»]
    4FWMX-ray2.95A2-397[»]
    4FWNX-ray3.00A2-402[»]
    4FWOX-ray2.90A2-402[»]
    4FWPX-ray2.50A2-402[»]
    4FWQX-ray2.65A2-402[»]
    4FWRX-ray3.00A2-402[»]
    4FWSX-ray2.69A2-402[»]
    4XH1X-ray2.00A2-397[»]
    4XH4X-ray1.80A1-402[»]
    4XH5X-ray2.11A4-397[»]
    ProteinModelPortaliO06961.
    SMRiO06961. Positions 4-397.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO06961.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the acetokinase family. TdcD subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105C6H. Bacteria.
    COG0282. LUCA.
    HOGENOMiHOG000288399.
    KOiK00932.
    OMAiTDEDLMI.
    OrthoDBiEOG69975F.
    PhylomeDBiO06961.

    Family and domain databases

    HAMAPiMF_00020. Acetate_kinase.
    MF_01881. Propion_kin_subfam1.
    InterProiIPR004372. Ac/propionate_kinase.
    IPR000890. Aliphatic_acid_kin_short-chain.
    IPR023865. Aliphatic_acid_kinase_CS.
    IPR024917. Propionate_kinase.
    [Graphical view]
    PANTHERiPTHR21060. PTHR21060. 1 hit.
    PfamiPF00871. Acetate_kinase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000722. Acetate_prop_kin. 1 hit.
    PRINTSiPR00471. ACETATEKNASE.
    TIGRFAMsiTIGR00016. ackA. 1 hit.
    PROSITEiPS01075. ACETATE_KINASE_1. 1 hit.
    PS01076. ACETATE_KINASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O06961-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNEFPVVLVI NCGSSSIKFS VLDVATCDVL MAGIADGMNT ENAFLSINGD
    60 70 80 90 100
    KPINLAHSNY EDALKAIAFE LEKRDLTDSV ALIGHRIAHG GELFTQSVII
    110 120 130 140 150
    TDEIIDNIRR VSPLAPLHNY ANLSGIDAAR HLFPAVRQVA VFDTSFHQTL
    160 170 180 190 200
    APEAYLYGLP WEYFSSLGVR RYGFHGTSHR YVSRRAYELL DLDEKDSGLI
    210 220 230 240 250
    VAHLGNGASI CAVRNGQSVD TSMGMTPLEG LMMGTRSGDV DFGAMAWIAK
    260 270 280 290 300
    ETGQTLSDLE RVVNKESGLL GISGLSSDLR VLEKAWHEGH ERARLAIKTF
    310 320 330 340 350
    VHRIARHIAG HAASLHRLDG IIFTGGIGEN SVLIRQLVIE HLGVLGLTLD
    360 370 380 390 400
    VEMNKQPNSH GERIISANPS QVICAVIPTN EEKMIALDAI HLGNVKAPVE

    FA
    Length:402
    Mass (Da):43,718
    Last modified:January 23, 2002 - v2
    Checksum:iEF387E43054FCAB3
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti135 – 1428AVRQVAVF → GRASGGGI in AAB53419 (PubMed:10498722).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U89718 Genomic DNA. Translation: AAB53419.1.
    AE006468 Genomic DNA. Translation: AAL22115.1.
    RefSeqiNP_462156.1. NC_003197.1.
    WP_001001853.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL22115; AAL22115; STM3242.
    GeneIDi1254765.
    KEGGistm:STM3242.
    PATRICi32385265. VBISalEnt20916_3438.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U89718 Genomic DNA. Translation: AAB53419.1.
    AE006468 Genomic DNA. Translation: AAL22115.1.
    RefSeqiNP_462156.1. NC_003197.1.
    WP_001001853.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1X3MX-ray2.20A2-402[»]
    1X3NX-ray2.30A2-402[»]
    2E1YX-ray2.60A2-402[»]
    2E1ZX-ray1.98A2-402[»]
    2E20X-ray2.40A2-402[»]
    4FWKX-ray2.80A2-402[»]
    4FWLX-ray2.40A2-397[»]
    4FWMX-ray2.95A2-397[»]
    4FWNX-ray3.00A2-402[»]
    4FWOX-ray2.90A2-402[»]
    4FWPX-ray2.50A2-402[»]
    4FWQX-ray2.65A2-402[»]
    4FWRX-ray3.00A2-402[»]
    4FWSX-ray2.69A2-402[»]
    4XH1X-ray2.00A2-397[»]
    4XH4X-ray1.80A1-402[»]
    4XH5X-ray2.11A4-397[»]
    ProteinModelPortaliO06961.
    SMRiO06961. Positions 4-397.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM3242.

    Proteomic databases

    PaxDbiO06961.
    PRIDEiO06961.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL22115; AAL22115; STM3242.
    GeneIDi1254765.
    KEGGistm:STM3242.
    PATRICi32385265. VBISalEnt20916_3438.

    Phylogenomic databases

    eggNOGiENOG4105C6H. Bacteria.
    COG0282. LUCA.
    HOGENOMiHOG000288399.
    KOiK00932.
    OMAiTDEDLMI.
    OrthoDBiEOG69975F.
    PhylomeDBiO06961.

    Enzyme and pathway databases

    UniPathwayiUPA00052; UER00510.
    BioCyciSENT99287:GCTI-3262-MONOMER.
    BRENDAi2.7.2.15. 5542.

    Miscellaneous databases

    EvolutionaryTraceiO06961.

    Family and domain databases

    HAMAPiMF_00020. Acetate_kinase.
    MF_01881. Propion_kin_subfam1.
    InterProiIPR004372. Ac/propionate_kinase.
    IPR000890. Aliphatic_acid_kin_short-chain.
    IPR023865. Aliphatic_acid_kinase_CS.
    IPR024917. Propionate_kinase.
    [Graphical view]
    PANTHERiPTHR21060. PTHR21060. 1 hit.
    PfamiPF00871. Acetate_kinase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000722. Acetate_prop_kin. 1 hit.
    PRINTSiPR00471. ACETATEKNASE.
    TIGRFAMsiTIGR00016. ackA. 1 hit.
    PROSITEiPS01075. ACETATE_KINASE_1. 1 hit.
    PS01076. ACETATE_KINASE_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Characterization of a group of anaerobically induced, fnr-dependent genes of Salmonella typhimurium."
      Wei Y., Miller C.G.
      J. Bacteriol. 181:6092-6097(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: LT2.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    3. "Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily."
      Simanshu D.K., Savithri H.S., Murthy M.R.
      J. Mol. Biol. 352:876-892(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH ATP ANALOGS, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
    4. "Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity."
      Simanshu D.K., Savithri H.S., Murthy M.R.
      Proteins 70:1379-1388(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEXES WITH ATP ANALOGS.

    Entry informationi

    Entry nameiTDCD_SALTY
    AccessioniPrimary (citable) accession number: O06961
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: January 23, 2002
    Last modified: May 11, 2016
    This is version 113 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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.