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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)DescriptionActionsGraphical viewLength
    Metal bindingi11MagnesiumUniRule annotation1
    Binding sitei11ATP1
    Binding sitei18ATPUniRule annotation1
    Binding sitei86SubstrateUniRule annotation1
    Active sitei143Proton donor/acceptorUniRule annotation1
    Binding sitei175ATP1
    Sitei175Transition state stabilizerUniRule annotation1
    Sitei236Transition state stabilizerUniRule annotation1
    Metal bindingi381MagnesiumUniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi203 – 207ATP5
    Nucleotide bindingi278 – 280ATP3
    Nucleotide bindingi326 – 330ATPUniRule annotation5

    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

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001076561 – 402Propionate kinaseAdd BLAST402

    Proteomic databases

    PaxDbiO06961.
    PRIDEiO06961.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM3242.

    Structurei

    Secondary structure

    1402
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi6 – 12Combined sources7
    Beta strandi17 – 23Combined sources7
    Turni24 – 26Combined sources3
    Beta strandi29 – 37Combined sources9
    Beta strandi40 – 48Combined sources9
    Beta strandi53 – 57Combined sources5
    Helixi60 – 73Combined sources14
    Helixi77 – 79Combined sources3
    Beta strandi80 – 88Combined sources9
    Turni91 – 93Combined sources3
    Helixi102 – 111Combined sources10
    Helixi112 – 114Combined sources3
    Helixi116 – 132Combined sources17
    Beta strandi136 – 142Combined sources7
    Helixi145 – 149Combined sources5
    Helixi152 – 155Combined sources4
    Helixi161 – 167Combined sources7
    Helixi176 – 190Combined sources15
    Helixi194 – 196Combined sources3
    Beta strandi198 – 214Combined sources17
    Beta strandi217 – 222Combined sources6
    Beta strandi229 – 231Combined sources3
    Helixi242 – 252Combined sources11
    Helixi256 – 265Combined sources10
    Helixi268 – 273Combined sources6
    Helixi279 – 287Combined sources9
    Helixi291 – 312Combined sources22
    Beta strandi315 – 317Combined sources3
    Beta strandi320 – 324Combined sources5
    Helixi325 – 330Combined sources6
    Helixi332 – 340Combined sources9
    Helixi341 – 345Combined sources5
    Helixi351 – 355Combined sources5
    Helixi358 – 360Combined sources3
    Beta strandi362 – 364Combined sources3
    Beta strandi371 – 376Combined sources6
    Helixi381 – 392Combined sources12

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    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.
    OMAiMIAREVI.
    PhylomeDBiO06961.

    Family and domain databases

    HAMAPiMF_00020. Acetate_kinase. 1 hit.
    MF_01881. Propion_kin_subfam1. 1 hit.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti135 – 142AVRQVAVF → GRASGGGI in AAB53419 (PubMed:10498722).Curated8

    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
    PDB 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.
    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.
    OMAiMIAREVI.
    PhylomeDBiO06961.

    Enzyme and pathway databases

    UniPathwayiUPA00052; UER00510.
    BRENDAi2.7.2.15. 5542.

    Miscellaneous databases

    EvolutionaryTraceiO06961.

    Family and domain databases

    HAMAPiMF_00020. Acetate_kinase. 1 hit.
    MF_01881. Propion_kin_subfam1. 1 hit.
    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...

    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: November 2, 2016
    This is version 116 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.