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Protein

Petal death protein

Gene

PDP

Organism
Dianthus caryophyllus (Carnation) (Clove pink)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes cleavage of the C2-C3 bond in oxaloacetate and in (2R)-alkyl malate derivatives to form oxalate and acetate, and alkyl carboxylates and R-ketocarboxylates, respectively.1 Publication

Catalytic activityi

Oxaloacetate + H2O = oxalate + acetate.1 Publication
(3S)-citramalate = acetate + pyruvate.1 Publication

Cofactori

Mg2+1 Publication, Mn2+1 Publication, Fe2+1 Publication, Co2+1 PublicationNote: Binds 1 Mg2+ ion per subunit. Can bind other divalent cations such as Mn2+, Fe2+ and Co2+.1 Publication

Kineticsi

  1. KM=290 µM for (R)-citramalate (at pH 7.5 and 25 degrees Celsius)1 Publication
  2. KM=130 µM for oxaloacetate (at pH 7.5 and 25 degrees Celsius)1 Publication
  3. KM=42 µM for (2R,3S)-isocitrate (at pH 7.5 and 25 degrees Celsius)1 Publication
  4. KM=104 µM for (2R,3R:2S,3S)-2-methyl isocitrate (at pH 7.5 and 25 degrees Celsius)1 Publication
  5. KM=69 µM for (2R,3S:2S,3R)-2-methyl isocitrate (at pH 7.5 and 25 degrees Celsius)1 Publication
  6. KM=1100 µM for (2R)-2-ethyl malate (at pH 7.5 and 25 degrees Celsius)1 Publication
  7. KM=26 µM for (2R,3S)-2,3-dimethyl malate (at pH 7.5 and 25 degrees Celsius)1 Publication
  8. KM=450 µM for (2R)-ethyl-(3S)-methyl malate (at pH 7.5 and 25 degrees Celsius)1 Publication
  9. KM=98 µM for (2R)-propyl-(3S)-methyl malate (at pH 7.5 and 25 degrees Celsius)1 Publication
  10. KM=8000 µM for (2R)-isobutyl-(3S)-methyl malate (at pH 7.5 and 25 degrees Celsius)1 Publication
  11. KM=19 µM for magnesium ion (at pH 7.5 and 25 degrees Celsius)1 Publication
  12. KM=0.7 µM for manganese ion (at pH 7.5 and 25 degrees Celsius)1 Publication
  13. KM=2 µM for cobalt ion (at pH 7.5 and 25 degrees Celsius)1 Publication
  14. KM=6 µM for iron ion (at pH 7.5 and 25 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 7.0.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi107Magnesium1
    Metal bindingi109Magnesium1
    Metal bindingi142Magnesium1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionHydrolase, Lyase, Transferase
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BRENDAi4.1.3.1 1925

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Petal death protein (EC:3.7.1.1, EC:4.1.3.22)
    Alternative name(s):
    Citramalate lyase
    Oxalacetic hydrolase
    PSR132
    Gene namesi
    Name:PDP
    OrganismiDianthus caryophyllus (Carnation) (Clove pink)
    Taxonomic identifieri3570 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesCaryophyllaceaeCaryophylleaeDianthus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi79D → A: Reduced catalytic activity. 1 Publication1
    Mutagenesisi144C → A: Loss of catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    PropeptideiPRO_00003160981 – 3Removed in mature form1 Publication3
    ChainiPRO_00000688234 – 318Petal death proteinAdd BLAST315

    Proteomic databases

    PRIDEiQ05957

    Expressioni

    Tissue specificityi

    Accumulates in senescing flower petals.1 Publication

    Inductioni

    By ethylene.1 Publication

    Interactioni

    Subunit structurei

    Homodimer and homotetramer formed by a dimer of homodimer.1 Publication

    Structurei

    Secondary structure

    1318
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliQ05957
    SMRiQ05957
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ05957

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    InterProiView protein in InterPro
    IPR018523 Isocitrate_lyase_ph_CS
    IPR015813 Pyrv/PenolPyrv_Kinase-like_dom
    SUPFAMiSSF51621 SSF51621, 1 hit
    PROSITEiView protein in PROSITE
    PS00161 ISOCITRATE_LYASE, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q05957-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MAPPNGTTNG ETEVATQGSY TAVSTGRKTT MHRLIEEHGS VLMPGVQDAL
    60 70 80 90 100
    SAAVVEKTGF HAAFVSGYSV SAAMLGLPDF GLLTTTEVVE ATRRITAAAP
    110 120 130 140 150
    NLCVVVDGDT GGGGPLNVQR FIRELISAGA KGVFLEDQVW PKKCGHMRGK
    160 170 180 190 200
    AVVPAEEHAL KIAAAREAIG DSDFFLVART DARAPHGLEE GIRRANLYKE
    210 220 230 240 250
    AGADATFVEA PANVDELKEV SAKTKGLRIA NMIEGGKTPL HTPEEFKEMG
    260 270 280 290 300
    FHLIAHSLTA VYATARALVN IMKILKEKGT TRDDLDQMAT FSEFNELISL
    310
    ESWYEMESKF KNFTPKAT
    Length:318
    Mass (Da):34,180
    Last modified:November 1, 1996 - v1
    Checksum:iE8051FE337DA8A14
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L11598 mRNA Translation: AAA02862.1
    PIRiS35145

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L11598 mRNA Translation: AAA02862.1
    PIRiS35145

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ZLPX-ray2.70A/B1-318[»]
    ProteinModelPortaliQ05957
    SMRiQ05957
    ModBaseiSearch...
    MobiDBiSearch...

    Proteomic databases

    PRIDEiQ05957

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi4.1.3.1 1925

    Miscellaneous databases

    EvolutionaryTraceiQ05957

    Family and domain databases

    InterProiView protein in InterPro
    IPR018523 Isocitrate_lyase_ph_CS
    IPR015813 Pyrv/PenolPyrv_Kinase-like_dom
    SUPFAMiSSF51621 SSF51621, 1 hit
    PROSITEiView protein in PROSITE
    PS00161 ISOCITRATE_LYASE, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPDP_DIACA
    AccessioniPrimary (citable) accession number: Q05957
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 1996
    Last modified: May 23, 2018
    This is version 78 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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