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Protein

Petal death protein

Gene

PDP

Organism
Dianthus caryophyllus (Carnation) (Clove pink)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes cleavage of the C(2)-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)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi107 – 1071Magnesium
    Metal bindingi109 – 1091Magnesium
    Metal bindingi142 – 1421Magnesium

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Lyase, Transferase

    Keywords - Ligandi

    Magnesium, 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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesCaryophyllaceaeDianthus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi79 – 791D → A: Reduced catalytic activity. 1 Publication
    Mutagenesisi144 – 1441C → A: Loss of catalytic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Propeptidei1 – 33Removed in mature form1 PublicationPRO_0000316098
    Chaini4 – 318315Petal death proteinPRO_0000068823Add
    BLAST

    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

    1
    318
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi30 – 378Combined sources
    Beta strandi38 – 469Combined sources
    Helixi49 – 579Combined sources
    Beta strandi61 – 655Combined sources
    Helixi67 – 737Combined sources
    Beta strandi79 – 813Combined sources
    Helixi85 – 9814Combined sources
    Beta strandi99 – 1079Combined sources
    Beta strandi112 – 1143Combined sources
    Helixi115 – 12713Combined sources
    Beta strandi132 – 1365Combined sources
    Beta strandi145 – 1484Combined sources
    Helixi155 – 16915Combined sources
    Beta strandi175 – 1806Combined sources
    Helixi183 – 20018Combined sources
    Beta strandi204 – 2085Combined sources
    Helixi214 – 22310Combined sources
    Beta strandi226 – 2327Combined sources
    Beta strandi236 – 2383Combined sources
    Helixi243 – 2497Combined sources
    Beta strandi253 – 2564Combined sources
    Helixi259 – 27820Combined sources
    Helixi285 – 2873Combined sources
    Helixi291 – 2988Combined sources
    Helixi300 – 30910Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ZLPX-ray2.70A/B1-318[»]
    ProteinModelPortaliQ05957.
    SMRiQ05957. Positions 28-312.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ05957.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    InterProiIPR018523. Isocitrate_lyase_ph_CS.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
    [Graphical view]

    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.

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ZLPX-ray2.70A/B1-318[»]
    ProteinModelPortaliQ05957.
    SMRiQ05957. Positions 28-312.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    BRENDAi4.1.3.1. 1925.

    Miscellaneous databases

    EvolutionaryTraceiQ05957.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    InterProiIPR018523. Isocitrate_lyase_ph_CS.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    PROSITEiPS00161. ISOCITRATE_LYASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "A flower senescence-related mRNA from carnation encodes a novel protein related to enzymes involved in phosphonate biosynthesis."
      Wang H., Brandt A.S., Woodson W.R.
      Plant Mol. Biol. 22:719-724(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION BY ETHYLENE, TISSUE SPECIFICITY.
      Strain: cv. White Sim.
      Tissue: Petal.
    2. "Diversity of function in the isocitrate lyase enzyme superfamily: the Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-hydroxycarboxylic acids."
      Lu Z., Feng X., Song L., Han Y., Kim A., Herzberg O., Woodson W.R., Martin B.M., Mariano P.S., Dunaway-Mariano D.
      Biochemistry 44:16365-16376(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 4-14, MUTAGENESIS OF ASP-79 AND CYS-144, PROPEPTIDE, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, CATALYTIC ACTIVITY.
    3. "Crystal structure of the petal death protein from carnation flower."
      Teplyakov A., Liu S., Lu Z., Howard A., Dunaway-Mariano D., Herzberg O.
      Biochemistry 44:16377-16384(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH MAGNESIUM ION, DIMERIZATION.

    Entry informationi

    Entry nameiPDP_DIACA
    AccessioniPrimary (citable) accession number: Q05957
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 1996
    Last modified: October 14, 2015
    This is version 72 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.