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Protein

Pheophorbidase

Gene

PPD

Organism
Raphanus sativus (Radish)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in chlorophyll degradation. Specific for the pheophorbides of the dihydroporphyrin and tetrahydroporphyrin types. Chlorophyllide a, pheophytin a and the nonfluorescent chlorophyll catabolite (NCC) are not used as substrates.

Catalytic activityi

Pheophorbide a + H2O = pyropheophorbide a + methanol + CO2.3 Publications

Enzyme regulationi

Inhibited by methanol and phenylmethylsulfonicfluoride (PMSF).

Kineticsi

  1. KM=15.1 µM for pheophorbide a (for the native enzyme)2 Publications
  2. KM=95.5 µM for pheophorbide a (for the PPD-GST recombinant enzyme)2 Publications
  3. KM=240 µM for pheophorbide b (for the native enzyme)2 Publications
  4. KM=40 µM for bacterio-pheophorbide a (for the native enzyme)2 Publications

    pH dependencei

    Optimum pH is 6.5 for the native enzyme and 7.0-7.5 for the PPD-GST recombinant enzyme.2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei88Acyl-ester intermediateBy similarity1
    Active sitei212Charge relay systemPROSITE-ProRule annotation1
    Active sitei240Charge relay systemPROSITE-ProRule annotation1

    GO - Molecular functioni

    • carboxylic ester hydrolase activity Source: UniProtKB
    • pheophoridase activity Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    • chlorophyll a catabolic process Source: UniProtKB
    • demethylation Source: UniProtKB
    • leaf senescence Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Chlorophyll catabolism

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14131.

    Protein family/group databases

    ESTHERirapsa-q2v0w1. Hydroxynitrile_lyase.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pheophorbidase (EC:3.1.1.82)
    Short name:
    RsPPD
    Gene namesi
    Name:PPD
    OrganismiRaphanus sativus (Radish)
    Taxonomic identifieri3726 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeBrassiceaeRaphanus

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00003913501 – 263PheophorbidaseAdd BLAST263

    Expressioni

    Inductioni

    Up-regulated by senescence.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Structurei

    3D structure databases

    ProteinModelPortaliQ2V0W1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini13 – 244AB hydrolase-1Sequence analysisAdd BLAST232

    Sequence similaritiesi

    Belongs to the AB hydrolase superfamily.Curated

    Phylogenomic databases

    KOiK13544.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    [Graphical view]
    PfamiPF00561. Abhydrolase_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53474. SSF53474. 1 hit.
    PROSITEiPS00120. LIPASE_SER. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q2V0W1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MGGEGGADDS VVHFVFVHGA SHGAWCWYKL TTLLVAAGFK ATSVDLTGAG
    60 70 80 90 100
    INLTDSNTVF DFDHYNRPLF SLLSDLPSHH KIVLVGHSIG GGSVTEALCK
    110 120 130 140 150
    FTDKISMVVY LAADMVQPGS TSSTHDSIMT VGEEDIWEYI YGEGADKPPT
    160 170 180 190 200
    GVLMKEEFRR HYYYSQSPLE DVSLASKLLR PAPVRALGGA DKLSPNPEAE
    210 220 230 240 250
    KVPRVYIKTA KDNLFDPLRQ DRLVEKWPPS QLYILEESDH SAFFSVPTTL
    260
    FAYLLRAVSF LQL
    Length:263
    Mass (Da):28,974
    Last modified:January 24, 2006 - v1
    Checksum:iC375CE13930E1FA1
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB218276 mRNA. Translation: BAE54383.1.

    Genome annotation databases

    KEGGiag:BAE54383.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB218276 mRNA. Translation: BAE54383.1.

    3D structure databases

    ProteinModelPortaliQ2V0W1.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    ESTHERirapsa-q2v0w1. Hydroxynitrile_lyase.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:BAE54383.

    Phylogenomic databases

    KOiK13544.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14131.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    [Graphical view]
    PfamiPF00561. Abhydrolase_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53474. SSF53474. 1 hit.
    PROSITEiPS00120. LIPASE_SER. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPPD_RAPSA
    AccessioniPrimary (citable) accession number: Q2V0W1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 9, 2010
    Last sequence update: January 24, 2006
    Last modified: November 2, 2016
    This is version 49 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    An additional type 1 isoform with the same enzymatic activity seems to exist.

    Keywords - Technical termi

    Direct protein sequencing

    Documents

    1. 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.