PPD_RAPSA
ID PPD_RAPSA Reviewed; 263 AA.
AC Q2V0W1;
DT 09-FEB-2010, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 64.
DE RecName: Full=Pheophorbidase;
DE Short=RsPPD;
DE EC=3.1.1.82;
GN Name=PPD;
OS Raphanus sativus (Radish) (Raphanus raphanistrum var. sativus).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus.
OX NCBI_TaxID=3726;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 8-35 AND 133-163,
RP INDUCTION, SUBUNIT, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=16384908; DOI=10.1104/pp.105.071290;
RA Suzuki Y., Amano T., Shioi Y.;
RT "Characterization and cloning of the chlorophyll-degrading enzyme
RT pheophorbidase from cotyledons of radish.";
RL Plant Physiol. 140:716-725(2006).
RN [2]
RP IDENTIFICATION, CATALYTIC ACTIVITY, AND INHIBITION BY METHANOL AND PMSF.
RX PubMed=16228561; DOI=10.1023/a:1020919929608;
RA Suzuki Y., Doi M., Shioi Y.;
RT "Two enzymatic reaction pathways in the formation of pyropheophorbide a.";
RL Photosyn. Res. 74:225-233(2002).
RN [3]
RP CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=18846292; DOI=10.1039/b810271f;
RA Suzuki Y., Soga K., Yoshimatsu K., Shioi Y.;
RT "Expression and purification of pheophorbidase, an enzyme catalyzing the
RT formation of pyropheophorbide during chlorophyll degradation: comparison
RT with the native enzyme.";
RL Photochem. Photobiol. Sci. 7:1260-1266(2008).
CC -!- FUNCTION: Involved in chlorophyll degradation. Specific for the
CC pheophorbides of the dihydroporphyrin and tetrahydroporphyrin types.
CC Chlorophyllide a, pheophytin a and the nonfluorescent chlorophyll
CC catabolite (NCC) are not used as substrates.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + H2O + pheophorbide a = CO2 + methanol +
CC pyropheophorbide a; Xref=Rhea:RHEA:32483, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:17790,
CC ChEBI:CHEBI:58687, ChEBI:CHEBI:58742; EC=3.1.1.82;
CC Evidence={ECO:0000269|PubMed:16228561, ECO:0000269|PubMed:16384908,
CC ECO:0000269|PubMed:18846292};
CC -!- ACTIVITY REGULATION: Inhibited by methanol and
CC phenylmethylsulfonicfluoride (PMSF).
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15.1 uM for pheophorbide a (for the native enzyme)
CC {ECO:0000269|PubMed:16384908, ECO:0000269|PubMed:18846292};
CC KM=95.5 uM for pheophorbide a (for the PPD-GST recombinant enzyme)
CC {ECO:0000269|PubMed:16384908, ECO:0000269|PubMed:18846292};
CC KM=240 uM for pheophorbide b (for the native enzyme)
CC {ECO:0000269|PubMed:16384908, ECO:0000269|PubMed:18846292};
CC KM=40 uM for bacterio-pheophorbide a (for the native enzyme)
CC {ECO:0000269|PubMed:16384908, ECO:0000269|PubMed:18846292};
CC pH dependence:
CC Optimum pH is 6.5 for the native enzyme and 7.0-7.5 for the PPD-GST
CC recombinant enzyme. {ECO:0000269|PubMed:16384908,
CC ECO:0000269|PubMed:18846292};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16384908}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: Up-regulated by senescence. {ECO:0000269|PubMed:16384908}.
CC -!- MISCELLANEOUS: An additional type 1 isoform with the same enzymatic
CC activity seems to exist.
CC -!- SIMILARITY: Belongs to the AB hydrolase superfamily. {ECO:0000305}.
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DR EMBL; AB218276; BAE54383.1; -; mRNA.
DR AlphaFoldDB; Q2V0W1; -.
DR SMR; Q2V0W1; -.
DR ESTHER; rapsa-q2v0w1; Hydroxynitrile_lyase.
DR KEGG; ag:BAE54383; -.
DR BioCyc; MetaCyc:MON-14131; -.
DR Proteomes; UP000504610; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0052689; F:carboxylic ester hydrolase activity; IDA:UniProtKB.
DR GO; GO:0035560; F:pheophorbidase activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0033310; P:chlorophyll a catabolic process; IDA:UniProtKB.
DR GO; GO:0070988; P:demethylation; IDA:UniProtKB.
DR GO; GO:0010150; P:leaf senescence; IEP:UniProtKB.
DR Gene3D; 3.40.50.1820; -; 1.
DR InterPro; IPR029058; AB_hydrolase.
DR InterPro; IPR000073; AB_hydrolase_1.
DR InterPro; IPR045889; MES/HNL.
DR PANTHER; PTHR10992; PTHR10992; 1.
DR Pfam; PF12697; Abhydrolase_6; 1.
DR SUPFAM; SSF53474; SSF53474; 1.
DR PROSITE; PS00120; LIPASE_SER; 1.
PE 1: Evidence at protein level;
KW Chlorophyll catabolism; Cytoplasm; Direct protein sequencing; Hydrolase;
KW Reference proteome.
FT CHAIN 1..263
FT /note="Pheophorbidase"
FT /id="PRO_0000391350"
FT DOMAIN 13..244
FT /note="AB hydrolase-1"
FT /evidence="ECO:0000255"
FT ACT_SITE 88
FT /note="Acyl-ester intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 212
FT /note="Charge relay system"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10037"
FT ACT_SITE 240
FT /note="Charge relay system"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10037"
SQ SEQUENCE 263 AA; 28974 MW; C375CE13930E1FA1 CRC64;
MGGEGGADDS VVHFVFVHGA SHGAWCWYKL TTLLVAAGFK ATSVDLTGAG INLTDSNTVF
DFDHYNRPLF SLLSDLPSHH KIVLVGHSIG GGSVTEALCK FTDKISMVVY LAADMVQPGS
TSSTHDSIMT VGEEDIWEYI YGEGADKPPT GVLMKEEFRR HYYYSQSPLE DVSLASKLLR
PAPVRALGGA DKLSPNPEAE KVPRVYIKTA KDNLFDPLRQ DRLVEKWPPS QLYILEESDH
SAFFSVPTTL FAYLLRAVSF LQL
