PDP_DIACA
ID PDP_DIACA Reviewed; 318 AA.
AC Q05957;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=Petal death protein {ECO:0000303|PubMed:16342929};
DE EC=3.7.1.1 {ECO:0000269|PubMed:16342929};
DE AltName: Full=(R)-2-methylmalate lyase {ECO:0000305|PubMed:16342929};
DE Short=D-citramalate lyase {ECO:0000305};
DE EC=4.1.3.- {ECO:0000269|PubMed:16342929};
DE AltName: Full=Oxalacetic hydrolase {ECO:0000305};
DE AltName: Full=PSR132 {ECO:0000303|PubMed:8393719};
DE Flags: Precursor;
GN Name=PDP {ECO:0000303|PubMed:16342929};
OS Dianthus caryophyllus (Carnation) (Clove pink).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC Caryophyllales; Caryophyllaceae; Caryophylleae; Dianthus.
OX NCBI_TaxID=3570;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], INDUCTION BY ETHYLENE, AND TISSUE SPECIFICITY.
RC STRAIN=cv. White Sim; TISSUE=Petal;
RX PubMed=8393719; DOI=10.1007/bf00047414;
RA Wang H., Brandt A.S., Woodson W.R.;
RT "A flower senescence-related mRNA from carnation encodes a novel protein
RT related to enzymes involved in phosphonate biosynthesis.";
RL Plant Mol. Biol. 22:719-724(1993).
RN [2]
RP PROTEIN SEQUENCE OF 4-14, MUTAGENESIS OF ASP-79 AND CYS-144, PROPEPTIDE,
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND CATALYTIC ACTIVITY.
RX PubMed=16342929; DOI=10.1021/bi051776l;
RA Lu Z., Feng X., Song L., Han Y., Kim A., Herzberg O., Woodson W.R.,
RA Martin B.M., Mariano P.S., Dunaway-Mariano D.;
RT "Diversity of function in the isocitrate lyase enzyme superfamily: the
RT Dianthus caryophyllus petal death protein cleaves alpha-keto and alpha-
RT hydroxycarboxylic acids.";
RL Biochemistry 44:16365-16376(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH MAGNESIUM ION, AND
RP DIMERIZATION.
RX PubMed=16342930; DOI=10.1021/bi051779y;
RA Teplyakov A., Liu S., Lu Z., Howard A., Dunaway-Mariano D., Herzberg O.;
RT "Crystal structure of the petal death protein from carnation flower.";
RL Biochemistry 44:16377-16384(2005).
CC -!- FUNCTION: Catalyzes cleavage of the C(2)-C(3) bond in oxaloacetate and
CC in (2R)-alkyl malate derivatives to form oxalate and acetate, and alkyl
CC carboxylates and R-ketocarboxylates, respectively.
CC {ECO:0000269|PubMed:16342929}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + oxaloacetate = acetate + H(+) + oxalate;
CC Xref=Rhea:RHEA:24432, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16452, ChEBI:CHEBI:30089, ChEBI:CHEBI:30623; EC=3.7.1.1;
CC Evidence={ECO:0000269|PubMed:16342929};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16342929};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:16342929};
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:16342929};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:16342929};
CC Note=Binds 1 Mg(2+) ion per subunit. Can bind other divalent cations
CC such as Mn(2+), Fe(2+) and Co(2+). {ECO:0000269|PubMed:16342929};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=290 uM for (R)-citramalate (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC KM=130 uM for oxaloacetate (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC KM=42 uM for (2R,3S)-isocitrate (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC KM=104 uM for (2R,3R:2S,3S)-2-methyl isocitrate (at pH 7.5 and 25
CC degrees Celsius) {ECO:0000269|PubMed:16342929};
CC KM=69 uM for (2R,3S:2S,3R)-2-methyl isocitrate (at pH 7.5 and 25
CC degrees Celsius) {ECO:0000269|PubMed:16342929};
CC KM=1100 uM for (2R)-2-ethyl malate (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC KM=26 uM for (2R,3S)-2,3-dimethyl malate (at pH 7.5 and 25 degrees
CC Celsius) {ECO:0000269|PubMed:16342929};
CC KM=450 uM for (2R)-ethyl-(3S)-methyl malate (at pH 7.5 and 25 degrees
CC Celsius) {ECO:0000269|PubMed:16342929};
CC KM=98 uM for (2R)-propyl-(3S)-methyl malate (at pH 7.5 and 25 degrees
CC Celsius) {ECO:0000269|PubMed:16342929};
CC KM=8000 uM for (2R)-isobutyl-(3S)-methyl malate (at pH 7.5 and 25
CC degrees Celsius) {ECO:0000269|PubMed:16342929};
CC KM=19 uM for magnesium ion (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC KM=0.7 uM for manganese ion (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC KM=2 uM for cobalt ion (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC KM=6 uM for iron ion (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:16342929};
CC pH dependence:
CC Optimum pH is 7.0. {ECO:0000269|PubMed:16342929};
CC -!- SUBUNIT: Homodimer and homotetramer formed by a dimer of homodimer.
CC {ECO:0000269|PubMed:16342930}.
CC -!- TISSUE SPECIFICITY: Accumulates in senescing flower petals.
CC {ECO:0000269|PubMed:8393719}.
CC -!- INDUCTION: By ethylene. {ECO:0000269|PubMed:8393719}.
CC -!- SIMILARITY: Belongs to the isocitrate lyase/PEP mutase superfamily.
CC {ECO:0000305}.
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DR EMBL; L11598; AAA02862.1; -; mRNA.
DR PIR; S35145; S35145.
DR PDB; 1ZLP; X-ray; 2.70 A; A/B=1-318.
DR PDBsum; 1ZLP; -.
DR AlphaFoldDB; Q05957; -.
DR SMR; Q05957; -.
DR BRENDA; 4.1.3.1; 1925.
DR EvolutionaryTrace; Q05957; -.
DR GO; GO:0047776; F:citramalate lyase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030603; F:oxaloacetase activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR GO; GO:0006107; P:oxaloacetate metabolic process; IDA:UniProtKB.
DR CDD; cd00377; ICL_PEPM; 1.
DR Gene3D; 3.20.20.60; -; 1.
DR InterPro; IPR039556; ICL/PEPM.
DR InterPro; IPR018523; Isocitrate_lyase_ph_CS.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR SUPFAM; SSF51621; SSF51621; 1.
DR PROSITE; PS00161; ISOCITRATE_LYASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Lyase; Magnesium;
KW Metal-binding; Transferase.
FT PROPEP 1..3
FT /note="Removed in mature form"
FT /evidence="ECO:0000269|PubMed:16342929"
FT /id="PRO_0000316098"
FT CHAIN 4..318
FT /note="Petal death protein"
FT /id="PRO_0000068823"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 107
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16342930,
FT ECO:0007744|PDB:1ZLP"
FT BINDING 109
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16342930,
FT ECO:0007744|PDB:1ZLP"
FT BINDING 142
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:16342930,
FT ECO:0007744|PDB:1ZLP"
FT MUTAGEN 79
FT /note="D->A: Reduces catalytic efficiency 1000-fold."
FT /evidence="ECO:0000269|PubMed:16342929"
FT MUTAGEN 144
FT /note="C->A: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:16342929"
FT HELIX 30..37
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 38..46
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 49..57
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 61..65
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 67..73
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 85..98
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 99..107
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 115..127
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 145..148
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 155..169
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 175..180
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 183..200
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 204..208
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 214..223
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 226..232
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 236..238
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 243..249
FT /evidence="ECO:0007829|PDB:1ZLP"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 259..278
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 285..287
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 291..298
FT /evidence="ECO:0007829|PDB:1ZLP"
FT HELIX 300..309
FT /evidence="ECO:0007829|PDB:1ZLP"
SQ SEQUENCE 318 AA; 34180 MW; E8051FE337DA8A14 CRC64;
MAPPNGTTNG ETEVATQGSY TAVSTGRKTT MHRLIEEHGS VLMPGVQDAL SAAVVEKTGF
HAAFVSGYSV SAAMLGLPDF GLLTTTEVVE ATRRITAAAP NLCVVVDGDT GGGGPLNVQR
FIRELISAGA KGVFLEDQVW PKKCGHMRGK AVVPAEEHAL KIAAAREAIG DSDFFLVART
DARAPHGLEE GIRRANLYKE AGADATFVEA PANVDELKEV SAKTKGLRIA NMIEGGKTPL
HTPEEFKEMG FHLIAHSLTA VYATARALVN IMKILKEKGT TRDDLDQMAT FSEFNELISL
ESWYEMESKF KNFTPKAT
