PSD2_ARATH
ID PSD2_ARATH Reviewed; 635 AA.
AC F4KAK5; A4GNA9; Q9LU67;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=Phosphatidylserine decarboxylase proenzyme 2;
DE EC=4.1.1.65 {ECO:0000255|HAMAP-Rule:MF_03209};
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 2 beta chain;
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 2 alpha chain;
GN Name=PSD2; OrderedLocusNames=At5g57190; ORFNames=MUL3.14;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=17449644; DOI=10.1104/pp.107.095414;
RA Nerlich A., von Orlow M., Rontein D., Hanson A.D., Dormann P.;
RT "Deficiency in phosphatidylserine decarboxylase activity in the psd1 psd2
RT psd3 triple mutant of Arabidopsis affects phosphatidylethanolamine
RT accumulation in mitochondria.";
RL Plant Physiol. 144:904-914(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
CC -!- FUNCTION: Catalyzes the formation of phosphatidylethanolamine (PtdEtn)
CC from phosphatidylserine (PtdSer). Plays a central role in phospholipid
CC metabolism and in the interorganelle trafficking of phosphatidylserine.
CC Contributes only to a minor proportion of PtdEtn production.
CC {ECO:0000255|HAMAP-Rule:MF_03209, ECO:0000269|PubMed:17449644}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-
CC diacyl-sn-glycero-3-phosphoethanolamine + CO2; Xref=Rhea:RHEA:20828,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57262,
CC ChEBI:CHEBI:64612; EC=4.1.1.65; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03209};
CC -!- COFACTOR:
CC Name=pyruvate; Xref=ChEBI:CHEBI:15361;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03209};
CC Note=Binds 1 pyruvoyl group covalently per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03209};
CC -!- PATHWAY: Phospholipid metabolism; phosphatidylethanolamine
CC biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step
CC 2/2. {ECO:0000255|HAMAP-Rule:MF_03209}.
CC -!- SUBUNIT: Heterodimer of a large membrane-associated beta subunit and a
CC small pyruvoyl-containing alpha subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03209}.
CC -!- SUBCELLULAR LOCATION: Vacuole membrane {ECO:0000305|PubMed:17449644};
CC Peripheral membrane protein {ECO:0000305|PubMed:17449644}.
CC Note=Tonoplast.
CC -!- TISSUE SPECIFICITY: Highly expressed in flowers and at lower levels in
CC leaves. {ECO:0000269|PubMed:17449644}.
CC -!- DOMAIN: The C2 domains have an essential, but non-catalytic function.
CC They may facilitate interactions with other proteins and are required
CC for lipid transport function. {ECO:0000255|HAMAP-Rule:MF_03209}.
CC -!- PTM: Is synthesized initially as an inactive proenzyme. Formation of
CC the active enzyme involves a self-maturation process in which the
CC active site pyruvoyl group is generated from an internal serine residue
CC via an autocatalytic post-translational modification. Two non-identical
CC subunits are generated from the proenzyme in this reaction, and the
CC pyruvate is formed at the N-terminus of the alpha chain, which is
CC derived from the carboxyl end of the proenzyme. The autoendoproteolytic
CC cleavage occurs by a canonical serine protease mechanism, in which the
CC side chain hydroxyl group of the serine supplies its oxygen atom to
CC form the C-terminus of the beta chain, while the remainder of the
CC serine residue undergoes an oxidative deamination to produce ammonia
CC and the pyruvoyl prosthetic group on the alpha chain. During this
CC reaction, the Ser that is part of the protease active site of the
CC proenzyme becomes the pyruvoyl prosthetic group, which constitutes an
CC essential element of the active site of the mature decarboxylase.
CC {ECO:0000255|HAMAP-Rule:MF_03209}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:17449644}.
CC -!- SIMILARITY: Belongs to the phosphatidylserine decarboxylase family.
CC PSD-B subfamily. Eukaryotic type II sub-subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_03209}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABO26298.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAA97369.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; EF203902; ABO26298.1; ALT_INIT; mRNA.
DR EMBL; AB023042; BAA97369.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED96864.1; -; Genomic_DNA.
DR RefSeq; NP_200529.4; NM_125101.5.
DR AlphaFoldDB; F4KAK5; -.
DR SMR; F4KAK5; -.
DR STRING; 3702.AT5G57190.1; -.
DR PaxDb; F4KAK5; -.
DR PRIDE; F4KAK5; -.
DR ProteomicsDB; 226061; -.
DR EnsemblPlants; AT5G57190.1; AT5G57190.1; AT5G57190.
DR GeneID; 835825; -.
DR Gramene; AT5G57190.1; AT5G57190.1; AT5G57190.
DR KEGG; ath:AT5G57190; -.
DR Araport; AT5G57190; -.
DR TAIR; locus:2175574; AT5G57190.
DR eggNOG; KOG2419; Eukaryota.
DR HOGENOM; CLU_034900_0_0_1; -.
DR InParanoid; F4KAK5; -.
DR OrthoDB; 707062at2759; -.
DR BioCyc; ARA:AT5G57190-MON; -.
DR BioCyc; MetaCyc:AT5G57190-MON; -.
DR BRENDA; 4.1.1.65; 399.
DR UniPathway; UPA00558; UER00616.
DR PRO; PR:F4KAK5; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; F4KAK5; baseline and differential.
DR Genevisible; F4KAK5; AT.
DR GO; GO:0009705; C:plant-type vacuole membrane; IDA:TAIR.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0004609; F:phosphatidylserine decarboxylase activity; IDA:TAIR.
DR GO; GO:0006646; P:phosphatidylethanolamine biosynthetic process; IBA:GO_Central.
DR GO; GO:0016540; P:protein autoprocessing; IEA:UniProtKB-UniRule.
DR CDD; cd00051; EFh; 1.
DR Gene3D; 2.60.40.150; -; 1.
DR HAMAP; MF_00663; PS_decarb_PSD_B_type2; 1.
DR InterPro; IPR000008; C2_dom.
DR InterPro; IPR035892; C2_domain_sf.
DR InterPro; IPR011992; EF-hand-dom_pair.
DR InterPro; IPR018247; EF_Hand_1_Ca_BS.
DR InterPro; IPR002048; EF_hand_dom.
DR InterPro; IPR003817; PS_Dcarbxylase.
DR InterPro; IPR033177; PSD.
DR InterPro; IPR033179; PSD_type2_pro.
DR PANTHER; PTHR10067; PTHR10067; 1.
DR Pfam; PF00168; C2; 1.
DR Pfam; PF13833; EF-hand_8; 1.
DR Pfam; PF02666; PS_Dcarbxylase; 1.
DR SMART; SM00054; EFh; 2.
DR SUPFAM; SSF47473; SSF47473; 1.
DR SUPFAM; SSF49562; SSF49562; 1.
DR TIGRFAMs; TIGR00163; PS_decarb; 1.
DR PROSITE; PS50004; C2; 1.
DR PROSITE; PS00018; EF_HAND_1; 2.
DR PROSITE; PS50222; EF_HAND_2; 2.
PE 2: Evidence at transcript level;
KW Calcium; Decarboxylase; Lipid biosynthesis; Lipid metabolism; Lyase;
KW Membrane; Metal-binding; Phospholipid biosynthesis;
KW Phospholipid metabolism; Pyruvate; Reference proteome; Repeat; Vacuole;
KW Zymogen.
FT CHAIN 1..635
FT /note="Phosphatidylserine decarboxylase proenzyme 2"
FT /id="PRO_0000429514"
FT CHAIN 1..586
FT /note="Phosphatidylserine decarboxylase 2 beta chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000429515"
FT CHAIN 587..635
FT /note="Phosphatidylserine decarboxylase 2 alpha chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000429516"
FT DOMAIN 20..146
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 174..209
FT /note="EF-hand 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT DOMAIN 210..245
FT /note="EF-hand 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 443
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 499
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 587
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 587
FT /note="Schiff-base intermediate with substrate; via pyruvic
FT acid; for decarboxylase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 187
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 189
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 191
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 193
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 198
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 223
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 225
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 227
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 234
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT SITE 586..587
FT /note="Cleavage (non-hydrolytic); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT MOD_RES 587
FT /note="Pyruvic acid (Ser); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT CONFLICT 397
FT /note="D -> G (in Ref. 1; ABO26298)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 635 AA; 71000 MW; FFDDA6408A793DAF CRC64;
MGNGNSREAK ESRRSRLRHK LQKFRIHRRH LRSSRNSAGM VIQRTVSAED FSGIALLTLI
GAEMKFKDKW LACVSFGEQT FRTEISDTTQ KPIWNSEKKL LLEKNGPSLA RVSVFETNRV
ARNKIIGYCE LDIFDFVVQE PESTCKSFNL LDPTSSNVVG SIFLSCAIED PVETERRFAK
RILSIVDYNE DGQLSFSEFS DLIKAFGNLV AANKKEELFK AADLNGDGVV TIDELAALLA
LQQEQEPIIN NCPVCGEALQ VSDKLNAMIH MTLCFDEGTG NQVMTGGFLT DRQASYGWMF
KLSEWTHLST YDVGLNTGSS ASYIVVIDRK SKRLVEELID SKIVLSMRAI YQSKIGLRLM
DQGAKEILQR LSEKQGKKMS SVESAQKIPR FLEFFKDQIN MAEVKYPLQH FKTFNEFFIR
ELKPGARPIA CMNRNDVAVC AADCRLMAFQ SVEDSTRFWI KGKKFSIRGL LGKNVNPNAF
LDGSLVIFRL APQDYHRFHV PVSGVIEQFV DVSGSLYTVN PIAVNSKYCN VFTENKRTVA
IISTAEFGKV AFVAIGATMV GSINFVRKEG EHVKKGDELG YFSFGGSTVI CVFEKDAIGI
DNDLLVNSGR SLETLVSVGM QLGVSTRTFA RSTLI
