PSD2_ORYSJ
ID PSD2_ORYSJ Reviewed; 624 AA.
AC Q5JN42; Q0JFV3; Q5JN41;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 17-FEB-2016, sequence version 3.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Phosphatidylserine decarboxylase proenzyme 2 {ECO:0000255|HAMAP-Rule:MF_03209};
DE EC=4.1.1.65 {ECO:0000255|HAMAP-Rule:MF_03209};
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 2 beta chain {ECO:0000255|HAMAP-Rule:MF_03209};
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 2 alpha chain {ECO:0000255|HAMAP-Rule:MF_03209};
GN Name=PSD2 {ECO:0000255|HAMAP-Rule:MF_03209};
GN OrderedLocusNames=Os01g0959800, LOC_Os01g72940; ORFNames=P0401G10.19;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
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 {ECO:0000255|HAMAP-Rule:MF_03209}.
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:0000250|UniProtKB:F4KAK5};
CC Peripheral membrane protein {ECO:0000250|UniProtKB:F4KAK5}. Endoplasmic
CC reticulum membrane {ECO:0000250|UniProtKB:A4GNA8}; Peripheral membrane
CC protein {ECO:0000250|UniProtKB:A4GNA8}.
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 -!- 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=BAD87120.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes.; Evidence={ECO:0000305};
CC Sequence=BAD87121.1; Type=Erroneous gene model prediction; Note=Was originally thought to correspond to two different genes.; Evidence={ECO:0000305};
CC Sequence=BAF07375.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP003238; BAD87120.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP003238; BAD87121.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008207; BAF07375.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR AlphaFoldDB; Q5JN42; -.
DR SMR; Q5JN42; -.
DR STRING; 4530.OS01T0959800-01; -.
DR PRIDE; Q5JN42; -.
DR eggNOG; KOG2419; Eukaryota.
DR InParanoid; Q5JN42; -.
DR PlantReactome; R-OSA-1119402; Phospholipid biosynthesis I.
DR UniPathway; UPA00558; UER00616.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005774; C:vacuolar membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0004609; F:phosphatidylserine decarboxylase activity; IBA:GO_Central.
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 HAMAP; MF_00663; PS_decarb_PSD_B_type2; 1.
DR InterPro; IPR000008; C2_dom.
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; PF13499; EF-hand_7; 1.
DR Pfam; PF02666; PS_Dcarbxylase; 1.
DR SMART; SM00054; EFh; 2.
DR SUPFAM; SSF47473; SSF47473; 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 3: Inferred from homology;
KW Calcium; Decarboxylase; Endoplasmic reticulum; Lipid biosynthesis;
KW Lipid metabolism; Lyase; Membrane; Metal-binding;
KW Phospholipid biosynthesis; Phospholipid metabolism; Pyruvate;
KW Reference proteome; Repeat; Vacuole; Zymogen.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:A4GNA8"
FT CHAIN 2..624
FT /note="Phosphatidylserine decarboxylase proenzyme 2"
FT /id="PRO_0000429523"
FT CHAIN 2..568
FT /note="Phosphatidylserine decarboxylase 2 beta chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000429524"
FT CHAIN 569..624
FT /note="Phosphatidylserine decarboxylase 2 alpha chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000429525"
FT DOMAIN 16..129
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 156..191
FT /note="EF-hand 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT DOMAIN 192..227
FT /note="EF-hand 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 425
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 481
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 569
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 569
FT /note="Schiff-base intermediate with substrate; via pyruvic
FT acid; for decarboxylase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 169
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 171
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 173
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 175
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 180
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 205
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 207
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 209
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 216
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT SITE 568..569
FT /note="Cleavage (non-hydrolytic); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT MOD_RES 569
FT /note="Pyruvic acid (Ser); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
SQ SEQUENCE 624 AA; 69055 MW; F1540411747C072D CRC64;
MGHSPSRHNA CGGGGGDGES PPSPLPSRFE RFRRRLRLRH RDRAGRPGGD AHASESGTGR
AIAVDEFAGI ARIRIVKEKK VVVETNGPHI ARISVFETNR FSKNTLVGYC EVDLFELLTK
DLDEHSEVLS LLDPSSSATI VGSISISCYI EDPVETEQSF ARRVLAIVDY NEDGELSLSE
FSDLMKAFGN KLAVAKIEEL FRQADKNGDG IVDMDELAAL LANQQEKEPL ISNCPVCGEI
LGKHDKINDM IHMTLCFDEG TGNQIMTGGF LTDKQASYGW MFKLSEWAHF SSYDVGLHSG
STASHILVFD RRTKRLVEEV IDGKIVLSMR ALYQSKVGLT LIDTGVKDLL KNLSEKQGKK
MSSPESAKDI PKFLELFKDQ INLDEVKDPL ESFKTFNEFF VRQLKPGARP IACYEQDTIA
TCAADSRLMT FSSVDESTRL WIKGRKFSIE GLLGKDVHSD ALCNGSLVIF RLAPQDYHRF
HVPVSGTLEK FVEIPGCLYT VNPIAVNSKY CNVFTENKRV VSIISTSEFG KVAFVAIGAT
MVGSIEFLKE EGDYVHKGDE FGYFAFGGST VICVFEKDAI EFDADLLANS ARSLETLVSV
GMRLGVSTRN RDLQPQELEK CSLE
