PSD2_KOMPG
ID PSD2_KOMPG Reviewed; 1010 AA.
AC C4R360;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 07-JUL-2009, sequence version 1.
DT 03-AUG-2022, entry version 72.
DE RecName: Full=Phosphatidylserine decarboxylase proenzyme 2 {ECO:0000255|HAMAP-Rule:MF_03209, ECO:0000303|PubMed:19656201};
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, ECO:0000303|PubMed:19656201};
GN OrderedLocusNames=PAS_chr3_1127;
OS Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) (Pichia pastoris).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Phaffomycetaceae; Komagataella.
OX NCBI_TaxID=644223;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GS115 / ATCC 20864;
RX PubMed=19465926; DOI=10.1038/nbt.1544;
RA De Schutter K., Lin Y.-C., Tiels P., Van Hecke A., Glinka S.,
RA Weber-Lehmann J., Rouze P., Van de Peer Y., Callewaert N.;
RT "Genome sequence of the recombinant protein production host Pichia
RT pastoris.";
RL Nat. Biotechnol. 27:561-566(2009).
RN [2]
RP FUNCTION.
RX PubMed=19656201; DOI=10.1111/j.1567-1364.2009.00544.x;
RA Wriessnegger T., Sunga A.J., Cregg J.M., Daum G.;
RT "Identification of phosphatidylserine decarboxylases 1 and 2 from Pichia
RT pastoris.";
RL FEMS Yeast Res. 9:911-922(2009).
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, ECO:0000269|PubMed:19656201}.
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 -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00041};
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. Interacts with pstB2. This
CC interaction may be a means to structurally tether the donor membrane
CC (ER) harboring PstB2 to acceptor membranes (Golgi/endosomes) harboring
CC PSD2 during PtdSer transport to the site of PtdEtn synthesis.
CC {ECO:0000255|HAMAP-Rule:MF_03209}.
CC -!- SUBCELLULAR LOCATION: Golgi apparatus membrane {ECO:0000255|HAMAP-
CC Rule:MF_03209}; Peripheral membrane protein {ECO:0000255|HAMAP-
CC Rule:MF_03209}; Cytoplasmic side {ECO:0000255|HAMAP-Rule:MF_03209}.
CC Endosome membrane {ECO:0000255|HAMAP-Rule:MF_03209}; Peripheral
CC membrane protein {ECO:0000255|HAMAP-Rule:MF_03209}; Cytoplasmic side
CC {ECO:0000255|HAMAP-Rule:MF_03209}.
CC -!- DOMAIN: The C2 domains have an essential, but non-catalytic function.
CC They may facilitate interaction with PstB2 and are required for lipid
CC 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 -!- SIMILARITY: Belongs to the phosphatidylserine decarboxylase family.
CC PSD-B subfamily. Eukaryotic type II sub-subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_03209}.
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DR EMBL; FN392321; CAY71194.1; -; Genomic_DNA.
DR RefSeq; XP_002493373.1; XM_002493328.1.
DR AlphaFoldDB; C4R360; -.
DR SMR; C4R360; -.
DR STRING; 644223.C4R360; -.
DR EnsemblFungi; CAY71194; CAY71194; PAS_chr3_1127.
DR GeneID; 8200159; -.
DR KEGG; ppa:PAS_chr3_1127; -.
DR eggNOG; KOG2419; Eukaryota.
DR HOGENOM; CLU_002661_0_0_1; -.
DR InParanoid; C4R360; -.
DR OMA; NMTRTSF; -.
DR UniPathway; UPA00558; UER00616.
DR Proteomes; UP000000314; Chromosome 3.
DR GO; GO:0010008; C:endosome membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0000139; C:Golgi membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005795; C:Golgi stack; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004609; F:phosphatidylserine decarboxylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006656; P:phosphatidylcholine biosynthetic process; IEA:EnsemblFungi.
DR GO; GO:0006646; P:phosphatidylethanolamine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0016540; P:protein autoprocessing; IEA:UniProtKB-UniRule.
DR Gene3D; 2.60.40.150; -; 2.
DR HAMAP; MF_00663; PS_decarb_PSD_B_type2; 1.
DR InterPro; IPR000008; C2_dom.
DR InterPro; IPR035892; C2_domain_sf.
DR InterPro; IPR003817; PS_Dcarbxylase.
DR InterPro; IPR033177; PSD.
DR InterPro; IPR033179; PSD_type2_pro.
DR PANTHER; PTHR10067; PTHR10067; 1.
DR Pfam; PF00168; C2; 2.
DR Pfam; PF02666; PS_Dcarbxylase; 1.
DR SMART; SM00239; C2; 2.
DR SUPFAM; SSF49562; SSF49562; 2.
DR TIGRFAMs; TIGR00163; PS_decarb; 1.
DR PROSITE; PS50004; C2; 2.
PE 3: Inferred from homology;
KW Calcium; Decarboxylase; Endosome; Golgi apparatus; Lipid biosynthesis;
KW Lipid metabolism; Lyase; Membrane; Metal-binding;
KW Phospholipid biosynthesis; Phospholipid metabolism; Pyruvate;
KW Reference proteome; Repeat; Zymogen.
FT CHAIN 1..1010
FT /note="Phosphatidylserine decarboxylase proenzyme 2"
FT /id="PRO_0000435597"
FT CHAIN 1..879
FT /note="Phosphatidylserine decarboxylase 2 beta chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000435598"
FT CHAIN 880..1010
FT /note="Phosphatidylserine decarboxylase 2 alpha chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000435599"
FT DOMAIN 1..114
FT /note="C2 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 247..370
FT /note="C2 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 458..493
FT /note="EF-hand"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 734
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 793
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 880
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 880
FT /note="Schiff-base intermediate with substrate; via pyruvic
FT acid; for decarboxylase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 342
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT BINDING 345
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT BINDING 348
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT SITE 879..880
FT /note="Cleavage (non-hydrolytic); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT MOD_RES 880
FT /note="Pyruvic acid (Ser); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
SQ SEQUENCE 1010 AA; 116241 MW; DA5A769F27974BE1 CRC64;
MSQAFNLVLF TEIKQAQNVK TGNDKEPNSK LRAIVRISER SSKKTPRATP RDDFVYTWNS
TISLKLRSQL KLPLIQISVW DKQAHRSVYV GEVRFFLIGL LKSLAYNEHT SSWESTPQWY
QLYSSEDKKS FSSGTILVQF RVQQHLSKKN LFFNAKSDVT LSDQTGSSDL LNQYIQAIET
STPRSLQKKA FDLSNPNEQR FYPDIETNAL ASSILDCEID SMLEDFTYRK PNITESSLHD
DTLTDTDFES IHSDPTIPSS ALVPKRILFI EILSVTDLPP YKSFTRATFD MDPFVVISFG
KRTYRTSWRK HTLTPVFNER LAFEVCDYEK NYDLQFSVLD KDKFSFHDQV ATGFVSVSEL
LEEKTTDKPC TDFKPTSSNL ILLDKPMNAN ESADNLLDTK KKKYKRNVNT DATLQGGLLR
KYELVMSLDG KKNWSRKTKD EYIPILKFNT RFERYEILRR QLWMHLLQGN DTQMKGTLDL
IELNYFVDCL GSNLSDKTLA SFFEYYDKNP WVGETLTIEQ VIDSLERLVF KRQCANTHEN
YIINIDTCPL CGQGRLSLRQ DLDILKHLSI CASRDWSTVN KVLKPSFVSS KAATRRWYSR
LLIKLTFGQY TLGGNSANIL IQDRDTGYIL EEKMNIHVRL GIKLLYKSFD KANSRKIKTL
LRKLSIRQGI KFDSPSSVSQ IPSFIKFHKL DVDDCLLQLD EYKTFNEFFY RKLKPGSRPQ
EDENNSNIAT SPADCRCTVF ESITFAKTFW IKGRNFTTKK LFGSFYSREM ADLYDECSIG
IFRLAPQDYH RFHSPVTGTV GKVQSISGEY FTVNPMAIRS DLDVFGENVR CLLPIQTKEF
GRVLVVPVGA MMVGSIILSV KENQEVKKGD ELGYFKFGGS TLLVLFPNKR FKFDSDLLAN
SNNKIETLIK VGMSIGHTPE EPQFERHYRS FEEEPVDQQL RIIRCITGGS TFEESKQATQ
RRNELLGNEG SPQEKDLQVE NLSWEAKNMN LEELEENESL LLYDLVNDGT
