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HAMAP rule MF_03209

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General rule information [?]

Accession MF_03209
Dates 6-JAN-2016 (Created)
1-JUN-2023 (Last updated, Version 6)
Name PS_decarb_PSD_B_type2_euk
Scope(s) Eukaryota
Template(s) P53037 (PSD2_YEAST); [ Recover all ]
Triggered by
case c? <OC:Eukaryota>
HAMAP; MF_00663 (Get profile general information and statistics)
end case

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier PSD2
Protein name RecName: Full=Phosphatidylserine decarboxylase proenzyme 2;
                 EC=4.1.1.65;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase 2 beta chain;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase 2 alpha chain;
Gene name Name=PSD2;

Comments [?]

FUNCTIONCatalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Plays a central role in phospholipid metabolism and in the interorganelle trafficking of phosphatidylserine.
CATALYTIC ACTIVITY Reaction=a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2- diacyl-sn-glycero-3-phosphoethanolamine + CO2; Xref=Rhea:RHEA:20828, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57262, ChEBI:CHEBI:64612; EC=4.1.1.65;
COFACTOR Name=pyruvate; Xref=ChEBI:CHEBI:15361; Note=Binds 1 pyruvoyl group covalently per subunit
PATHWAYPhospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2.
case <OC:Ascomycota>
SUBUNITHeterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit. Interacts with pstB2. This interaction may be a means to structurally tether the donor membrane (ER) harboring PstB2 to acceptor membranes (Golgi/endosomes) harboring PSD2 during PtdSer transport to the site of PtdEtn synthesis.
else
SUBUNITHeterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit.
end case
case <OC:Fungi>
SUBCELLULAR LOCATIONGolgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side. Endosome membrane; Peripheral membrane protein; Cytoplasmic side.
end case
case <Feature:PS50004> and <OC:Saccharomycetales>
DOMAINThe C2 domains have an essential, but non-catalytic function. They may facilitate interaction with PstB2 and are required for lipid transport function.
else case <Feature:PS50004>
DOMAINThe C2 domains have an essential, but non-catalytic function. They may facilitate interactions with other proteins and are required for lipid transport function.
end case
PTMIs synthesized initially as an inactive proenzyme. Formation of the active enzyme involves a self-maturation process in which the active site pyruvoyl group is generated from an internal serine residue via an autocatalytic post-translational modification. Two non-identical subunits are generated from the proenzyme in this reaction, and the pyruvate is formed at the N-terminus of the alpha chain, which is derived from the carboxyl end of the proenzyme. The autoendoproteolytic cleavage occurs by a canonical serine protease mechanism, in which the side chain hydroxyl group of the serine supplies its oxygen atom to form the C-terminus of the beta chain, while the remainder of the serine residue undergoes an oxidative deamination to produce ammonia and the pyruvoyl prosthetic group on the alpha chain. During this reaction, the Ser that is part of the protease active site of the proenzyme becomes the pyruvoyl prosthetic group, which constitutes an essential element of the active site of the mature decarboxylase.
SIMILARITYBelongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Eukaryotic type II sub-subfamily.

Keywords [?]


Gene Ontology [?]

case <OCellular component:Fungi>
GO:0005768; Cellular component:endosome
GO:0005795; Cellular component:Golgi stack
end case
GO:0004609; Molecular function:phosphatidylserine decarboxylase activity
GO:0006646; Biological process:phosphatidylethanolamine biosynthetic process
GO:0016540; Biological process:protein autoprocessing

Cross-references [?]

PROSITE PS50004; C2; 1-2;
PROSITE PS00018; EF_HAND_1; 0-2;
PROSITE PS50222; EF_HAND_2; 0-2;
Pfam PF00168; C2; 1-2;
Pfam PF02666; PS_Dcarbxylase; 1;
Pfam PF13499; EF-hand_7; 0-1;
NCBIfam TIGR00163; PS_decarb; 1;

Features [?]

From: PSD2_YEAST (P53037)
Key From To Description Tag Condition FTGroup
CHAIN Nter 1042 /note="Phosphatidylserine decarboxylase 2 beta chain"
CHAIN 1043 Cter /note="Phosphatidylserine decarboxylase 2 alpha chain"
ACT_SITE 899 899 /note="Charge relay system; for autoendoproteolytic cleavage activity" D
ACT_SITE 956 956 /note="Charge relay system; for autoendoproteolytic cleavage activity" H
ACT_SITE 1043 1043 /note="Charge relay system; for autoendoproteolytic cleavage activity" S
ACT_SITE 1043 1043 /note="Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activity" S
SITE 1042 1043 /note="Cleavage (non-hydrolytic); by autocatalysis" G-S
MOD_RES 1043 1043 /note="Pyruvic acid (Ser); by autocatalysis" S

Additional information [?]

Size range 383-1400 amino acids
Related rules None
Fusion Nter: None Cter: None
Comments Classification of phosphatidylserine decarboxylase into subfamilies was done according to Daiyasu at al.(2005) (PubMed:16243780) for PSD-A and PSD-B and Voelker D.R.(1997) (PubMed:9370338) for type I and type II.



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