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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
Eukaryota
Template P53037 (PSD2_YEAST)
case <OC:Eukaryota>
Triggered by
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
PSD2

Comments [?]

Function Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Plays a central role in phospholipid metabolism and in the interorganelle trafficking of phosphatidylserine.
Catalytic activity RHEA:20828: a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CO2
EC 4.1.1.65
Cofactor pyruvate
Note: Binds 1 pyruvoyl group covalently per subunit
Pathway Phospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2.
case <OC:Ascomycota>
Subunit Heterodimer 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
Subunit Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit.
end case
case <OC:Fungi>
Subcellular location Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side. Endosome membrane; Peripheral membrane protein; Cytoplasmic side.
end case
case <Feature:PS50004> and <OC:Saccharomycetales>
Domain The 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>
Domain The 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
Ptm Is 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.
Similarity Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Eukaryotic type II sub-subfamily.

Keywords [?]

Decarboxylase
case <OC:Fungi>
Endosome
Golgi apparatus
end case
Lipid biosynthesis
Lipid metabolism
Lyase
Membrane
Phospholipid biosynthesis
Phospholipid metabolism
Pyruvate
Zymogen

Gene Ontology [?]

case <OC: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; trigger=PRU00041;
PS00018; EF_HAND_1; 0-2;
PS50222; EF_HAND_2; 0-2; trigger=PRU00448;
Pfam PF00168; C2; 1-2;
PF02666; PS_Dcarbxylase; 1;
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       Phosphatidylserine decarboxylase 2 beta chain        
CHAIN     1043     Cter       Phosphatidylserine decarboxylase 2 alpha chain        
ACT_SITE     899     899       Charge relay system; for autoendoproteolytic cleavage activity     D  
ACT_SITE     956     956       Charge relay system; for autoendoproteolytic cleavage activity     H  
ACT_SITE     1043     1043       Charge relay system; for autoendoproteolytic cleavage activity     S  
ACT_SITE     1043     1043       Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activity     S  
SITE     1042     1043       Cleavage (non-hydrolytic); by autocatalysis     G-S  
MOD_RES     1043     1043       Pyruvic acid (Ser); by autocatalysis     S  

Additional information [?]

Size range 383-1400 amino acids
Related rules None
Fusion 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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