HAMAP rule MF_03209
General rule information
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| 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
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Identifier, protein and gene names
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| 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
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| 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 | 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 |
| 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
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| Decarboxylase | |
| case <OC:Fungi> | |
| Endosome | |
| Golgi apparatus | |
| end case | |
| Lipid biosynthesis | |
| Lipid metabolism | |
| Lyase | |
| Membrane | |
| Phospholipid biosynthesis | |
| Phospholipid metabolism | |
| Pyruvate | |
| Zymogen | |
Gene Ontology
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| 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
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| 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
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| 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
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| 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. |