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HAMAP rule MF_03208

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General rule information [?]

Accession MF_03208
Dates 6-JAN-2016 (Created)
1-JUN-2023 (Last updated, Version 8)
Name PS_decarb_PSD_B_type1_euk
Scope(s) Eukaryota
Template(s) B3L2V1 (PSD_PLAKH); P39006 (PSD1_YEAST); [ Recover all ]
Triggered by HAMAP; MF_03208 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

case <OC:Plasmodiidae>
Identifier PSD
Protein name RecName: Full=Phosphatidylserine decarboxylase proenzyme;
                 EC=4.1.1.65;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase beta chain;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase alpha chain;
                 Flags: Precursor;
else case <OC:Fungi> or <OC:Viridiplantae>
Identifier PSD1
Protein name RecName: Full=Phosphatidylserine decarboxylase proenzyme 1, mitochondrial;
                 EC=4.1.1.65;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase 1 beta chain;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase 1 alpha chain;
                 Flags: Precursor;
else
Identifier PISD
Protein name RecName: Full=Phosphatidylserine decarboxylase proenzyme, mitochondrial;
                 EC=4.1.1.65;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase beta chain;
                 Contains:
RecName: Full=Phosphatidylserine decarboxylase alpha chain;
                 Flags: Precursor;
end case
case <OC:Vertebrata>
Gene name Name=PISD;
else case <OC:Caenorhabditis>
Gene name Name=psd-1;
else case <OC:Fungi>
Gene name Name=PSD1;
end case

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.;
case not <OC:Vertebrata>
PATHWAYPhospholipid metabolism; phosphatidylethanolamine biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step 2/2.
end case
SUBUNITHeterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit.
case <OC:Plasmodiidae>
SUBCELLULAR LOCATIONEndoplasmic reticulum membrane; Single-pass membrane protein. Note=Equally found in the membrane-bound as well as in the soluble fraction.
else case (<OC:Fungi> or <OC:Viridiplantae>)
SUBCELLULAR LOCATIONPhosphatidylserine decarboxylase 1 beta chain: Mitochondrion inner membrane; Single-pass membrane protein; Intermembrane side.
SUBCELLULAR LOCATIONPhosphatidylserine decarboxylase 1 alpha chain: Mitochondrion inner membrane; Peripheral membrane protein; Intermembrane side. Note=Anchored to the mitochondrial inner membrane through its interaction with the integral membrane beta chain.
else
SUBCELLULAR LOCATIONPhosphatidylserine decarboxylase beta chain: Mitochondrion inner membrane; Single-pass membrane protein; Intermembrane side.
SUBCELLULAR LOCATIONPhosphatidylserine decarboxylase alpha chain: Mitochondrion inner membrane; Peripheral membrane protein; Intermembrane side. Note=Anchored to the mitochondrial inner membrane through its interaction with the integral membrane beta chain.
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 I sub-subfamily.
case not <AnyFeature:TransitM> and not <OC:Apicomplexa>
MISCELLANEOUSThis protein may be expected to contain an N-terminal transit peptide but none has been predicted.
end case

Keywords [?]

Decarboxylase
Lipid biosynthesis
Lipid metabolism
Lyase
Membrane
Transmembrane
Transmembrane helix
case <OC:Plasmodiidae>
Endoplasmic reticulum
else
Mitochondrion
Mitochondrion inner membrane
end case
Phospholipid biosynthesis
Phospholipid metabolism
Pyruvate
Zymogen

Gene Ontology [?]

case <OCellular component:Plasmodiidae>
GO:0005789; Cellular component:endoplasmic reticulum membrane
else; https://www.ebi.ac.uk/QuickGO/term/else
GO:0005743; Cellular component:mitochondrial inner membrane
end case
GO:0004609; Molecular function:phosphatidylserine decarboxylase activity
GO:0006646; Biological process:phosphatidylethanolamine biosynthetic process
GO:0016540; Biological process:protein autoprocessing

Cross-references [?]

Pfam PF02666; PS_Dcarbxylase; 1;
NCBIfam TIGR00163; PS_decarb; 1;
General TransitM; -; 0-1;

Features [?]

From: PSD_PLAKH (B3L2V1)
Key From To Description Tag Condition FTGroup
case <OC:Fungi> or <OC:Viridiplantae>
CHAIN Nter 307 /note="Phosphatidylserine decarboxylase 1 beta chain"
CHAIN 308 Cter /note="Phosphatidylserine decarboxylase 1 alpha chain"
else
CHAIN Nter 307 /note="Phosphatidylserine decarboxylase beta chain"
CHAIN 308 Cter /note="Phosphatidylserine decarboxylase alpha chain"
end case
TRANSMEM 18 36 /note="Helical"
case not <OC:Plasmodiidae>
TOPO_DOM Nter 17 /note="Mitochondrial matrix"
TOPO_DOM 37 Cter /note="Mitochondrial intermembrane"
end case
ACT_SITE 139 139 /note="Charge relay system; for autoendoproteolytic cleavage activity" D
ACT_SITE 198 198 /note="Charge relay system; for autoendoproteolytic cleavage activity" H
ACT_SITE 308 308 /note="Charge relay system; for autoendoproteolytic cleavage activity" S
ACT_SITE 308 308 /note="Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activity" S
SITE 307 308 /note="Cleavage (non-hydrolytic); by autocatalysis" G-S
MOD_RES 308 308 /note="Pyruvic acid (Ser); by autocatalysis" S

Additional information [?]

Size range 336-655 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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