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Protein

Phosphatidylserine decarboxylase proenzyme

Gene

psd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Only decarboxylates the lipid-linked form of the serine moiety, and not serine alone or derivatives like phosphoserine or glycerophosphoserine.UniRule annotation1 Publication

Catalytic activityi

Phosphatidyl-L-serine = phosphatidylethanolamine + CO2.UniRule annotation1 Publication

Cofactori

pyruvateUniRule annotation1 PublicationNote: Binds 1 pyruvoyl group covalently per subunit.UniRule annotation1 Publication

Enzyme regulationi

Inhibited by ionic detergents such as Barlox-12, an amine oxide, and sodium dodecyl sulfate.1 Publication

pH dependencei

Optimum pH is 6.5-7.5.1 Publication

Pathwayi: phosphatidylethanolamine biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes phosphatidylethanolamine from CDP-diacylglycerol.UniRule annotation1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Phosphatidylserine decarboxylase proenzyme (psd)
This subpathway is part of the pathway phosphatidylethanolamine biosynthesis, which is itself part of Phospholipid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes phosphatidylethanolamine from CDP-diacylglycerol, the pathway phosphatidylethanolamine biosynthesis and in Phospholipid metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei90Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity1
Active sitei147Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity1
Active sitei254Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity1
Active sitei254Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activityUniRule annotation1 Publication1

GO - Molecular functioni

  • phosphatidylserine decarboxylase activity Source: EcoCyc

GO - Biological processi

Keywordsi

Molecular functionDecarboxylase, Lyase
Biological processLipid biosynthesis, Lipid metabolism, Phospholipid biosynthesis, Phospholipid metabolism
LigandPyruvate

Enzyme and pathway databases

BioCyciEcoCyc:PSD-MONOMER.
MetaCyc:PSD-MONOMER.
UniPathwayiUPA00558; UER00616.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphatidylserine decarboxylase proenzymeUniRule annotation (EC:4.1.1.65UniRule annotation)
Cleaved into the following 2 chains:
Phosphatidylserine decarboxylase alpha chainUniRule annotation
Phosphatidylserine decarboxylase beta chainUniRule annotation
Gene namesi
Name:psdUniRule annotation
Ordered Locus Names:b4160, JW4121
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10775. psd.

Subcellular locationi

  • Cell membrane UniRule annotation1 Publication; Peripheral membrane protein UniRule annotation1 Publication

GO - Cellular componenti

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi254S → A: No processing of the proenzyme, complete loss of activity. 1 Publication1
Mutagenesisi254S → C: Reduced processing, 16% wild-type activity. 1 Publication1
Mutagenesisi254S → T: Reduced processing, 2% wild-type activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000296471 – 253Phosphatidylserine decarboxylase beta chainUniRule annotationAdd BLAST253
ChainiPRO_0000029648254 – 322Phosphatidylserine decarboxylase alpha chainUniRule annotationAdd BLAST69

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-formylmethionine1 Publication1
Modified residuei254Pyruvic acid (Ser); by autocatalysisUniRule annotation1 Publication1

Post-translational modificationi

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 (PubMed:3042771, PubMed:2406271). 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 (By similarity).UniRule annotationBy similarity2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei253 – 254Cleavage (non-hydrolytic); by autocatalysisUniRule annotation1 Publication2

Keywords - PTMi

Formylation, Zymogen

Proteomic databases

PaxDbiP0A8K1.
PRIDEiP0A8K1.

Interactioni

Subunit structurei

Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit.UniRule annotation1 Publication

Protein-protein interaction databases

BioGridi4261081. 64 interactors.
IntActiP0A8K1. 2 interactors.
STRINGi316385.ECDH10B_4355.

Structurei

3D structure databases

ProteinModelPortaliP0A8K1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Prokaryotic type I sub-subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DJ4. Bacteria.
COG0688. LUCA.
HOGENOMiHOG000282407.
InParanoidiP0A8K1.
KOiK01613.
PhylomeDBiP0A8K1.

Family and domain databases

HAMAPiMF_00662. PS_decarb_PSD_B_type1. 1 hit.
InterProiView protein in InterPro
IPR003817. PS_Dcarbxylase.
IPR033177. PSD.
IPR033178. PSD_type1_pro.
PANTHERiPTHR10067. PTHR10067. 1 hit.
PfamiView protein in Pfam
PF02666. PS_Dcarbxylase. 1 hit.
TIGRFAMsiTIGR00163. PS_decarb. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A8K1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLNSFKLSLQ YILPKLWLTR LAGWGASKRA GWLTKLVIDL FVKYYKVDMK
60 70 80 90 100
EAQKPDTASY RTFNEFFVRP LRDEVRPIDT DPNVLVMPAD GVISQLGKIE
110 120 130 140 150
EDKILQAKGH NYSLEALLAG NYLMADLFRN GTFVTTYLSP RDYHRVHMPC
160 170 180 190 200
NGILREMIYV PGDLFSVNHL TAQNVPNLFA RNERVICLFD TEFGPMAQIL
210 220 230 240 250
VGATIVGSIE TVWAGTITPP REGIIKRWTW PAGENDGSVA LLKGQEMGRF
260 270 280 290 300
KLGSTVINLF APGKVNLVEQ LESLSVTKIG QPLAVSTETF VTPDAEPAPL
310 320
PAEEIEAEHD ASPLVDDKKD QV
Length:322
Mass (Da):35,934
Last modified:June 7, 2005 - v1
Checksum:i45195A6689610599
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03916 Genomic DNA. Translation: AAA83896.1.
U14003 Genomic DNA. Translation: AAA97059.1.
U00096 Genomic DNA. Translation: AAC77120.1.
AP009048 Genomic DNA. Translation: BAE78164.1.
PIRiA29234.
RefSeqiNP_418584.1. NC_000913.3.
WP_000934920.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77120; AAC77120; b4160.
BAE78164; BAE78164; BAE78164.
GeneIDi948673.
KEGGiecj:JW4121.
eco:b4160.
PATRICifig|1411691.4.peg.2538.

Similar proteinsi

Entry informationi

Entry nameiPSD_ECOLI
AccessioniPrimary (citable) accession number: P0A8K1
Secondary accession number(s): P10740, Q2M6E2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: August 30, 2017
This is version 94 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families