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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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei90 – 901Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity
Active sitei147 – 1471Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity
Active sitei254 – 2541Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity
Active sitei254 – 2541Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activityUniRule annotation1 Publication

GO - Molecular functioni

  • phosphatidylserine decarboxylase activity Source: EcoCyc

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Lipid biosynthesis, Lipid metabolism, Phospholipid biosynthesis, Phospholipid metabolism

Keywords - Ligandi

Pyruvate

Enzyme and pathway databases

BioCyciEcoCyc:PSD-MONOMER.
ECOL316407:JW4121-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi254 – 2541S → A: No processing of the proenzyme, complete loss of activity. 1 Publication
Mutagenesisi254 – 2541S → C: Reduced processing, 16% wild-type activity. 1 Publication
Mutagenesisi254 – 2541S → T: Reduced processing, 2% wild-type activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 253253Phosphatidylserine decarboxylase beta chainUniRule annotationPRO_0000029647Add
BLAST
Chaini254 – 32269Phosphatidylserine decarboxylase alpha chainUniRule annotationPRO_0000029648Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-formylmethionine1 Publication
Modified residuei254 – 2541Pyruvic acid (Ser); by autocatalysisUniRule annotation1 Publication

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)LengthDescriptionGraphical viewFeature identifierActions
Sitei253 – 2542Cleavage (non-hydrolytic); by autocatalysisUniRule annotation1 Publication

Keywords - PTMi

Formylation, Zymogen

Proteomic databases

EPDiP0A8K1.
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 interactions.
IntActiP0A8K1. 2 interactions.
STRINGi511145.b4160.

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.
OMAiGSMATVW.
PhylomeDBiP0A8K1.

Family and domain databases

HAMAPiMF_00662. PS_decarb_PSD_B_type1. 1 hit.
InterProiIPR003817. PS_Dcarbxylase.
IPR033177. PSD.
IPR033178. PSD_type1_pro.
[Graphical view]
PANTHERiPTHR10067. PTHR10067. 1 hit.
PfamiPF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
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.
PATRICi32123893. VBIEscCol129921_4294.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP0A8K1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261081. 64 interactions.
IntActiP0A8K1. 2 interactions.
STRINGi511145.b4160.

Proteomic databases

EPDiP0A8K1.
PaxDbiP0A8K1.
PRIDEiP0A8K1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77120; AAC77120; b4160.
BAE78164; BAE78164; BAE78164.
GeneIDi948673.
KEGGiecj:JW4121.
eco:b4160.
PATRICi32123893. VBIEscCol129921_4294.

Organism-specific databases

EchoBASEiEB0768.
EcoGeneiEG10775. psd.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00558; UER00616.
BioCyciEcoCyc:PSD-MONOMER.
ECOL316407:JW4121-MONOMER.
MetaCyc:PSD-MONOMER.

Miscellaneous databases

PROiP0A8K1.

Family and domain databases

HAMAPiMF_00662. PS_decarb_PSD_B_type1. 1 hit.
InterProiIPR003817. PS_Dcarbxylase.
IPR033177. PSD.
IPR033178. PSD_type1_pro.
[Graphical view]
PANTHERiPTHR10067. PTHR10067. 1 hit.
PfamiPF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00163. PS_decarb. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPSD_ECOLI
AccessioniPrimary (citable) accession number: P0A8K1
Secondary accession number(s): P10740, Q2M6E2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: September 7, 2016
This is version 88 of the entry and version 1 of the sequence. [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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.