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Protein

Phosphatidylserine decarboxylase proenzyme

Gene

psd

Organism
Rhizobium etli (strain CIAT 652)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer).UniRule annotation

Catalytic activityi

Phosphatidyl-L-serine = phosphatidylethanolamine + CO2.UniRule annotation

Cofactori

pyruvateUniRule annotationNote: Binds 1 pyruvoyl group covalently per subunit.UniRule annotation

Pathwayi: phosphatidylethanolamine biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes phosphatidylethanolamine from CDP-diacylglycerol.UniRule annotation
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 sitei190 – 1901Schiff-base intermediate with substrate; via pyruvic acidUniRule annotation

GO - Molecular functioni

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

BioCyciRETL1328306-WGS:GSTH-1422-MONOMER.
RETL491916:GH4T-1479-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:RHECIAT_CH0001480
OrganismiRhizobium etli (strain CIAT 652)
Taxonomic identifieri491916 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupRhizobium
Proteomesi
  • UP000008817 Componenti: Chromosome

Subcellular locationi

  • Cell membrane UniRule annotation; Peripheral membrane protein UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 189189Phosphatidylserine decarboxylase beta chainUniRule annotationPRO_1000131486Add
BLAST
Chaini190 – 23243Phosphatidylserine decarboxylase alpha chainUniRule annotationPRO_1000131487Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei190 – 1901Pyruvic acid (Ser); by autocatalysisUniRule annotation

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 post-translation cleavage follows an unusual pathway, termed non-hydrolytic serinolysis, 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.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei189 – 1902Cleavage (non-hydrolytic); by autocatalysisUniRule annotation

Keywords - PTMi

Zymogen

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi491916.RHECIAT_CH0001480.

Family & Domainsi

Sequence similaritiesi

Belongs to the phosphatidylserine decarboxylase family. PSD-A subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG41071I4. Bacteria.
COG0688. LUCA.
HOGENOMiHOG000229359.
KOiK01613.
OMAiFNVHSNR.
OrthoDBiEOG6KT2P7.

Family and domain databases

HAMAPiMF_00664. PS_decarb_PSD_A.
InterProiIPR003817. PS_Dcarbxylase.
IPR033175. PSD-A.
[Graphical view]
PfamiPF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00164. PS_decarb_rel. 1 hit.

Sequencei

Sequence statusi: Complete.

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

B3PUR0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLFNTVRNT IVPVHKEGYP FVAAFFVASL ILGWIFKPLF WIGMIFTLWC
60 70 80 90 100
AYFFRDPERV TPQDDDLVIS PADGKVSAIQ MVTPPAELDL GSEPMLRISV
110 120 130 140 150
FMNVFNCHVN RAPMRGRIVS INYRSGSFVN AELDKASEDN ERNGLVIETK
160 170 180 190 200
HGQIGVVQIA GLVARRILCW ANTNEPMDAG ERFGLIRFGS RLDVFLPAGA
210 220 230
APRVSLGQTA IAGETVIAEF ASAKGPVISR RS
Length:232
Mass (Da):25,575
Last modified:September 2, 2008 - v1
Checksum:iCC3DF4D7D555FDCD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001074 Genomic DNA. Translation: ACE90459.1.
RefSeqiWP_012483280.1. NC_010994.1.

Genome annotation databases

EnsemblBacteriaiACE90459; ACE90459; RHECIAT_CH0001480.
KEGGirec:RHECIAT_CH0001480.
PATRICi23096407. VBIRhiEtl120572_1459.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001074 Genomic DNA. Translation: ACE90459.1.
RefSeqiWP_012483280.1. NC_010994.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi491916.RHECIAT_CH0001480.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACE90459; ACE90459; RHECIAT_CH0001480.
KEGGirec:RHECIAT_CH0001480.
PATRICi23096407. VBIRhiEtl120572_1459.

Phylogenomic databases

eggNOGiENOG41071I4. Bacteria.
COG0688. LUCA.
HOGENOMiHOG000229359.
KOiK01613.
OMAiFNVHSNR.
OrthoDBiEOG6KT2P7.

Enzyme and pathway databases

UniPathwayiUPA00558; UER00616.
BioCyciRETL1328306-WGS:GSTH-1422-MONOMER.
RETL491916:GH4T-1479-MONOMER.

Family and domain databases

HAMAPiMF_00664. PS_decarb_PSD_A.
InterProiIPR003817. PS_Dcarbxylase.
IPR033175. PSD-A.
[Graphical view]
PfamiPF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00164. PS_decarb_rel. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Genome diversity and DNA divergence of Rhizobium etli."
    Gonzalez V., Acosta J.L., Santamaria R.I., Bustos P., Hernandez-Gonzalez I.L., Fernandez J.L., Diaz R., Flores M., Mora J., Palacios R., Davila G.
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CIAT 652.

Entry informationi

Entry nameiPSD_RHIE6
AccessioniPrimary (citable) accession number: B3PUR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: September 2, 2008
Last modified: April 13, 2016
This is version 49 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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.