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Protein

Phosphatidylserine decarboxylase proenzyme 2

Gene

PSD2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Plays a central role in phospholipid metabolism and in the interorganelle trafficking of phosphatidylserine (PubMed:7890740, PubMed:7890739, PubMed:24366873). Phosphatidylethanolamine produced by PSD2 is insufficient to completely provide the PtdEtn pool required by mitochondria under respiratory conditions (PubMed:11294902). PSD2 is also involved in the PtdSer transport step to the site of PtdEtn synthesis on the Golgi/endosome membranes (PubMed:24366873). Required for normal heavy metal resistance (PubMed:20016005).UniRule annotation5 Publications

Catalytic activityi

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

Cofactori

pyruvateUniRule annotationBy similarityNote: Binds 1 pyruvoyl group covalently per subunit.UniRule annotationBy similarity

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. CDP-diacylglycerol--serine O-phosphatidyltransferase (CHO1)
  2. Phosphatidylserine decarboxylase proenzyme 2 (PSD2), Phosphatidylserine decarboxylase proenzyme 1, mitochondrial (PSD1)
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 sitei899Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity1
Active sitei956Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity1
Active sitei1043Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity1
Active sitei1043Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activityUniRule annotationBy similarity1

GO - Molecular functioni

  • phosphatidylserine decarboxylase activity Source: SGD

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciYEAST:YGR170W-MONOMER
UniPathwayiUPA00558; UER00616

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphatidylserine decarboxylase proenzyme 2UniRule annotation1 Publication (EC:4.1.1.65UniRule annotation1 Publication)
Cleaved into the following 2 chains:
Phosphatidylserine decarboxylase 2 beta chainUniRule annotation1 Publication
Phosphatidylserine decarboxylase 2 alpha chainUniRule annotation1 Publication
Gene namesi
Name:PSD21 PublicationUniRule annotation
Ordered Locus Names:YGR170WImported
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGR170W
SGDiS000003402 PSD2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Endosome, Golgi apparatus, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1041 – 1043GGS → AAA: No processing of the proenzyme, complete loss of activity. 1 Publication3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000452001 – 1138Phosphatidylserine decarboxylase proenzyme 2Add BLAST1138
ChainiPRO_00000452011 – 1042Phosphatidylserine decarboxylase 2 beta chainUniRule annotationAdd BLAST1042
ChainiPRO_00000452021043 – 1138Phosphatidylserine decarboxylase 2 alpha chainUniRule annotationAdd BLAST96

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1043Pyruvic acid (Ser); by autocatalysisUniRule annotationBy similarity1

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. 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.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei1042 – 1043Cleavage (non-hydrolytic); by autocatalysisUniRule annotationBy similarity2

Keywords - PTMi

Zymogen

Proteomic databases

MaxQBiP53037
PaxDbiP53037
PRIDEiP53037

PTM databases

iPTMnetiP53037

Interactioni

Subunit structurei

Heterodimer of a large membrane-associated beta subunit and a small pyruvoyl-containing alpha subunit (By similarity). Interacts with pstB2/PDR17 (PubMed:20016005, PubMed:24366873). This interaction may be a means to structurally tether the donor membrane (ER) harboring PstB2/PDR17 to acceptor membranes (Golgi/endosomes) harboring PSD2 during PtdSer transport to the site of PtdEtn synthesis (PubMed:24366873).By similarity1 Publication2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
PDR17P538443EBI-14018,EBI-2076838

Protein-protein interaction databases

BioGridi33422, 182 interactors
DIPiDIP-6756N
IntActiP53037, 3 interactors
MINTiP53037
STRINGi4932.YGR170W

Structurei

3D structure databases

ProteinModelPortaliP53037
SMRiP53037
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini14 – 87C2 1; degenerate1 PublicationAdd BLAST74
Domaini500 – 583C2 2UniRule annotationAdd BLAST84

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi108 – 159Ser-richPROSITE-ProRule annotationAdd BLAST52

Domaini

The C2 domains have an essential, but non-catalytic function (Probable) (PubMed:24366873). Both C2-1 and C2-2 facilitate interaction with PstB2/PDR17 and are required for lipid transport function (PubMed:24366873).1 Publication1 Publication

Sequence similaritiesi

Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Eukaryotic type II sub-subfamily.UniRule annotationBy similarity

Phylogenomic databases

HOGENOMiHOG000199289
InParanoidiP53037
KOiK01613
OMAiMRIIYNG
OrthoDBiEOG092C5DKH

Family and domain databases

Gene3Di2.60.40.150, 1 hit
HAMAPiMF_00663 PS_decarb_PSD_B_type2, 1 hit
InterProiView protein in InterPro
IPR000008 C2_dom
IPR035892 C2_domain_sf
IPR003817 PS_Dcarbxylase
IPR033177 PSD
IPR033179 PSD_type2_pro
PANTHERiPTHR10067 PTHR10067, 1 hit
PfamiView protein in Pfam
PF00168 C2, 2 hits
PF02666 PS_Dcarbxylase, 1 hit
SMARTiView protein in SMART
SM00239 C2, 2 hits
TIGRFAMsiTIGR00163 PS_decarb, 1 hit

Sequencei

Sequence statusi: Complete.

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

P53037-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIIKGRKRG KNKKPTLILK IHVIQAENIE ALKTFNCNPV CFVTTNTFYS
60 70 80 90 100
QKTNKLKNSN THWNQTLRIK LPRNPTSEWL RIIVYDALPT GAPPTTPSRP
110 120 130 140 150
RTTTANTSSS TLSNSGLSSH SHSSRNLNVT SKGNQTSTSI NSVSSSATPA
160 170 180 190 200
PSHSSSSLST TGPGSTHKNR INSYLYLGEA KISLLDLFKR KDTTTSYKFS
210 220 230 240 250
IEAQRYHLYD MKGGKDQDSL NCNFLVGDIL LGFKLECNVK RTPTFQAFNA
260 270 280 290 300
WRNELNTYLG RIDRNKARMR SSSSLPPPLE DMLSNSSAVS GNEIRREKPY
310 320 330 340 350
SDTDLAHDEE VNAEDEIDAE ESIEDMNSSG SICTERRYDI DNDTIFDSIS
360 370 380 390 400
EVVSLNDEEL DILNDFEEAD HPNVPDINVH DIDEDTRISL SSMITALDEY
410 420 430 440 450
DIVEPEDVAK LPAVSENDIT SVDDEESENQ QESDEEFDIY NEDEREDSDF
460 470 480 490 500
QSKEYIGSRL LHLQRGKHNK SYANYLYRRA KSNFFISKKE HAMGVVFMHI
510 520 530 540 550
GAIKNLPALR NRLSKTNYEM DPFIVISFGR RVFKTSWRKH TLNPEFNEYA
560 570 580 590 600
AFEVFPHETN FAFSIKVVDK DSFSFNDDVA KCELAWFDML QQQQHENEWI
610 620 630 640 650
PYEIPLDLTV EPAHAPKQPV LYSSFKYVSY PFLKKSFWKE AVDTSVNLER
660 670 680 690 700
LDIIQVMLYL ERLGSFTMAD SFELFQHFNK SAWAGQSITR SQLVEGLQSW
710 720 730 740 750
RKSTNFKRIW TCPRCMRSCK PTRNARRSKL VLENDLITHF AICTFSKEHK
760 770 780 790 800
TLKPSYVSSA FASKRWFSKV LIKLTYGKYA LGSNNANILV QDRDTGIIIE
810 820 830 840 850
EKISAHVKLG MRIIYNGKSP ESKKFRSLLK TLSIRQGKKF DSTASAKQIE
860 870 880 890 900
PFIKFHSLDL SQCRDKDFKT FNEFFYRKLK PGSRLPESNN KEILFSPADS
910 920 930 940 950
RCTVFPTIQE SKEIWVKGRK FSIKKLANNY NPETFNDNNC SIGIFRLAPQ
960 970 980 990 1000
DYHRFHSPCN GTIGKPVYVD GEYYTVNPMA VRSELDVFGE NIRVIIPIDS
1010 1020 1030 1040 1050
PQFGKLLYIP IGAMMVGSIL LTCKENDVVE SGQELGYFKF GGSTIIIIIP
1060 1070 1080 1090 1100
HNNFMFDSDL VKNSSERIET LVKVGMSIGH TSNVNELKRI RIKVDDPKKI
1110 1120 1130
ERIKRTISVS DENAKSTGNV TWEYHTLREM MNKDFAGL
Length:1,138
Mass (Da):130,065
Last modified:October 1, 1996 - v1
Checksum:i934BA6579E121053
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti801E → G in AAA69819 (PubMed:7890740).Curated1
Sequence conflicti974Y → N in AAA69819 (PubMed:7890740).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U19910 Genomic DNA Translation: AAA69819.1
Z72955 Genomic DNA Translation: CAA97196.1
BK006941 Genomic DNA Translation: DAA08265.1
PIRiS64484
RefSeqiNP_011686.1, NM_001181299.1

Genome annotation databases

EnsemblFungiiYGR170W; YGR170W; YGR170W
GeneIDi853080
KEGGisce:YGR170W

Similar proteinsi

Entry informationi

Entry nameiPSD2_YEAST
AccessioniPrimary (citable) accession number: P53037
Secondary accession number(s): D6VUV4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: May 23, 2018
This is version 162 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

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