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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: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei899 – 8991Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity
Active sitei956 – 9561Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity
Active sitei1043 – 10431Charge relay system; for autoendoproteolytic cleavage activityUniRule annotationBy similarity
Active sitei1043 – 10431Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activityUniRule annotationBy similarity

GO - Molecular functioni

  • phosphatidylserine decarboxylase activity Source: SGD

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

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

  • Golgi apparatus membrane UniRule annotation1 Publication; Peripheral membrane protein UniRule annotation2 Publications; Cytoplasmic side UniRule annotation1 Publication
  • Endosome membrane UniRule annotation1 Publication; Peripheral membrane protein UniRule annotation2 Publications; Cytoplasmic side UniRule annotation1 Publication

GO - Cellular componenti

  • endosome Source: SGD
  • endosome membrane Source: UniProtKB-SubCell
  • Golgi membrane Source: UniProtKB-SubCell
  • Golgi stack Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Endosome, Golgi apparatus, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1041 – 10433GGS → AAA: No processing of the proenzyme, complete loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11381138Phosphatidylserine decarboxylase proenzyme 2PRO_0000045200Add
BLAST
Chaini1 – 10421042Phosphatidylserine decarboxylase 2 beta chainUniRule annotationPRO_0000045201Add
BLAST
Chaini1043 – 113896Phosphatidylserine decarboxylase 2 alpha chainUniRule annotationPRO_0000045202Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1043 – 10431Pyruvic acid (Ser); by autocatalysisUniRule annotationBy similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Sitei1042 – 10432Cleavage (non-hydrolytic); by autocatalysisUniRule annotationBy similarity

Keywords - PTMi

Zymogen

Proteomic databases

MaxQBiP53037.

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

Protein-protein interaction databases

BioGridi33422. 118 interactions.
DIPiDIP-6756N.
IntActiP53037. 2 interactions.
MINTiMINT-654217.

Structurei

3D structure databases

ProteinModelPortaliP53037.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 8774C2 1; degenerate1 PublicationAdd
BLAST
Domaini500 – 58384C2 2UniRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi108 – 15952Ser-richPROSITE-ProRule annotationAdd
BLAST

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
Contains 2 C2 domains.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000199289.
InParanoidiP53037.
KOiK01613.
OMAiMRIIYNG.
OrthoDBiEOG725DRT.

Family and domain databases

Gene3Di2.60.40.150. 3 hits.
HAMAPiMF_00663. PS_decarb_PSD_B_type2.
InterProiIPR000008. C2_dom.
IPR003817. PS_Dcarbxylase.
IPR033177. PSD.
IPR033179. PSD_type2_pro.
[Graphical view]
PANTHERiPTHR10067. PTHR10067. 1 hit.
PfamiPF00168. C2. 2 hits.
PF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
SMARTiSM00239. C2. 2 hits.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti801 – 8011E → G in AAA69819 (PubMed:7890740).Curated
Sequence conflicti974 – 9741Y → N in AAA69819 (PubMed:7890740).Curated

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP53037.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33422. 118 interactions.
DIPiDIP-6756N.
IntActiP53037. 2 interactions.
MINTiMINT-654217.

PTM databases

iPTMnetiP53037.

Proteomic databases

MaxQBiP53037.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGR170W; YGR170W; YGR170W.
GeneIDi853080.
KEGGisce:YGR170W.

Organism-specific databases

EuPathDBiFungiDB:YGR170W.
SGDiS000003402. PSD2.

Phylogenomic databases

HOGENOMiHOG000199289.
InParanoidiP53037.
KOiK01613.
OMAiMRIIYNG.
OrthoDBiEOG725DRT.

Enzyme and pathway databases

UniPathwayiUPA00558; UER00616.
BioCyciYEAST:YGR170W-MONOMER.

Miscellaneous databases

PROiP53037.

Family and domain databases

Gene3Di2.60.40.150. 3 hits.
HAMAPiMF_00663. PS_decarb_PSD_B_type2.
InterProiIPR000008. C2_dom.
IPR003817. PS_Dcarbxylase.
IPR033177. PSD.
IPR033179. PSD_type2_pro.
[Graphical view]
PANTHERiPTHR10067. PTHR10067. 1 hit.
PfamiPF00168. C2. 2 hits.
PF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
SMARTiSM00239. C2. 2 hits.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 2 hits.
TIGRFAMsiTIGR00163. PS_decarb. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Phosphatidylserine decarboxylase 2 of Saccharomyces cerevisiae. Cloning and mapping of the gene, heterologous expression, and creation of the null allele."
    Trotter P.J., Pedretti J., Yates R., Voelker D.R.
    J. Biol. Chem. 270:6071-6080(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, SUBCELLULAR LOCATION.
    Strain: PTY36.
  2. "Sequence analysis of 203 kilobases from Saccharomyces cerevisiae chromosome VII."
    Rieger M., Brueckner M., Schaefer M., Mueller-Auer S.
    Yeast 13:1077-1090(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
    Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
    , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
    Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. "Identification of a non-mitochondrial phosphatidylserine decarboxylase activity (PSD2) in the yeast Saccharomyces cerevisiae."
    Trotter P.J., Voelker D.R.
    J. Biol. Chem. 270:6062-6070(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION.
  6. "Characterization of phosphatidylserine transport to the locus of phosphatidylserine decarboxylase 2 in permeabilized yeast."
    Wu W.I., Voelker D.R.
    J. Biol. Chem. 276:7114-7121(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  7. "Roles of phosphatidylethanolamine and of its several biosynthetic pathways in Saccharomyces cerevisiae."
    Birner R., Buergermeister M., Schneiter R., Daum G.
    Mol. Biol. Cell 12:997-1007(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "The C2 domain of phosphatidylserine decarboxylase 2 is not required for catalysis but is essential for in vivo function."
    Kitamura H., Wu W.I., Voelker D.R.
    J. Biol. Chem. 277:33720-33726(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN.
  9. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "Compartment-specific synthesis of phosphatidylethanolamine is required for normal heavy metal resistance."
    Gulshan K., Shahi P., Moye-Rowley W.S.
    Mol. Biol. Cell 21:443-455(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF 1041-GLY--SER-1043, INTERACTION WITH PDR17.
  11. "An assembly of proteins and lipid domains regulates transport of phosphatidylserine to phosphatidylserine decarboxylase 2 in Saccharomyces cerevisiae."
    Riekhof W.R., Wu W.I., Jones J.L., Nikrad M., Chan M.M., Loewen C.J., Voelker D.R.
    J. Biol. Chem. 289:5809-5819(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DOMAIN, INTERACTION WITH PDR17.

Entry informationi

Entry nameiPSD2_YEAST
AccessioniPrimary (citable) accession number: P53037
Secondary accession number(s): D6VUV4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: July 6, 2016
This is version 145 of the entry and version 1 of the sequence. [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

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.