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Protein

Phosphatidylserine decarboxylase proenzyme 3

Gene

psd3

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the formation of phosphatidylethanolamine (PtdEtn) from phosphatidylserine (PtdSer). Plays a central role in phospholipid metabolism and in the interorganelle trafficking of phosphatidylserine (By similarity). Together with psd1 and psd2, responsible for the majority of phosphatidylethanolamine synthesis (PubMed:19286980).UniRule annotation1 Publication

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. CDP-diacylglycerol--serine O-phosphatidyltransferase (pps1)
  2. Phosphatidylserine decarboxylase proenzyme 3 (psd3), Phosphatidylserine decarboxylase proenzyme 1, mitochondrial (psd1), Phosphatidylserine decarboxylase proenzyme 2, mitochondrial (psd2)
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 sitei769 – 7691Charge relay system; for autoendoproteolytic cleavage activityUniRule annotation
Active sitei825 – 8251Charge relay system; for autoendoproteolytic cleavage activityUniRule annotation
Active sitei912 – 9121Charge relay system; for autoendoproteolytic cleavage activityUniRule annotation
Active sitei912 – 9121Schiff-base intermediate with substrate; via pyruvic acid; for decarboxylase activityUniRule annotation

GO - Molecular functioni

  • phosphatidylserine decarboxylase activity Source: PomBase
  • phospholipid binding Source: PomBase

GO - Biological processi

  • phosphatidylcholine biosynthetic process Source: PomBase
  • phosphatidylethanolamine biosynthetic process Source: PomBase
  • protein autoprocessing Source: UniProtKB-HAMAP
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

UniPathwayiUPA00558; UER00616.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphatidylserine decarboxylase proenzyme 31 Publication (EC:4.1.1.65UniRule annotation)
Cleaved into the following 2 chains:
Gene namesi
Name:psd31 Publication
ORF Names:SPAC31G5.15Imported
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAC31G5.15.
PomBaseiSPAC31G5.15. psd3.

Subcellular locationi

GO - Cellular componenti

  • cell division site Source: PomBase
  • cytosol Source: PomBase
  • endosome membrane Source: UniProtKB-SubCell
  • fungal-type vacuole membrane Source: PomBase
  • Golgi membrane Source: PomBase
  • Golgi stack Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endosome, Golgi apparatus, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 967967Phosphatidylserine decarboxylase proenzyme 3PRO_0000303954Add
BLAST
Chaini1 – 911911Phosphatidylserine decarboxylase 3 beta chainCuratedPRO_0000416837Add
BLAST
Chaini912 – 96756Phosphatidylserine decarboxylase 3 alpha chainCuratedPRO_0000416838Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei912 – 9121Pyruvic 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 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
Sitei911 – 9122Cleavage (non-hydrolytic); by autocatalysisUniRule annotation

Keywords - PTMi

Zymogen

Proteomic databases

MaxQBiO14111.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi279608. 8 interactions.
MINTiMINT-4670569.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini269 – 35789C2UniRule annotationAdd
BLAST

Domaini

The C2 domains have an essential, but non-catalytic function. They may facilitate interactions with other proteins and are required for lipid transport function.UniRule annotation

Sequence similaritiesi

Belongs to the phosphatidylserine decarboxylase family. PSD-B subfamily. Eukaryotic type II sub-subfamily.UniRule annotation
Contains 1 C2 domain.UniRule annotation

Phylogenomic databases

InParanoidiO14111.
KOiK01613.
OMAiPADCRMM.
OrthoDBiEOG725DRT.

Family and domain databases

Gene3Di2.60.40.150. 1 hit.
HAMAPiMF_00663. PS_decarb_PSD_B_type2.
InterProiIPR000008. C2_dom.
IPR003817. PS_Dcarbxylase.
IPR033177. PSD.
[Graphical view]
PANTHERiPTHR10067. PTHR10067. 3 hits.
PfamiPF00168. C2. 1 hit.
PF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
SMARTiSM00239. C2. 1 hit.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 1 hit.
TIGRFAMsiTIGR00163. PS_decarb. 1 hit.
PROSITEiPS50004. C2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

O14111-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPFTKSCRSA NTLRKGIKNG KLILKIIVND IDNVESCLSG DESNDSKKSS
60 70 80 90 100
ASFYMKLKYG SYRALADNIL STDENRKEDI AVFDVPLPNG LQIDTFTLCL
110 120 130 140 150
YRKSKWKKQI VGEAYIGIQA LLLSTNPDET CKYPVISPPS GRNKENQSPS
160 170 180 190 200
HQICNLSLKW IIYDPEDADA DSKTLAKAWL QQIKMNQTSI DPMSNISKSL
210 220 230 240 250
KELEVDNVES DLEDSSFIAE PDSSIPPSES SVSISTDTGK ETPPSKSKKS
260 270 280 290 300
SNQPYVSIGE GNSDLLGFVF LEIISVSNLP PLKNVFRTGF DMDPFVITAF
310 320 330 340 350
SKNIFRTKWL RHNLNPVYNE KFLFEVGAFE SNYDLVFKVV DHDKMSLNDS
360 370 380 390 400
IAVGSFNVQS IINSSAQVDP ETGLYSFNIE TSSPSQDTSS KAEDSPTVQK
410 420 430 440 450
IADDFSSAVG KDLRTDIIEQ IIPLTLCCKH DFSTPRDVKL SFKAMFFPIA
460 470 480 490 500
ALRQKFWRVM LAQYGDIEDG HIGKLGMYAV LDTLGSNIPN SMVDDIYTEL
510 520 530 540 550
SSKNHDDTSD SITVDEAVIC LERLVDLVCH QDQQATQTPQ SPSSNEESGP
560 570 580 590 600
GTPTQTSDQY EDSEDSRNFP SKLYLVYLSN CPLCLKFKLS KVNQQKATVH
610 620 630 640 650
LATCASHDWK RVDRLMMTSY VSLNQAQRRW FSKAFAKVVY GSSKVGSTSA
660 670 680 690 700
TTLVQNRQTG QIQEEKMNAY VRIGIRLLYR GIRNRRIEGS KVKKILRSLT
710 720 730 740 750
LKQGMKYDSP ISVKEIKPFI RFFDLNMNEV DMPVGGFKTF NEFFYRKLKP
760 770 780 790 800
GSRPCAFPDN PDILVSPADS RIVAYECIEK ATTYWIKGTE FTVERLLGYS
810 820 830 840 850
NEAQRFVGGS ICISRLAPQD YHRFHSPVNG CIGPITKIEG QYYTVNPMAI
860 870 880 890 900
RSYLDVFGEN VRVLIPIDSN EFGKVMLVAV GAMMVGSTVL TVDEGKIVQR
910 920 930 940 950
SDELGYFKFG GSTVITLFEP NVTSFDEDLL RNSKTKIETL VKMGERIGQK
960
IDPNKPTDAE DHSKSDS
Length:967
Mass (Da):108,213
Last modified:April 18, 2012 - v2
Checksum:i5B2115FB91FA42BC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB11699.2.
PIRiT38632.
RefSeqiNP_594016.2. NM_001019442.2.

Genome annotation databases

EnsemblFungiiSPAC31G5.15.1; SPAC31G5.15.1:pep; SPAC31G5.15.
GeneIDi2543178.
KEGGispo:SPAC31G5.15.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB11699.2.
PIRiT38632.
RefSeqiNP_594016.2. NM_001019442.2.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi279608. 8 interactions.
MINTiMINT-4670569.

Proteomic databases

MaxQBiO14111.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC31G5.15.1; SPAC31G5.15.1:pep; SPAC31G5.15.
GeneIDi2543178.
KEGGispo:SPAC31G5.15.

Organism-specific databases

EuPathDBiFungiDB:SPAC31G5.15.
PomBaseiSPAC31G5.15. psd3.

Phylogenomic databases

InParanoidiO14111.
KOiK01613.
OMAiPADCRMM.
OrthoDBiEOG725DRT.

Enzyme and pathway databases

UniPathwayiUPA00558; UER00616.

Miscellaneous databases

NextBioi20804202.
PROiO14111.

Family and domain databases

Gene3Di2.60.40.150. 1 hit.
HAMAPiMF_00663. PS_decarb_PSD_B_type2.
InterProiIPR000008. C2_dom.
IPR003817. PS_Dcarbxylase.
IPR033177. PSD.
[Graphical view]
PANTHERiPTHR10067. PTHR10067. 3 hits.
PfamiPF00168. C2. 1 hit.
PF02666. PS_Dcarbxylase. 1 hit.
[Graphical view]
SMARTiSM00239. C2. 1 hit.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 1 hit.
TIGRFAMsiTIGR00163. PS_decarb. 1 hit.
PROSITEiPS50004. C2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "Comparative functional genomics of the fission yeasts."
    Rhind N., Chen Z., Yassour M., Thompson D.A., Haas B.J., Habib N., Wapinski I., Roy S., Lin M.F., Heiman D.I., Young S.K., Furuya K., Guo Y., Pidoux A., Chen H.M., Robbertse B., Goldberg J.M., Aoki K.
    , Bayne E.H., Berlin A.M., Desjardins C.A., Dobbs E., Dukaj L., Fan L., FitzGerald M.G., French C., Gujja S., Hansen K., Keifenheim D., Levin J.Z., Mosher R.A., Mueller C.A., Pfiffner J., Priest M., Russ C., Smialowska A., Swoboda P., Sykes S.M., Vaughn M., Vengrova S., Yoder R., Zeng Q., Allshire R., Baulcombe D., Birren B.W., Brown W., Ekwall K., Kellis M., Leatherwood J., Levin H., Margalit H., Martienssen R., Nieduszynski C.A., Spatafora J.W., Friedman N., Dalgaard J.Z., Baumann P., Niki H., Regev A., Nusbaum C.
    Science 332:930-936(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVISION OF GENE MODEL.
  3. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  4. "Phosphatidylethanolamine is required for normal cell morphology and cytokinesis in the fission yeast Schizosaccharomyces pombe."
    Luo J., Matsuo Y., Gulis G., Hinz H., Patton-Vogt J., Marcus S.
    Eukaryot. Cell 8:790-799(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiPSD3_SCHPO
AccessioniPrimary (citable) accession number: O14111
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: April 18, 2012
Last modified: April 13, 2016
This is version 99 of the entry and version 2 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. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  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.