PSD1_ARATH
ID PSD1_ARATH Reviewed; 453 AA.
AC Q84V22; O23513;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Phosphatidylserine decarboxylase proenzyme 1, mitochondrial {ECO:0000255|HAMAP-Rule:MF_03208};
DE EC=4.1.1.65 {ECO:0000255|HAMAP-Rule:MF_03208};
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 1 beta chain {ECO:0000255|HAMAP-Rule:MF_03208};
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 1 alpha chain {ECO:0000255|HAMAP-Rule:MF_03208};
DE Flags: Precursor;
GN Name=PSD1; OrderedLocusNames=At4g16700; ORFNames=dl4375c, FCAALL.4;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=12857846; DOI=10.1104/pp.103.023242;
RA Rontein D., Wu W.-I., Voelker D.R., Hanson A.D.;
RT "Mitochondrial phosphatidylserine decarboxylase from higher plants.
RT Functional complementation in yeast, localization in plants, and
RT overexpression in Arabidopsis.";
RL Plant Physiol. 132:1678-1687(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9461215; DOI=10.1038/35140;
RA Bevan M., Bancroft I., Bent E., Love K., Goodman H.M., Dean C.,
RA Bergkamp R., Dirkse W., van Staveren M., Stiekema W., Drost L., Ridley P.,
RA Hudson S.-A., Patel K., Murphy G., Piffanelli P., Wedler H., Wedler E.,
RA Wambutt R., Weitzenegger T., Pohl T., Terryn N., Gielen J., Villarroel R.,
RA De Clercq R., van Montagu M., Lecharny A., Aubourg S., Gy I., Kreis M.,
RA Lao N., Kavanagh T., Hempel S., Kotter P., Entian K.-D., Rieger M.,
RA Schaefer M., Funk B., Mueller-Auer S., Silvey M., James R., Monfort A.,
RA Pons A., Puigdomenech P., Douka A., Voukelatou E., Milioni D.,
RA Hatzopoulos P., Piravandi E., Obermaier B., Hilbert H., Duesterhoeft A.,
RA Moores T., Jones J.D.G., Eneva T., Palme K., Benes V., Rechmann S.,
RA Ansorge W., Cooke R., Berger C., Delseny M., Voet M., Volckaert G.,
RA Mewes H.-W., Klosterman S., Schueller C., Chalwatzis N.;
RT "Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis
RT thaliana.";
RL Nature 391:485-488(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Kim C.J., Chen H., Quinitio C., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=17449644; DOI=10.1104/pp.107.095414;
RA Nerlich A., von Orlow M., Rontein D., Hanson A.D., Dormann P.;
RT "Deficiency in phosphatidylserine decarboxylase activity in the psd1 psd2
RT psd3 triple mutant of Arabidopsis affects phosphatidylethanolamine
RT accumulation in mitochondria.";
RL Plant Physiol. 144:904-914(2007).
CC -!- FUNCTION: Catalyzes the formation of phosphatidylethanolamine (PtdEtn)
CC from phosphatidylserine (PtdSer). Plays a central role in phospholipid
CC metabolism and in the interorganelle trafficking of phosphatidylserine.
CC Contributes only to a minor proportion of PtdEtn production.
CC {ECO:0000255|HAMAP-Rule:MF_03208, ECO:0000269|PubMed:12857846,
CC ECO:0000269|PubMed:17449644}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycero-3-phospho-L-serine + H(+) = a 1,2-
CC diacyl-sn-glycero-3-phosphoethanolamine + CO2; Xref=Rhea:RHEA:20828,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57262,
CC ChEBI:CHEBI:64612; EC=4.1.1.65; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_03208, ECO:0000305|PubMed:12857846};
CC -!- COFACTOR:
CC Name=pyruvate; Xref=ChEBI:CHEBI:15361;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03208};
CC Note=Binds 1 pyruvoyl group covalently per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03208};
CC -!- PATHWAY: Phospholipid metabolism; phosphatidylethanolamine
CC biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step
CC 2/2. {ECO:0000255|HAMAP-Rule:MF_03208, ECO:0000305|PubMed:12857846}.
CC -!- SUBUNIT: Heterodimer of a large membrane-associated beta subunit and a
CC small pyruvoyl-containing alpha subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03208}.
CC -!- SUBCELLULAR LOCATION: [Phosphatidylserine decarboxylase 1 beta chain]:
CC Mitochondrion {ECO:0000269|PubMed:17449644}. Mitochondrion inner
CC membrane {ECO:0000255|HAMAP-Rule:MF_03208}; Single-pass membrane
CC protein {ECO:0000255|HAMAP-Rule:MF_03208}; Intermembrane side
CC {ECO:0000255|HAMAP-Rule:MF_03208}.
CC -!- SUBCELLULAR LOCATION: [Phosphatidylserine decarboxylase 1 alpha chain]:
CC Mitochondrion {ECO:0000269|PubMed:17449644}. Mitochondrion inner
CC membrane {ECO:0000255|HAMAP-Rule:MF_03208}; Peripheral membrane protein
CC {ECO:0000255|HAMAP-Rule:MF_03208}; Intermembrane side
CC {ECO:0000255|HAMAP-Rule:MF_03208}. Note=Anchored to the mitochondrial
CC inner membrane through its interaction with the integral membrane beta
CC chain. {ECO:0000255|HAMAP-Rule:MF_03208}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers.
CC {ECO:0000269|PubMed:12857846, ECO:0000269|PubMed:17449644}.
CC -!- PTM: Is synthesized initially as an inactive proenzyme. Formation of
CC the active enzyme involves a self-maturation process in which the
CC active site pyruvoyl group is generated from an internal serine residue
CC via an autocatalytic post-translational modification. Two non-identical
CC subunits are generated from the proenzyme in this reaction, and the
CC pyruvate is formed at the N-terminus of the alpha chain, which is
CC derived from the carboxyl end of the proenzyme. The autoendoproteolytic
CC cleavage occurs by a canonical serine protease mechanism, in which the
CC side chain hydroxyl group of the serine supplies its oxygen atom to
CC form the C-terminus of the beta chain, while the remainder of the
CC serine residue undergoes an oxidative deamination to produce ammonia
CC and the pyruvoyl prosthetic group on the alpha chain. During this
CC reaction, the Ser that is part of the protease active site of the
CC proenzyme becomes the pyruvoyl prosthetic group, which constitutes an
CC essential element of the active site of the mature decarboxylase.
CC {ECO:0000255|HAMAP-Rule:MF_03208}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype under normal growth
CC conditions. {ECO:0000269|PubMed:17449644}.
CC -!- SIMILARITY: Belongs to the phosphatidylserine decarboxylase family.
CC PSD-B subfamily. Eukaryotic type I sub-subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_03208}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB10445.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB78712.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY189805; AAO38842.1; -; mRNA.
DR EMBL; Z97341; CAB10445.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161544; CAB78712.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE83788.1; -; Genomic_DNA.
DR EMBL; BT026135; ABG48491.1; -; mRNA.
DR PIR; C71434; C71434.
DR RefSeq; NP_193403.2; NM_117771.3.
DR AlphaFoldDB; Q84V22; -.
DR SMR; Q84V22; -.
DR STRING; 3702.AT4G16700.1; -.
DR PaxDb; Q84V22; -.
DR PRIDE; Q84V22; -.
DR ProteomicsDB; 226353; -.
DR EnsemblPlants; AT4G16700.1; AT4G16700.1; AT4G16700.
DR GeneID; 827373; -.
DR Gramene; AT4G16700.1; AT4G16700.1; AT4G16700.
DR KEGG; ath:AT4G16700; -.
DR Araport; AT4G16700; -.
DR TAIR; locus:2129046; AT4G16700.
DR eggNOG; KOG2420; Eukaryota.
DR HOGENOM; CLU_029061_3_0_1; -.
DR InParanoid; Q84V22; -.
DR OMA; RLWGKFN; -.
DR OrthoDB; 1226492at2759; -.
DR PhylomeDB; Q84V22; -.
DR BioCyc; ARA:AT4G16700-MON; -.
DR BioCyc; MetaCyc:AT4G16700-MON; -.
DR UniPathway; UPA00558; UER00616.
DR PRO; PR:Q84V22; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q84V22; baseline and differential.
DR Genevisible; Q84V22; AT.
DR GO; GO:0031305; C:integral component of mitochondrial inner membrane; IEA:UniProtKB-UniRule.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0004609; F:phosphatidylserine decarboxylase activity; IMP:TAIR.
DR GO; GO:0006646; P:phosphatidylethanolamine biosynthetic process; IBA:GO_Central.
DR GO; GO:0016540; P:protein autoprocessing; IEA:UniProtKB-UniRule.
DR HAMAP; MF_03208; PS_decarb_PSD_B_type1_euk; 1.
DR InterPro; IPR003817; PS_Dcarbxylase.
DR InterPro; IPR033177; PSD.
DR InterPro; IPR033661; PSD_type1_euk.
DR PANTHER; PTHR10067; PTHR10067; 1.
DR Pfam; PF02666; PS_Dcarbxylase; 1.
DR TIGRFAMs; TIGR00163; PS_decarb; 1.
PE 2: Evidence at transcript level;
KW Decarboxylase; Lipid biosynthesis; Lipid metabolism; Lyase; Membrane;
KW Mitochondrion; Mitochondrion inner membrane; Phospholipid biosynthesis;
KW Phospholipid metabolism; Pyruvate; Reference proteome; Transit peptide;
KW Transmembrane; Transmembrane helix; Zymogen.
FT TRANSIT 1..29
FT /note="Mitochondrion"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT CHAIN 30..453
FT /note="Phosphatidylserine decarboxylase proenzyme 1,
FT mitochondrial"
FT /id="PRO_0000429511"
FT CHAIN 30..407
FT /note="Phosphatidylserine decarboxylase 1 beta chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT /id="PRO_0000429512"
FT CHAIN 408..453
FT /note="Phosphatidylserine decarboxylase 1 alpha chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT /id="PRO_0000429513"
FT TOPO_DOM 30..74
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT TRANSMEM 75..93
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT TOPO_DOM 94..453
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 199
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 296
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 408
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 408
FT /note="Schiff-base intermediate with substrate; via pyruvic
FT acid; for decarboxylase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT SITE 407..408
FT /note="Cleavage (non-hydrolytic); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT MOD_RES 408
FT /note="Pyruvic acid (Ser); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
SQ SEQUENCE 453 AA; 50560 MW; 4004511B1A7CDE1D CRC64;
MKPRFPQNVY FLARYSYLRR FQHSQRRTFS SFLNNIRSNY SGARASPLGG SSGAGAGAGG
GGTGDSKGNA FLVPGATMAT ILMLGALHAR RLYEDKKIEE KREKGIELEF HPDIKASFLG
VLPLRSISRA WGSFMSLEIP VWMRPYAYKA WARAFHSNLE EAALPLEEYT SLQDFFVRSL
KEGCRPIDPD PCCLVSPVDG TVLRFGELKG NRGMIEQVKG HSYSVPALLG NNSLLPMEPE
GKNESKEEAV GDKSDKSWLR VSLASPKLRE NVSASPMKGL YYCVIYLKPG DYHRIHSPAD
WNATVRRHFA GRLFPVNERA TRTIRNLYVE NERVVLEGIW KEGFMALAAV GATNIGSIEL
FIEPELRTNK PKKKLFPTEP PEERVYDPEG LGLRLEKGKE VAVFNMGSTV VLIFQAPTAN
TPEGSSSSSD YRFCVKQGDR VRVGQALGRW KEE
