PSD3_ARATH
ID PSD3_ARATH Reviewed; 635 AA.
AC A4GNA8; Q9SZH1;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 17-APR-2007, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Phosphatidylserine decarboxylase proenzyme 3;
DE EC=4.1.1.65 {ECO:0000255|HAMAP-Rule:MF_03209};
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 3 beta chain;
DE Contains:
DE RecName: Full=Phosphatidylserine decarboxylase 3 alpha chain;
GN Name=PSD3; OrderedLocusNames=At4g25970; ORFNames=F20B18.80;
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, SUBCELLULAR LOCATION, TISSUE
RP SPECIFICITY, AND DISRUPTION 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).
RN [2]
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 [3]
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 [4]
RP MYRISTOYLATION AT GLY-2, CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE
RP ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
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_03209, 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_03209};
CC -!- COFACTOR:
CC Name=pyruvate; Xref=ChEBI:CHEBI:15361;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03209};
CC Note=Binds 1 pyruvoyl group covalently per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03209};
CC -!- PATHWAY: Phospholipid metabolism; phosphatidylethanolamine
CC biosynthesis; phosphatidylethanolamine from CDP-diacylglycerol: step
CC 2/2. {ECO:0000255|HAMAP-Rule:MF_03209}.
CC -!- SUBUNIT: Heterodimer of a large membrane-associated beta subunit and a
CC small pyruvoyl-containing alpha subunit. {ECO:0000255|HAMAP-
CC Rule:MF_03209}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
CC {ECO:0000305|PubMed:17449644}; Lipid-anchor {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems and flowers.
CC {ECO:0000269|PubMed:17449644}.
CC -!- DOMAIN: The C2 domains have an essential, but non-catalytic function.
CC They may facilitate interactions with other proteins and are required
CC for lipid transport function. {ECO:0000250|UniProtKB:P53037}.
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_03209}.
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 II sub-subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_03209}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAB39662.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79452.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; EF203901; ABO26297.1; -; mRNA.
DR EMBL; AL049483; CAB39662.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161564; CAB79452.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE85138.1; -; Genomic_DNA.
DR PIR; T04252; T04252.
DR RefSeq; NP_567736.3; NM_118730.4.
DR AlphaFoldDB; A4GNA8; -.
DR SMR; A4GNA8; -.
DR STRING; 3702.AT4G25970.1; -.
DR iPTMnet; A4GNA8; -.
DR PaxDb; A4GNA8; -.
DR PRIDE; A4GNA8; -.
DR ProteomicsDB; 226062; -.
DR EnsemblPlants; AT4G25970.1; AT4G25970.1; AT4G25970.
DR GeneID; 828703; -.
DR Gramene; AT4G25970.1; AT4G25970.1; AT4G25970.
DR KEGG; ath:AT4G25970; -.
DR Araport; AT4G25970; -.
DR TAIR; locus:2120820; AT4G25970.
DR eggNOG; KOG2419; Eukaryota.
DR HOGENOM; CLU_034900_0_0_1; -.
DR InParanoid; A4GNA8; -.
DR OMA; ISCYIED; -.
DR OrthoDB; 707062at2759; -.
DR PhylomeDB; A4GNA8; -.
DR BioCyc; ARA:AT4G25970-MON; -.
DR BioCyc; MetaCyc:AT4G25970-MON; -.
DR UniPathway; UPA00558; UER00616.
DR PRO; PR:A4GNA8; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; A4GNA8; baseline and differential.
DR Genevisible; A4GNA8; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
DR GO; GO:0005789; C:endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0004609; F:phosphatidylserine decarboxylase activity; IDA:TAIR.
DR GO; GO:0006646; P:phosphatidylethanolamine biosynthetic process; IBA:GO_Central.
DR GO; GO:0016540; P:protein autoprocessing; IEA:UniProtKB-UniRule.
DR CDD; cd00051; EFh; 1.
DR Gene3D; 2.60.40.150; -; 1.
DR HAMAP; MF_00663; PS_decarb_PSD_B_type2; 1.
DR InterPro; IPR000008; C2_dom.
DR InterPro; IPR035892; C2_domain_sf.
DR InterPro; IPR011992; EF-hand-dom_pair.
DR InterPro; IPR018247; EF_Hand_1_Ca_BS.
DR InterPro; IPR002048; EF_hand_dom.
DR InterPro; IPR003817; PS_Dcarbxylase.
DR InterPro; IPR033177; PSD.
DR InterPro; IPR033179; PSD_type2_pro.
DR PANTHER; PTHR10067; PTHR10067; 1.
DR Pfam; PF13833; EF-hand_8; 1.
DR Pfam; PF02666; PS_Dcarbxylase; 1.
DR SMART; SM00054; EFh; 2.
DR SUPFAM; SSF47473; SSF47473; 1.
DR SUPFAM; SSF49562; SSF49562; 1.
DR TIGRFAMs; TIGR00163; PS_decarb; 1.
DR PROSITE; PS50004; C2; 1.
DR PROSITE; PS00018; EF_HAND_1; 2.
DR PROSITE; PS50222; EF_HAND_2; 2.
PE 1: Evidence at protein level;
KW Calcium; Decarboxylase; Endoplasmic reticulum; Lipid biosynthesis;
KW Lipid metabolism; Lipoprotein; Lyase; Membrane; Metal-binding; Myristate;
KW Phospholipid biosynthesis; Phospholipid metabolism; Pyruvate;
KW Reference proteome; Repeat; Zymogen.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:22223895,
FT ECO:0007744|PubMed:22223895"
FT CHAIN 2..635
FT /note="Phosphatidylserine decarboxylase proenzyme 3"
FT /id="PRO_0000429517"
FT CHAIN 2..585
FT /note="Phosphatidylserine decarboxylase 3 beta chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000429518"
FT CHAIN 586..635
FT /note="Phosphatidylserine decarboxylase 3 alpha chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT /id="PRO_0000429519"
FT DOMAIN 22..147
FT /note="C2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00041"
FT DOMAIN 180..210
FT /note="EF-hand 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT DOMAIN 211..246
FT /note="EF-hand 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 28..42
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 442
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 498
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 586
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT ACT_SITE 586
FT /note="Schiff-base intermediate with substrate; via pyruvic
FT acid; for decarboxylase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 188
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 190
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 192
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 194
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 199
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 224
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 226
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 228
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT BINDING 235
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT SITE 585..586
FT /note="Cleavage (non-hydrolytic); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT MOD_RES 586
FT /note="Pyruvic acid (Ser); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03209"
FT LIPID 2
FT /note="N-myristoyl glycine"
FT /evidence="ECO:0000269|PubMed:22223895"
SQ SEQUENCE 635 AA; 70352 MW; 03ED131D298BE5E8 CRC64;
MGNGNSTETK ESRRSKMRKK IQNFRSRRRL SRPGSGSVSG LASQRSVSAD DFAGIALLTL
IGAEMKFKDK WLACVSFGEQ TFRSEISDST EKPIWNSEKK LLLEKNGPSL ARISVFETNR
LLKNNIVGYC ELDLLDFVVQ EPDSTCKSFD LLDPASSNVV GSMFVSCSVE DPVETETCFA
KRILSIVDYD EDGKLSFSEF SDLMNAFGNV VAANKKEELF KAADLNGDGV VTIDELAALL
AVQQEQEPII NSCPVCGEAL QLDKLNAMIH MTLCFDEGTG NQMTGGFLTD RQASYGWMFK
LSEWTHLSTY DVGLNTGSSA SHIVVIDRKT KRLVEELIDS KIVMSMRAIY QSKIGLRLMD
QGAKEILQNL SEKQGKKMNS VESAQNIPSF LEFFKDQINM AEVKYPLDHF KTFNEFFVRE
LKPGARPIAC MDQDDVAVSA ADCRLMAFQS VDDSTRFWIK GRKFSIKGLL GNDVQSDAFL
DGSLVIFRLA PQDYHRFHSP VSGVIEKFVN VSGSLYTVNP IAVNSKYCNV FTENKRTIVI
ISTAEFGKVA FVAIGATMVG SISFVRQEGD HVKKGDELGY FSFGGSTVIC VFEKDSIKID
EDLLANSARS LETLVTVGMQ LGVSFPKLEN CVLEP
