PSD1_ORYSJ
ID PSD1_ORYSJ Reviewed; 438 AA.
AC Q10T43; A0A0P0VRT9;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 107.
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=Os03g0101900, LOC_Os03g01216;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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 {ECO:0000255|HAMAP-Rule:MF_03208}.
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};
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}.
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 inner membrane {ECO:0000255|HAMAP-Rule:MF_03208}; Single-
CC pass membrane protein {ECO:0000255|HAMAP-Rule:MF_03208}; Intermembrane
CC side {ECO:0000255|HAMAP-Rule:MF_03208}.
CC -!- SUBCELLULAR LOCATION: [Phosphatidylserine decarboxylase 1 alpha chain]:
CC Mitochondrion inner membrane {ECO:0000255|HAMAP-Rule:MF_03208};
CC Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_03208};
CC Intermembrane side {ECO:0000255|HAMAP-Rule:MF_03208}. Note=Anchored to
CC the mitochondrial inner membrane through its interaction with the
CC integral membrane beta chain. {ECO:0000255|HAMAP-Rule:MF_03208}.
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 -!- SIMILARITY: Belongs to the phosphatidylserine decarboxylase family.
CC PSD-B subfamily. Eukaryotic type I sub-subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_03208}.
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DR EMBL; DP000009; ABF93486.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF10572.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS81828.1; -; Genomic_DNA.
DR EMBL; AK072180; BAG92859.1; -; mRNA.
DR RefSeq; XP_015631994.1; XM_015776508.1.
DR AlphaFoldDB; Q10T43; -.
DR SMR; Q10T43; -.
DR STRING; 4530.OS03T0101900-01; -.
DR PaxDb; Q10T43; -.
DR PRIDE; Q10T43; -.
DR EnsemblPlants; Os03t0101900-01; Os03t0101900-01; Os03g0101900.
DR EnsemblPlants; Os03t0101900-02; Os03t0101900-02; Os03g0101900.
DR GeneID; 4331292; -.
DR Gramene; Os03t0101900-01; Os03t0101900-01; Os03g0101900.
DR Gramene; Os03t0101900-02; Os03t0101900-02; Os03g0101900.
DR KEGG; osa:4331292; -.
DR eggNOG; KOG2420; Eukaryota.
DR HOGENOM; CLU_029061_3_0_1; -.
DR InParanoid; Q10T43; -.
DR OMA; RLWGKFN; -.
DR OrthoDB; 1226492at2759; -.
DR PlantReactome; R-OSA-1119402; Phospholipid biosynthesis I.
DR UniPathway; UPA00558; UER00616.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q10T43; OS.
DR GO; GO:0031305; C:integral component of mitochondrial inner membrane; IEA:UniProtKB-UniRule.
DR GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
DR GO; GO:0004609; F:phosphatidylserine decarboxylase activity; IBA:GO_Central.
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..21
FT /note="Mitochondrion"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT CHAIN 22..438
FT /note="Phosphatidylserine decarboxylase proenzyme 1,
FT mitochondrial"
FT /id="PRO_0000429520"
FT CHAIN 22..386
FT /note="Phosphatidylserine decarboxylase 1 beta chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT /id="PRO_0000429521"
FT CHAIN 387..438
FT /note="Phosphatidylserine decarboxylase 1 alpha chain"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT /id="PRO_0000429522"
FT TOPO_DOM 22..48
FT /note="Mitochondrial matrix"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT TRANSMEM 49..67
FT /note="Helical"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT TOPO_DOM 68..438
FT /note="Mitochondrial intermembrane"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 173
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 273
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 387
FT /note="Charge relay system; for autoendoproteolytic
FT cleavage activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT ACT_SITE 387
FT /note="Schiff-base intermediate with substrate; via pyruvic
FT acid; for decarboxylase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT SITE 386..387
FT /note="Cleavage (non-hydrolytic); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
FT MOD_RES 387
FT /note="Pyruvic acid (Ser); by autocatalysis"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03208"
SQ SEQUENCE 438 AA; 49288 MW; B706B76F9965EABC CRC64;
MRRFRVWPPS PSPWPLLASR PCPHSHHHRS PFHASANSGA RQGNFILPGA TAATLVMFGI
LHARRMYEDQ KVVERKEKGI EPEFSPDFKA SFLRLLPLRS MSRLWGSLME VELPVFMRPA
IYKAWARAFH SNLQEAAMPL EEYPSLQAFF IRSLKEGSRP IDADPNCLVS PVDGKVLRLG
ELRGPGTMIE QVKGFSYSAA SLLGASSSLH GAEEEDFSRE HTEQSNPADS NAKSWWRVSV
AKPKLWDQTL LSPKKGIFYC VIYLHPGDYH RVHSPVDWNI IKRRHFSGHL FPQNERAVRT
IRNLYVENER VVLEGQWKEG FVAIAAIGAT NVGSIKLYIE PELRTNRAGS KILNSQPEPP
DDRVYEPVGT GVMVKKGEEI AGFKMGSTVV MVFEAPVVSK ARWREDGSGT VTSDFDFCIK
AGDRIRVGEA IGRWTSRE
