SPS3_ARATH
ID SPS3_ARATH Reviewed; 422 AA.
AC Q5HZ00; F4IHY6; O64684; Q8RWM1; Q9FT89;
DT 25-JAN-2012, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial {ECO:0000303|PubMed:21950843};
DE EC=2.5.1.85 {ECO:0000269|PubMed:21220764};
DE AltName: Full=All-trans-nonaprenyl-diphosphate synthase 3 (geranylgeranyl-diphosphate specific) {ECO:0000303|PubMed:21220764};
DE AltName: Full=Geranyl diphosphate synthase 1 {ECO:0000303|PubMed:11069698};
DE AltName: Full=Trans-type polyprenyl pyrophosphate synthase {ECO:0000303|PubMed:21220764};
DE Short=AtPPPS {ECO:0000303|PubMed:21220764};
DE Flags: Precursor;
GN Name=SPS3 {ECO:0000303|PubMed:21950843};
GN Synonyms=GPS1 {ECO:0000303|PubMed:11069698};
GN OrderedLocusNames=At2g34630 {ECO:0000312|Araport:AT2G34630};
GN ORFNames=T31E10.3;
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] (ISOFORM 1), FUNCTION, ALTERNATIVE SPLICING, AND
RP SUBCELLULAR LOCATION.
RX PubMed=11069698; DOI=10.1046/j.1365-313x.2000.00875.x;
RA Bouvier F., Suire C., d'Harlingue A., Backhaus R.A., Camara B.;
RT "Molecular cloning of geranyl diphosphate synthase and compartmentation of
RT monoterpene synthesis in plant cells.";
RL Plant J. 24:241-252(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=15653808; DOI=10.1093/pcp/pch211;
RA Luo J., Saiki R., Tatsumi K., Nakagawa T., Kawamukai M.;
RT "Identification and subcellular localization of two solanesyl diphosphate
RT synthases from Arabidopsis thaliana.";
RL Plant Cell Physiol. 45:1882-1888(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RA Kim C.J., Chen H., Cheuk R., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JAN-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=17877699; DOI=10.1111/j.1365-313x.2007.03273.x;
RA van Schie C.C., Ament K., Schmidt A., Lange T., Haring M.A.,
RA Schuurink R.C.;
RT "Geranyl diphosphate synthase is required for biosynthesis of
RT gibberellins.";
RL Plant J. 52:752-762(2007).
RN [8]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=21950843; DOI=10.1111/j.1365-313x.2011.04796.x;
RA Ducluzeau A.L., Wamboldt Y., Elowsky C.G., Mackenzie S.A., Schuurink R.C.,
RA Basset G.J.;
RT "Gene network reconstruction identifies the authentic trans-prenyl
RT diphosphate synthase that makes the solanesyl moiety of ubiquinone-9 in
RT Arabidopsis.";
RL Plant J. 69:366-375(2012).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 76-422 IN COMPLEX WITH
RP DIPHOSPHATE AND MAGNESIUM IONS, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND
RP MUTAGENESIS OF ILE-173; VAL-236; GLU-252; GLN-253; GLU-355 AND LYS-356.
RX PubMed=21220764; DOI=10.1104/pp.110.168799;
RA Hsieh F.L., Chang T.H., Ko T.P., Wang A.H.;
RT "Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl
RT pyrophosphate synthase.";
RL Plant Physiol. 155:1079-1090(2011).
CC -!- FUNCTION: May be involved in the supply of solanesyl diphosphate for
CC ubiquinone-9 (UQ-9) biosynthesis in mitochondria (PubMed:21950843).
CC Synthesizes C25 to C45 medium / long-chain products depending on the
CC type of substrate available (PubMed:21220764). Can use geranyl
CC diphosphate, farnesyl diphosphate or geranylgeranyl diphosphate as
CC substrates, but not dimethylallyl diphosphate (PubMed:11069698,
CC PubMed:17877699, PubMed:21220764). {ECO:0000269|PubMed:11069698,
CC ECO:0000269|PubMed:17877699, ECO:0000269|PubMed:21220764,
CC ECO:0000269|PubMed:21950843}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2E,6E,10E)-geranylgeranyl diphosphate + 5 isopentenyl
CC diphosphate = all-trans-nonaprenyl diphosphate + 5 diphosphate;
CC Xref=Rhea:RHEA:27594, ChEBI:CHEBI:33019, ChEBI:CHEBI:58391,
CC ChEBI:CHEBI:58756, ChEBI:CHEBI:128769; EC=2.5.1.85;
CC Evidence={ECO:0000269|PubMed:21220764};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:21220764};
CC Note=Binds 2 Mg(2+) ions per subunit. {ECO:0000250};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:21220764}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:11069698, ECO:0000269|PubMed:21950843}.
CC Mitochondrion {ECO:0000269|PubMed:21950843}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q5HZ00-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5HZ00-2; Sequence=VSP_042136;
CC Name=3;
CC IsoId=Q5HZ00-3; Sequence=VSP_042135;
CC -!- TISSUE SPECIFICITY: Ubiquitous. Highest expression in seeds and shoot
CC apical meristem. {ECO:0000269|PubMed:21950843}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethal. {ECO:0000269|PubMed:17877699,
CC ECO:0000269|PubMed:21950843}.
CC -!- MISCELLANEOUS: Silencing of At2g34630 decreases ubiquinone-9
CC biosynthesis (UQ-9) in mitochondria but has no effect on plastoquinone-
CC 9 (PQ-9) biosynthesis in chloroplast, and maybe due to the redundancy
CC with At1g17050. {ECO:0000269|PubMed:21950843}.
CC -!- SIMILARITY: Belongs to the FPP/GGPP synthase family. {ECO:0000305}.
CC -!- CAUTION: Was proposed to be a geranyl diphosphate synthase involved in
CC gibberellins biosynthesis. {ECO:0000305|PubMed:11069698,
CC ECO:0000305|PubMed:17877699}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC26705.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; Y17376; CAC16849.1; -; mRNA.
DR EMBL; AC004077; AAC26705.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002685; AEC09000.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC09001.1; -; Genomic_DNA.
DR EMBL; AY093006; AAM13005.1; -; mRNA.
DR EMBL; BT020524; AAW39025.1; -; mRNA.
DR PIR; A84759; A84759.
DR RefSeq; NP_001031483.1; NM_001036406.3. [Q5HZ00-1]
DR RefSeq; NP_850234.1; NM_179903.3. [Q5HZ00-3]
DR PDB; 3APZ; X-ray; 2.60 A; A/B=76-422.
DR PDB; 3AQ0; X-ray; 2.65 A; A/B/C/D/E/F/G/H=76-422.
DR PDBsum; 3APZ; -.
DR PDBsum; 3AQ0; -.
DR AlphaFoldDB; Q5HZ00; -.
DR SMR; Q5HZ00; -.
DR STRING; 3702.AT2G34630.2; -.
DR PaxDb; Q5HZ00; -.
DR PRIDE; Q5HZ00; -.
DR ProteomicsDB; 228257; -. [Q5HZ00-1]
DR EnsemblPlants; AT2G34630.1; AT2G34630.1; AT2G34630. [Q5HZ00-3]
DR EnsemblPlants; AT2G34630.2; AT2G34630.2; AT2G34630. [Q5HZ00-1]
DR GeneID; 818028; -.
DR Gramene; AT2G34630.1; AT2G34630.1; AT2G34630. [Q5HZ00-3]
DR Gramene; AT2G34630.2; AT2G34630.2; AT2G34630. [Q5HZ00-1]
DR KEGG; ath:AT2G34630; -.
DR Araport; AT2G34630; -.
DR TAIR; locus:2062315; AT2G34630.
DR eggNOG; KOG0776; Eukaryota.
DR OMA; RVAKYYT; -.
DR PhylomeDB; Q5HZ00; -.
DR BioCyc; MetaCyc:AT2G34630-MON; -.
DR PRO; PR:Q5HZ00; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q5HZ00; baseline and differential.
DR Genevisible; Q5HZ00; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:1990234; C:transferase complex; IBA:GO_Central.
DR GO; GO:0052924; F:all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004659; F:prenyltransferase activity; IDA:TAIR.
DR GO; GO:0050347; F:trans-octaprenyltranstransferase activity; IMP:TAIR.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IBA:GO_Central.
DR GO; GO:0006744; P:ubiquinone biosynthetic process; IMP:TAIR.
DR CDD; cd00685; Trans_IPPS_HT; 1.
DR Gene3D; 1.10.600.10; -; 1.
DR InterPro; IPR008949; Isoprenoid_synthase_dom_sf.
DR InterPro; IPR000092; Polyprenyl_synt.
DR InterPro; IPR033749; Polyprenyl_synt_CS.
DR Pfam; PF00348; polyprenyl_synt; 1.
DR SUPFAM; SSF48576; SSF48576; 1.
DR PROSITE; PS00723; POLYPRENYL_SYNTHASE_1; 1.
DR PROSITE; PS00444; POLYPRENYL_SYNTHASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Chloroplast; Isoprene biosynthesis;
KW Magnesium; Metal-binding; Mitochondrion; Plastid; Reference proteome;
KW Transferase; Transit peptide.
FT TRANSIT 1..32
FT /note="Chloroplast and mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 33..422
FT /note="Solanesyl diphosphate synthase 3,
FT chloroplastic/mitochondrial"
FT /id="PRO_0000414850"
FT BINDING 125
FT /ligand="isopentenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:128769"
FT /evidence="ECO:0000250|UniProtKB:P14324"
FT BINDING 128
FT /ligand="isopentenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:128769"
FT /evidence="ECO:0000250|UniProtKB:P14324"
FT BINDING 174
FT /ligand="isopentenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:128769"
FT /evidence="ECO:0000250|UniProtKB:Q12051"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P14324"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P14324"
FT BINDING 185
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P14324"
FT BINDING 185
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P14324"
FT BINDING 190
FT /ligand="an all-trans-polyprenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:58914"
FT /evidence="ECO:0000250"
FT BINDING 191
FT /ligand="isopentenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:128769"
FT /evidence="ECO:0000250|UniProtKB:P14324"
FT BINDING 267
FT /ligand="an all-trans-polyprenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:58914"
FT /evidence="ECO:0000250"
FT BINDING 268
FT /ligand="an all-trans-polyprenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:58914"
FT /evidence="ECO:0000250"
FT BINDING 305
FT /ligand="an all-trans-polyprenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:58914"
FT /evidence="ECO:0000250"
FT BINDING 322
FT /ligand="an all-trans-polyprenyl diphosphate"
FT /ligand_id="ChEBI:CHEBI:58914"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..101
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_042135"
FT VAR_SEQ 48
FT /note="K -> KL (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172, ECO:0000303|Ref.6"
FT /id="VSP_042136"
FT MUTAGEN 173
FT /note="I->F: Shorter product chain length; when associated
FT with F-236."
FT /evidence="ECO:0000269|PubMed:21220764"
FT MUTAGEN 236
FT /note="V->F: Shorter product chain length; when associated
FT with F-173."
FT /evidence="ECO:0000269|PubMed:21220764"
FT MUTAGEN 252
FT /note="E->A: No effect; when associated with A-253; A-355
FT and A-356."
FT /evidence="ECO:0000269|PubMed:21220764"
FT MUTAGEN 253
FT /note="Q->A: No effect; when associated with A-252; A-355
FT and A-356."
FT /evidence="ECO:0000269|PubMed:21220764"
FT MUTAGEN 355
FT /note="E->A: No effect; when associated with A-252; A-253
FT and A-356."
FT /evidence="ECO:0000269|PubMed:21220764"
FT MUTAGEN 356
FT /note="K->A: No effect; when associated with A-252; A-253
FT and A-355."
FT /evidence="ECO:0000269|PubMed:21220764"
FT CONFLICT 140
FT /note="N -> D (in Ref. 1; CAC16849)"
FT /evidence="ECO:0000305"
FT TURN 84..88
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 89..97
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 98..101
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 108..115
FT /evidence="ECO:0007829|PDB:3AQ0"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:3AQ0"
FT HELIX 123..136
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 157..182
FT /evidence="ECO:0007829|PDB:3APZ"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:3AQ0"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:3AQ0"
FT HELIX 196..199
FT /evidence="ECO:0007829|PDB:3AQ0"
FT HELIX 202..222
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 226..247
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 251..254
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 257..268
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 270..281
FT /evidence="ECO:0007829|PDB:3APZ"
FT TURN 282..284
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 287..314
FT /evidence="ECO:0007829|PDB:3APZ"
FT TURN 315..318
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 326..329
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 335..343
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 347..352
FT /evidence="ECO:0007829|PDB:3APZ"
FT TURN 353..356
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 359..370
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 373..392
FT /evidence="ECO:0007829|PDB:3APZ"
FT HELIX 401..419
FT /evidence="ECO:0007829|PDB:3APZ"
SQ SEQUENCE 422 AA; 46401 MW; 3951282BFE1E0126 CRC64;
MLFTRSVARI SSKFLRNRSF YGSSQSLASH RFAIIPDQGH SCSDSPHKGY VCRTTYSLKS
PVFGGFSHQL YHQSSSLVEE ELDPFSLVAD ELSLLSNKLR EMVLAEVPKL ASAAEYFFKR
GVQGKQFRST ILLLMATALN VRVPEALIGE STDIVTSELR VRQRGIAEIT EMIHVASLLH
DDVLDDADTR RGVGSLNVVM GNKMSVLAGD FLLSRACGAL AALKNTEVVA LLATAVEHLV
TGETMEITSS TEQRYSMDYY MQKTYYKTAS LISNSCKAVA VLTGQTAEVA VLAFEYGRNL
GLAFQLIDDI LDFTGTSASL GKGSLSDIRH GVITAPILFA MEEFPQLREV VDQVEKDPRN
VDIALEYLGK SKGIQRAREL AMEHANLAAA AIGSLPETDN EDVKRSRRAL IDLTHRVITR
NK
