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Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial (EC 2.5.1.85) (All-trans-nonaprenyl-diphosphate synthase 3 (geranylgeranyl-diphosphate specific)) (Geranyl diphosphate synthase 1) (Trans-type polyprenyl pyrophosphate synthase) (AtPPPS)

 SPS3_ARATH              Reviewed;         422 AA.
Q5HZ00; F4IHY6; O64684; Q8RWM1; Q9FT89;
25-JAN-2012, integrated into UniProtKB/Swiss-Prot.
15-FEB-2005, sequence version 1.
25-APR-2018, entry version 89.
RecName: Full=Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial {ECO:0000303|PubMed:21950843};
EC=2.5.1.85 {ECO:0000269|PubMed:21220764};
AltName: Full=All-trans-nonaprenyl-diphosphate synthase 3 (geranylgeranyl-diphosphate specific) {ECO:0000303|PubMed:21220764};
AltName: Full=Geranyl diphosphate synthase 1 {ECO:0000303|PubMed:11069698};
AltName: Full=Trans-type polyprenyl pyrophosphate synthase {ECO:0000303|PubMed:21220764};
Short=AtPPPS {ECO:0000303|PubMed:21220764};
Flags: Precursor;
Name=SPS3 {ECO:0000303|PubMed:21950843};
Synonyms=GPS1 {ECO:0000303|PubMed:11069698};
OrderedLocusNames=At2g34630 {ECO:0000312|Araport:AT2G34630};
ORFNames=T31E10.3;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, ALTERNATIVE
SPLICING, AND SUBCELLULAR LOCATION.
PubMed=11069698; DOI=10.1046/j.1365-313x.2000.00875.x;
Bouvier F., Suire C., d'Harlingue A., Backhaus R.A., Camara B.;
"Molecular cloning of geranyl diphosphate synthase and
compartmentation of monoterpene synthesis in plant cells.";
Plant J. 24:241-252(2000).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=15653808; DOI=10.1093/pcp/pch211;
Luo J., Saiki R., Tatsumi K., Nakagawa T., Kawamukai M.;
"Identification and subcellular localization of two solanesyl
diphosphate synthases from Arabidopsis thaliana.";
Plant Cell Physiol. 45:1882-1888(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617197; DOI=10.1038/45471;
Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L.,
Moffat K.S., Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L.,
Tallon L.J., Gill J.E., Adams M.D., Carrera A.J., Creasy T.H.,
Goodman H.M., Somerville C.R., Copenhaver G.P., Preuss D.,
Nierman W.C., White O., Eisen J.A., Salzberg S.L., Fraser C.M.,
Venter J.C.;
"Sequence and analysis of chromosome 2 of the plant Arabidopsis
thaliana.";
Nature 402:761-768(1999).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Kim C.J., Chen H., Cheuk R., Shinn P., Ecker J.R.;
"Arabidopsis ORF clones.";
Submitted (JAN-2005) to the EMBL/GenBank/DDBJ databases.
[7]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=17877699; DOI=10.1111/j.1365-313X.2007.03273.x;
van Schie C.C., Ament K., Schmidt A., Lange T., Haring M.A.,
Schuurink R.C.;
"Geranyl diphosphate synthase is required for biosynthesis of
gibberellins.";
Plant J. 52:752-762(2007).
[8]
FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND DISRUPTION
PHENOTYPE.
PubMed=21950843; DOI=10.1111/j.1365-313X.2011.04796.x;
Ducluzeau A.L., Wamboldt Y., Elowsky C.G., Mackenzie S.A.,
Schuurink R.C., Basset G.J.;
"Gene network reconstruction identifies the authentic trans-prenyl
diphosphate synthase that makes the solanesyl moiety of ubiquinone-9
in Arabidopsis.";
Plant J. 69:366-375(2012).
[9]
X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 76-422 IN COMPLEX WITH
DIPHOSPHATE AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND
MUTAGENESIS OF ILE-173; VAL-236; GLU-252; GLN-253; GLU-355 AND
LYS-356.
PubMed=21220764; DOI=10.1104/pp.110.168799;
Hsieh F.L., Chang T.H., Ko T.P., Wang A.H.;
"Structure and mechanism of an Arabidopsis medium/long-chain-length
prenyl pyrophosphate synthase.";
Plant Physiol. 155:1079-1090(2011).
-!- FUNCTION: May be involved in the supply of solanesyl diphosphate
for ubiquinone-9 biosynthesis in mitochondria (PubMed:21950843).
Synthesizes C25 to C45 medium / long-chain products depending on
the type of substrate available (PubMed:21220764). Can use geranyl
diphosphate, farnesyl diphosphate or geranylgeranyl diphosphate as
substrates, but not dimethylallyl diphosphate (PubMed:11069698,
PubMed:17877699, PubMed:21220764). {ECO:0000269|PubMed:11069698,
ECO:0000269|PubMed:17877699, ECO:0000269|PubMed:21220764,
ECO:0000269|PubMed:21950843}.
-!- CATALYTIC ACTIVITY: Geranylgeranyl diphosphate + 5 isopentenyl
diphosphate = 5 diphosphate + all-trans-nonaprenyl diphosphate.
{ECO:0000269|PubMed:21220764}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000250};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:21220764}.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast
{ECO:0000269|PubMed:11069698, ECO:0000269|PubMed:21950843}.
Mitochondrion {ECO:0000269|PubMed:21950843}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1;
IsoId=Q5HZ00-1; Sequence=Displayed;
Name=2;
IsoId=Q5HZ00-2; Sequence=VSP_042136;
Note=No experimental confirmation available.;
Name=3;
IsoId=Q5HZ00-3; Sequence=VSP_042135;
Note=Derived from EST data. No experimental confirmation
available.;
-!- TISSUE SPECIFICITY: Ubiquitous. Highest expression in seeds and
shoot apical meristem. {ECO:0000269|PubMed:21950843}.
-!- DISRUPTION PHENOTYPE: Embryo lethal. {ECO:0000269|PubMed:17877699,
ECO:0000269|PubMed:21950843}.
-!- MISCELLANEOUS: Silencing of At2g34630 decreases ubiquinone-9
biosynthesis in mitochondria but has no effect on plastoquinone-9
biosynthesis in chloroplast, maybe due to the redundancy with
At1g17050.
-!- SIMILARITY: Belongs to the FPP/GGPP synthase family.
{ECO:0000305}.
-!- CAUTION: Was proposed to be a geranyl diphosphate synthase
involved in gibberellins biosynthesis.
{ECO:0000305|PubMed:11069698, ECO:0000305|PubMed:17877699}.
-!- SEQUENCE CAUTION:
Sequence=AAC26705.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; Y17376; CAC16849.1; -; mRNA.
EMBL; AC004077; AAC26705.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002685; AEC09000.1; -; Genomic_DNA.
EMBL; CP002685; AEC09001.1; -; Genomic_DNA.
EMBL; AY093006; AAM13005.1; -; mRNA.
EMBL; BT020524; AAW39025.1; -; mRNA.
PIR; A84759; A84759.
RefSeq; NP_001031483.1; NM_001036406.3. [Q5HZ00-1]
RefSeq; NP_850234.1; NM_179903.3. [Q5HZ00-3]
UniGene; At.25503; -.
PDB; 3APZ; X-ray; 2.60 A; A/B=76-422.
PDB; 3AQ0; X-ray; 2.65 A; A/B/C/D/E/F/G/H=76-422.
PDBsum; 3APZ; -.
PDBsum; 3AQ0; -.
ProteinModelPortal; Q5HZ00; -.
SMR; Q5HZ00; -.
STRING; 3702.AT2G34630.2; -.
PaxDb; Q5HZ00; -.
EnsemblPlants; AT2G34630.1; AT2G34630.1; AT2G34630. [Q5HZ00-3]
EnsemblPlants; AT2G34630.2; AT2G34630.2; AT2G34630. [Q5HZ00-1]
GeneID; 818028; -.
Gramene; AT2G34630.1; AT2G34630.1; AT2G34630. [Q5HZ00-3]
Gramene; AT2G34630.2; AT2G34630.2; AT2G34630. [Q5HZ00-1]
KEGG; ath:AT2G34630; -.
Araport; AT2G34630; -.
TAIR; locus:2062315; AT2G34630.
eggNOG; KOG0776; Eukaryota.
eggNOG; COG0142; LUCA.
HOGENOM; HOG000009104; -.
KO; K14066; -.
OMA; AFTNKMA; -.
OrthoDB; EOG09360G4R; -.
PhylomeDB; Q5HZ00; -.
BioCyc; MetaCyc:AT2G34630-MONOMER; -.
PRO; PR:Q5HZ00; -.
Proteomes; UP000006548; Chromosome 2.
ExpressionAtlas; Q5HZ00; baseline and differential.
Genevisible; Q5HZ00; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0005739; C:mitochondrion; IDA:TAIR.
GO; GO:0009536; C:plastid; IDA:TAIR.
GO; GO:0052924; F:all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity; IEA:UniProtKB-EC.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004659; F:prenyltransferase activity; IDA:TAIR.
GO; GO:0050347; F:trans-octaprenyltranstransferase activity; IMP:TAIR.
GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:TAIR.
GO; GO:0008299; P:isoprenoid biosynthetic process; IEA:UniProtKB-KW.
GO; GO:0006744; P:ubiquinone biosynthetic process; IMP:TAIR.
Gene3D; 1.10.600.10; -; 1.
InterPro; IPR008949; Isoprenoid_synthase_dom_sf.
InterPro; IPR000092; Polyprenyl_synt.
InterPro; IPR033749; Polyprenyl_synt_CS.
Pfam; PF00348; polyprenyl_synt; 1.
SUPFAM; SSF48576; SSF48576; 1.
PROSITE; PS00723; POLYPRENYL_SYNTHASE_1; 1.
PROSITE; PS00444; POLYPRENYL_SYNTHASE_2; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Chloroplast; Complete proteome;
Isoprene biosynthesis; Magnesium; Metal-binding; Mitochondrion;
Plastid; Reference proteome; Transferase; Transit peptide.
TRANSIT 1 32 Chloroplast and mitochondrion.
{ECO:0000255}.
CHAIN 33 422 Solanesyl diphosphate synthase 3,
chloroplastic/mitochondrial.
/FTId=PRO_0000414850.
COMPBIAS 388 391 Poly-Ala.
METAL 181 181 Magnesium 1. {ECO:0000250}.
METAL 181 181 Magnesium 2. {ECO:0000250}.
METAL 185 185 Magnesium 1. {ECO:0000250}.
METAL 185 185 Magnesium 2. {ECO:0000250}.
METAL 308 308 Magnesium 3. {ECO:0000250}.
BINDING 125 125 Isopentenyl diphosphate. {ECO:0000250}.
BINDING 128 128 Isopentenyl diphosphate. {ECO:0000250}.
BINDING 174 174 Isopentenyl diphosphate. {ECO:0000250}.
BINDING 190 190 Polyprenyl diphosphate. {ECO:0000250}.
BINDING 191 191 Isopentenyl diphosphate. {ECO:0000250}.
BINDING 267 267 Polyprenyl diphosphate. {ECO:0000250}.
BINDING 268 268 Polyprenyl diphosphate. {ECO:0000250}.
BINDING 305 305 Polyprenyl diphosphate. {ECO:0000250}.
BINDING 322 322 Polyprenyl diphosphate. {ECO:0000250}.
VAR_SEQ 1 101 Missing (in isoform 3). {ECO:0000305}.
/FTId=VSP_042135.
VAR_SEQ 48 48 K -> KL (in isoform 2).
{ECO:0000303|PubMed:14593172,
ECO:0000303|Ref.6}.
/FTId=VSP_042136.
MUTAGEN 173 173 I->F: Shorter product chain length; when
associated with F-236.
{ECO:0000269|PubMed:21220764}.
MUTAGEN 236 236 V->F: Shorter product chain length; when
associated with F-173.
{ECO:0000269|PubMed:21220764}.
MUTAGEN 252 252 E->A: No effect; when associated with A-
253; A-355 and A-356.
{ECO:0000269|PubMed:21220764}.
MUTAGEN 253 253 Q->A: No effect; when associated with A-
252; A-355 and A-356.
{ECO:0000269|PubMed:21220764}.
MUTAGEN 355 355 E->A: No effect; when associated with A-
252; A-253 and A-356.
{ECO:0000269|PubMed:21220764}.
MUTAGEN 356 356 K->A: No effect; when associated with A-
252; A-253 and A-355.
{ECO:0000269|PubMed:21220764}.
CONFLICT 140 140 N -> D (in Ref. 1; CAC16849).
{ECO:0000305}.
TURN 84 88 {ECO:0000244|PDB:3APZ}.
HELIX 89 97 {ECO:0000244|PDB:3APZ}.
HELIX 98 101 {ECO:0000244|PDB:3APZ}.
HELIX 108 115 {ECO:0000244|PDB:3AQ0}.
TURN 116 118 {ECO:0000244|PDB:3AQ0}.
HELIX 123 136 {ECO:0000244|PDB:3APZ}.
HELIX 157 182 {ECO:0000244|PDB:3APZ}.
TURN 184 186 {ECO:0000244|PDB:3AQ0}.
STRAND 188 190 {ECO:0000244|PDB:3AQ0}.
HELIX 196 199 {ECO:0000244|PDB:3AQ0}.
HELIX 202 222 {ECO:0000244|PDB:3APZ}.
HELIX 226 247 {ECO:0000244|PDB:3APZ}.
HELIX 251 254 {ECO:0000244|PDB:3APZ}.
HELIX 257 268 {ECO:0000244|PDB:3APZ}.
HELIX 270 281 {ECO:0000244|PDB:3APZ}.
TURN 282 284 {ECO:0000244|PDB:3APZ}.
HELIX 287 314 {ECO:0000244|PDB:3APZ}.
TURN 315 318 {ECO:0000244|PDB:3APZ}.
HELIX 326 329 {ECO:0000244|PDB:3APZ}.
HELIX 335 343 {ECO:0000244|PDB:3APZ}.
HELIX 347 352 {ECO:0000244|PDB:3APZ}.
TURN 353 356 {ECO:0000244|PDB:3APZ}.
HELIX 359 370 {ECO:0000244|PDB:3APZ}.
HELIX 373 392 {ECO:0000244|PDB:3APZ}.
HELIX 401 419 {ECO:0000244|PDB:3APZ}.
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


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