TPSGD_VITVI
ID TPSGD_VITVI Reviewed; 557 AA.
AC Q6Q3H3; A5BPP0; A5C4C3; E0CT34;
DT 21-SEP-2011, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=(-)-germacrene D synthase;
DE EC=4.2.3.22;
DE EC=4.2.3.75;
GN OrderedLocusNames=VIT_19s0014g04930;
GN ORFNames=VIT_00014569001, VITISV_013313, VITISV_030783, Vv19s0014g04930;
OS Vitis vinifera (Grape).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; Vitales; Vitaceae; Viteae; Vitis.
OX NCBI_TaxID=29760;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=cv. Gewuerztraminer;
RX PubMed=15464152; DOI=10.1016/j.phytochem.2004.08.017;
RA Lucker J., Bowen P., Bohlmann J.;
RT "Vitis vinifera terpenoid cyclases: functional identification of two
RT sesquiterpene synthase cDNAs encoding (+)-valencene synthase and (-)-
RT germacrene D synthase and expression of mono- and sesquiterpene synthases
RT in grapevine flowers and berries.";
RL Phytochemistry 65:2649-2659(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Gewuerztraminer;
RA Steinmetz A.A., Lommele A., Drescher B., Driesel A.J.;
RL Submitted (FEB-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Pinot noir / PN40024;
RX PubMed=17721507; DOI=10.1038/nature06148;
RA Jaillon O., Aury J.-M., Noel B., Policriti A., Clepet C., Casagrande A.,
RA Choisne N., Aubourg S., Vitulo N., Jubin C., Vezzi A., Legeai F.,
RA Hugueney P., Dasilva C., Horner D., Mica E., Jublot D., Poulain J.,
RA Bruyere C., Billault A., Segurens B., Gouyvenoux M., Ugarte E.,
RA Cattonaro F., Anthouard V., Vico V., Del Fabbro C., Alaux M.,
RA Di Gaspero G., Dumas V., Felice N., Paillard S., Juman I., Moroldo M.,
RA Scalabrin S., Canaguier A., Le Clainche I., Malacrida G., Durand E.,
RA Pesole G., Laucou V., Chatelet P., Merdinoglu D., Delledonne M.,
RA Pezzotti M., Lecharny A., Scarpelli C., Artiguenave F., Pe M.E., Valle G.,
RA Morgante M., Caboche M., Adam-Blondon A.-F., Weissenbach J., Quetier F.,
RA Wincker P.;
RT "The grapevine genome sequence suggests ancestral hexaploidization in major
RT angiosperm phyla.";
RL Nature 449:463-467(2007).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Pinot noir;
RX PubMed=18094749; DOI=10.1371/journal.pone.0001326;
RA Velasco R., Zharkikh A., Troggio M., Cartwright D.A., Cestaro A., Pruss D.,
RA Pindo M., FitzGerald L.M., Vezzulli S., Reid J., Malacarne G., Iliev D.,
RA Coppola G., Wardell B., Micheletti D., Macalma T., Facci M., Mitchell J.T.,
RA Perazzolli M., Eldredge G., Gatto P., Oyzerski R., Moretto M., Gutin N.,
RA Stefanini M., Chen Y., Segala C., Davenport C., Dematte L., Mraz A.,
RA Battilana J., Stormo K., Costa F., Tao Q., Si-Ammour A., Harkins T.,
RA Lackey A., Perbost C., Taillon B., Stella A., Solovyev V., Fawcett J.A.,
RA Sterck L., Vandepoele K., Grando S.M., Toppo S., Moser C., Lanchbury J.,
RA Bogden R., Skolnick M., Sgaramella V., Bhatnagar S.K., Fontana P.,
RA Gutin A., Van de Peer Y., Salamini F., Viola R.;
RT "A high quality draft consensus sequence of the genome of a heterozygous
RT grapevine variety.";
RL PLoS ONE 2:E1326-E1326(2007).
CC -!- FUNCTION: Involved in the biosynthesis of germacrene D. Can use
CC farnesyl diphosphate as substrate, but not geranyl diphosphate or
CC geranylgeranyl diphosphate. Produces mainly (-)-germacrene D along with
CC gamma-cadinene. {ECO:0000269|PubMed:15464152}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-
CC 1(10),5-dien-11-ol + diphosphate; Xref=Rhea:RHEA:22436,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:33019, ChEBI:CHEBI:46734,
CC ChEBI:CHEBI:175763; EC=4.2.3.22;
CC Evidence={ECO:0000269|PubMed:15464152};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2E,6E)-farnesyl diphosphate = (-)-germacrene D + diphosphate;
CC Xref=Rhea:RHEA:12016, ChEBI:CHEBI:33019, ChEBI:CHEBI:49044,
CC ChEBI:CHEBI:175763; EC=4.2.3.75;
CC Evidence={ECO:0000269|PubMed:15464152};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 3 Mg(2+) ions per subunit. {ECO:0000250};
CC -!- PATHWAY: Secondary metabolite biosynthesis; terpenoid biosynthesis.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in flowers. Detected in stems, young
CC leaves and tendrils.
CC -!- DEVELOPMENTAL STAGE: Expressed in flower buds and detected in open pre-
CC anthesis flowers, flowers after anthesis and in early stages of fruit
CC onset.
CC -!- DOMAIN: The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for
CC the catalytic activity, presumably through binding to Mg(2+).
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the terpene synthase family. Tpsa subfamily.
CC {ECO:0000305}.
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DR EMBL; AY561842; AAS66357.1; -; mRNA.
DR EMBL; FN595229; CBI20483.3; -; Genomic_DNA.
DR EMBL; FN597046; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AM481907; CAN68620.1; -; Genomic_DNA.
DR EMBL; AM466733; CAN83470.1; -; Genomic_DNA.
DR RefSeq; NP_001268213.1; NM_001281284.1.
DR AlphaFoldDB; Q6Q3H3; -.
DR SMR; Q6Q3H3; -.
DR STRING; 29760.VIT_19s0014g04930.t01; -.
DR PRIDE; Q6Q3H3; -.
DR GeneID; 100232954; -.
DR KEGG; vvi:100232954; -.
DR eggNOG; ENOG502QUCN; Eukaryota.
DR HOGENOM; CLU_003125_7_2_1; -.
DR InParanoid; Q6Q3H3; -.
DR OrthoDB; 360509at2759; -.
DR BRENDA; 4.2.3.75; 6671.
DR UniPathway; UPA00213; -.
DR Proteomes; UP000009183; Chromosome 19.
DR ExpressionAtlas; Q6Q3H3; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0034004; F:germacradienol synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0052577; F:germacrene-D synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0016102; P:diterpenoid biosynthetic process; IEA:InterPro.
DR CDD; cd00684; Terpene_cyclase_plant_C1; 1.
DR Gene3D; 1.10.600.10; -; 1.
DR Gene3D; 1.50.10.130; -; 1.
DR InterPro; IPR008949; Isoprenoid_synthase_dom_sf.
DR InterPro; IPR034741; Terpene_cyclase-like_1_C.
DR InterPro; IPR044814; Terpene_cyclase_plant_C1.
DR InterPro; IPR001906; Terpene_synth_N.
DR InterPro; IPR036965; Terpene_synth_N_sf.
DR InterPro; IPR005630; Terpene_synthase_metal-bd.
DR InterPro; IPR008930; Terpenoid_cyclase/PrenylTrfase.
DR Pfam; PF01397; Terpene_synth; 1.
DR Pfam; PF03936; Terpene_synth_C; 1.
DR SFLD; SFLDG01019; Terpene_Cyclase_Like_1_C_Termi; 1.
DR SUPFAM; SSF48239; SSF48239; 1.
DR SUPFAM; SSF48576; SSF48576; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Lyase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..557
FT /note="(-)-germacrene D synthase"
FT /id="PRO_0000412252"
FT MOTIF 310..314
FT /note="DDXXD motif"
FT BINDING 310
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 310
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 314
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 314
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 462
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT CONFLICT 7
FT /note="G -> V (in Ref. 3; CBI20483 and 4; CAN68620/
FT CAN83470)"
FT /evidence="ECO:0000305"
FT CONFLICT 191
FT /note="H -> Y (in Ref. 4; CAN68620/CAN83470)"
FT /evidence="ECO:0000305"
FT CONFLICT 421
FT /note="F -> L (in Ref. 4; CAN83470)"
FT /evidence="ECO:0000305"
FT CONFLICT 432
FT /note="S -> T (in Ref. 4; CAN83470)"
FT /evidence="ECO:0000305"
FT CONFLICT 458
FT /note="F -> S (in Ref. 3; CBI20483 and 4; CAN68620/
FT CAN83470)"
FT /evidence="ECO:0000305"
FT CONFLICT 487
FT /note="P -> H (in Ref. 3; CBI20483 and 4; CAN68620/
FT CAN83470)"
FT /evidence="ECO:0000305"
FT CONFLICT 491..496
FT /note="PQPVRE -> HKQVRD (in Ref. 3; CBI20483 and 4;
FT CAN68620/CAN83470)"
FT /evidence="ECO:0000305"
FT CONFLICT 539..541
FT /note="FGA -> SGT (in Ref. 3; CBI20483 and 4; CAN68620/
FT CAN83470)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 557 AA; 64269 MW; BE6F4E1965265928 CRC64;
MSVQSSGVLL APSKNLSPEV GRRCANFHPS IWGDHFLSYA SEFTNTDDHL KQHVQQLKEE
VRKMLMAADD DSAQKLLLID AIQRLGVAYH FESEIDEVLK HMFDGSVVSA EEDVYTASLR
FRLLRQQGYH VSCDLFNNFK DNEGNFKESL SSDVRGMLSL YEATHFRVHG EDILDEALAF
TTTHLQSATK HSSNPLAEQV VHALKQPIRK GLPRLEARHY FSVYQADDSH NKALLKLAKL
DFNLLQKLHQ KELSDISAWW KDLDFAHKLP FARDRVVECY FWILGVYFEP QFFFARRILT
KVIAMTSIID DIYDVYGTLE ELELFTEAVE RWDISAIDQL PEYMRVCYQA LLYVYSEIEE
EMAKEGRSYR LYYAKEAMKN QVRAYYEEAK WLQVQQIPTM EEYMPVALVT SAYSMLATTS
FVGMGDAVTK ESFDWIFSKP KIVRASAIVC RLMDDMVFHK FEQKRGHVAS AVECYMKQHG
ASEQETPNEF PQPVREAWKD INEECLIPTA VPMPILMRVL NLARVIDVIY KNEDGYTHFG
AVLKDFVTSM LIDPVPI
