RLC1_CITSI
ID RLC1_CITSI Reviewed; 607 AA.
AC A0A1C9J6A7;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 10-MAY-2017, sequence version 2.
DT 03-AUG-2022, entry version 24.
DE RecName: Full=(R)-limonene synthase 1, chloroplastic {ECO:0000303|PubMed:28272875};
DE EC=4.2.3.20 {ECO:0000269|PubMed:28272875, ECO:0000269|PubMed:28272876};
DE AltName: Full=(+)-limonene synthase 1;
DE Flags: Precursor;
OS Citrus sinensis (Sweet orange) (Citrus aurantium var. sinensis).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus.
OX NCBI_TaxID=2711 {ECO:0000312|EMBL:AOP12358.2};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF
RP APOPROTEIN, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF TYR-565.
RC STRAIN=cv. Washington Navel; TISSUE=Flavedo;
RX PubMed=28272875; DOI=10.1021/acs.biochem.7b00143;
RA Morehouse B.R., Kumar R.P., Matos J.O., Olsen S.N., Entova S., Oprian D.D.;
RT "Functional and Structural Characterization of a (+)-Limonene Synthase from
RT Citrus sinensis.";
RL Biochemistry 56:1706-1715(2017).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH MANGANESE AND
RP SUBSTRATE ANALOGS, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBSTRATE SPECIFICITY, AND ACTIVITY REGULATION.
RX PubMed=28272876; DOI=10.1021/acs.biochem.7b00144;
RA Kumar R.P., Morehouse B.R., Matos J.O., Malik K., Lin H., Krauss I.J.,
RA Oprian D.D.;
RT "Structural Characterization of early michaelis complexes in the reaction
RT catalyzed by (+)-limonene synthase from Citrus sinensis using fluorinated
RT substrate analogues.";
RL Biochemistry 56:1716-1725(2017).
CC -!- FUNCTION: Catalyzes the conversion of geranyl diphosphate to (+)-(4R)-
CC limonene (PubMed:28272875, PubMed:28272876). Produces exclusively the
CC (+)-enantiomer (PubMed:28272875). Can use neryl diphosphate as
CC substrate (PubMed:28272876). Has no activity with farnesyl diphosphate
CC (PubMed:28272875). {ECO:0000269|PubMed:28272875,
CC ECO:0000269|PubMed:28272876}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2E)-geranyl diphosphate = (4R)-limonene + diphosphate;
CC Xref=Rhea:RHEA:10940, ChEBI:CHEBI:15382, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:58057; EC=4.2.3.20;
CC Evidence={ECO:0000269|PubMed:28272875, ECO:0000269|PubMed:28272876};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:28272875};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:28272875};
CC Note=Binds 3 Mg(2+) or Mn(2+) ions per subunit (PubMed:28272876). The
CC best cofactor is Mn(2+) (PubMed:28272875). No effect with monovalent
CC cations (PubMed:28272875). {ECO:0000269|PubMed:28272875,
CC ECO:0000269|PubMed:28272876};
CC -!- ACTIVITY REGULATION: Inhibited by 2-fluorogeranyl diphosphate (FGPP)
CC and 2-fluoroneryl diphosphate (FNPP). {ECO:0000269|PubMed:28272876}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=13.1 uM for geranyl diphosphate in presence of manganese
CC {ECO:0000269|PubMed:28272875};
CC KM=35 uM for geranyl diphosphate in presence of magnesium
CC {ECO:0000269|PubMed:28272875};
CC KM=9 uM for neryl diphosphate {ECO:0000269|PubMed:28272876};
CC Note=kcat is 0.186 sec(-1) for geranyl diphosphate in presence of
CC manganese. kcat is 0.118 sec(-1) for geranyl diphosphate in presence
CC of magnesium. kcat is 0.43 sec(-1) for neryl diphosphate.
CC {ECO:0000269|PubMed:28272875, ECO:0000269|PubMed:28272876};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255}.
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:0000305}.
CC -!- SIMILARITY: Belongs to the terpene synthase family. {ECO:0000305}.
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DR EMBL; KU746814; AOP12358.2; -; mRNA.
DR PDB; 5UV0; X-ray; 2.30 A; A=1-607.
DR PDB; 5UV1; X-ray; 2.40 A; A=1-607.
DR PDB; 5UV2; X-ray; 2.20 A; A=1-607.
DR PDB; 6ONM; X-ray; 2.70 A; A=1-607.
DR PDBsum; 5UV0; -.
DR PDBsum; 5UV1; -.
DR PDBsum; 5UV2; -.
DR PDBsum; 6ONM; -.
DR AlphaFoldDB; A0A1C9J6A7; -.
DR SMR; A0A1C9J6A7; -.
DR eggNOG; ENOG502QUH3; Eukaryota.
DR BRENDA; 4.2.3.20; 1426.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0034002; F:(R)-limonene 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 3D-structure; Chloroplast; Lyase; Magnesium; Manganese; Metal-binding;
KW Plastid; Transit peptide.
FT TRANSIT 1..52
FT /note="Chloroplast"
FT /evidence="ECO:0000305|PubMed:28272875"
FT CHAIN 53..607
FT /note="(R)-limonene synthase 1, chloroplastic"
FT /id="PRO_0000440244"
FT MOTIF 343..347
FT /note="DDXXD motif"
FT /evidence="ECO:0000305"
FT BINDING 343
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 343
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 343
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 347
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 347
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 347
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 485
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 488
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 488
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28272876"
FT BINDING 504
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28272876"
FT MUTAGEN 565
FT /note="Y->F: 50-fold decreased catalytic activity."
FT /evidence="ECO:0000269|PubMed:28272875"
FT HELIX 65..70
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 74..76
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 78..96
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 101..113
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 121..134
FT /evidence="ECO:0007829|PDB:5UV2"
FT TURN 138..140
FT /evidence="ECO:0007829|PDB:5UV1"
FT HELIX 145..157
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 164..170
FT /evidence="ECO:0007829|PDB:5UV2"
FT TURN 173..175
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 182..192
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 200..215
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 227..238
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 241..243
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 247..249
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 250..258
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 265..296
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 298..301
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 309..319
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 323..325
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 326..347
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 352..364
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 367..373
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 376..400
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 405..427
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 434..444
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 447..458
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 464..471
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 475..490
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 494..499
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 505..513
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 517..540
FT /evidence="ECO:0007829|PDB:5UV2"
FT STRAND 544..546
FT /evidence="ECO:0007829|PDB:5UV2"
FT HELIX 548..566
FT /evidence="ECO:0007829|PDB:5UV2"
FT STRAND 567..570
FT /evidence="ECO:0007829|PDB:5UV0"
FT HELIX 581..586
FT /evidence="ECO:0007829|PDB:5UV2"
SQ SEQUENCE 607 AA; 70354 MW; F1A481732DDE2B95 CRC64;
MSSCINPSTL ATSVNGFKCL PLATNRAAIR IMAKNKPVQC LVSTKYDNLT VDRRSANYQP
SIWDHDFLQS LNSNYTDETY KRRAEELKGK VKTAIKDVTE PLDQLELIDN LQRLGLAYHF
EPEIRNILRN IHNHNKDYNW RKENLYATSL EFRLLRQHGY PVSQEVFSGF KDDKVGFICD
DFKGILSLHE ASYYSLEGES IMEEAWQFTS KHLKEMMITS NSKEEDVFVA EQAKRALELP
LHWKAPMLEA RWFIHVYEKR EDKNHLLLEL AKLEFNTLQA IYQEELKDIS GWWKDTGLGE
KLSFARNRLV ASFLWSMGIA FEPQFAYCRR VLTISIALIT VIDDIYDVYG TLDELEIFTD
AVARWDINYA LKHLPGYMKM CFLALYNFVN EFAYYVLKQQ DFDMLLSIKH AWLGLIQAYL
VEAKWYHSKY TPKLEEYLEN GLVSITGPLI ITISYLSGTN PIIKKELEFL ESNPDIVHWS
SKIFRLQDDL GTSSDEIQRG DVPKSIQCYM HETGASEEVA REHIKDMMRQ MWKKVNAYTA
DKDSPLTRTT AEFLLNLVRM SHFMYLHGDG HGVQNQETID VGFTLLFQPI PLEDKDMAFT
ASPGTKG
