PDS_ORYSI
ID PDS_ORYSI Reviewed; 578 AA.
AC A2XDA1; Q93Y74; Q9ZTN9;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 10-JUL-2007, sequence version 2.
DT 03-AUG-2022, entry version 73.
DE RecName: Full=15-cis-phytoene desaturase, chloroplastic/chromoplastic {ECO:0000305};
DE EC=1.3.5.5 {ECO:0000269|PubMed:26147209, ECO:0000269|PubMed:29176862};
DE AltName: Full=Phytoene dehydrogenase {ECO:0000303|PubMed:28669634};
DE AltName: Full=Phytoene desaturase {ECO:0000303|Ref.2};
DE Flags: Precursor;
GN Name=PDS1; Synonyms=PDS; ORFNames=OsI_010044;
OS Oryza sativa subsp. indica (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=39946;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. 93-11;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 14-578.
RC STRAIN=cv. IR36;
RA Vigneswaran A., Wurtzel E.T.;
RT "A rice cDNA encoding phytoene desaturase.";
RL (er) Plant Gene Register PGR99-131(1999).
RN [3]
RP PROTEIN SEQUENCE OF 122-136; 394-397; 413-425; 479-500; 521-536 AND
RP 550-564, IDENTIFICATION BY MASS SPECTROMETRY, CRYSTALLIZATION, FUNCTION,
RP CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, ACTIVITY REGULATION,
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=26147209; DOI=10.1371/journal.pone.0131717;
RA Gemmecker S., Schaub P., Koschmieder J., Brausemann A., Drepper F.,
RA Rodriguez-Franco M., Ghisla S., Warscheid B., Einsle O., Beyer P.;
RT "Phytoene Desaturase from Oryza sativa: Oligomeric Assembly, Membrane
RT Association and Preliminary 3D-Analysis.";
RL PLoS ONE 10:E0131717-E0131717(2015).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF PHE-162; ARG-300; TYR-506;
RP THR-508 AND LEU-538, AND REACTION MECHANISM.
RX PubMed=29176862; DOI=10.1371/journal.pone.0187628;
RA Koschmieder J., Fehling-Kaschek M., Schaub P., Ghisla S., Brausemann A.,
RA Timmer J., Beyer P.;
RT "Plant-type phytoene desaturase: Functional evaluation of structural
RT implications.";
RL PLoS ONE 12:E0187628-E0187628(2017).
RN [5] {ECO:0007744|PDB:5MOG}
RP X-RAY CRYSTALLOGRAPHY (2.77 ANGSTROMS) OF 88-578 IN COMPLEX WITH FAD AND
RP HERBICIDAL INHIBITOR, SUBUNIT, AND REACTION MECHANISM.
RX PubMed=28669634; DOI=10.1016/j.str.2017.06.002;
RA Brausemann A., Gemmecker S., Koschmieder J., Ghisla S., Beyer P.,
RA Einsle O.;
RT "Structure of Phytoene Desaturase Provides Insights into Herbicide Binding
RT and Reaction Mechanisms Involved in Carotene Desaturation.";
RL Structure 25:1222-1232(2017).
CC -!- FUNCTION: Converts phytoene into zeta-carotene via the intermediary of
CC phytofluene by the symmetrical introduction of two double bonds at the
CC C-11 and C-11' positions of phytoene with a concomitant isomerization
CC of two neighboring double bonds at the C9 and C9' positions from trans
CC to cis. Active with decylplastoquinone (DPQ) as substrate
CC (PubMed:26147209, PubMed:29176862). Also active with other
CC benzoquinones, which are strongly preferred over naphthoquinones as
CC substrates (PubMed:26147209). {ECO:0000269|PubMed:26147209,
CC ECO:0000269|PubMed:29176862}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=15-cis-phytoene + 2 a plastoquinone = 9,9',15-tri-cis-zeta-
CC carotene + 2 a plastoquinol; Xref=Rhea:RHEA:30287, Rhea:RHEA-
CC COMP:9561, Rhea:RHEA-COMP:9562, ChEBI:CHEBI:17757, ChEBI:CHEBI:27787,
CC ChEBI:CHEBI:48717, ChEBI:CHEBI:62192; EC=1.3.5.5;
CC Evidence={ECO:0000269|PubMed:26147209, ECO:0000269|PubMed:29176862};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:26147209, ECO:0000269|PubMed:28669634,
CC ECO:0000269|PubMed:29176862};
CC -!- ACTIVITY REGULATION: Inhibited by the herbicide norflurazon (NFZ).
CC {ECO:0000269|PubMed:26147209, ECO:0000269|PubMed:29176862}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.3 mM for decylplastoquinone (DPQ) {ECO:0000269|PubMed:29176862};
CC KM=53.9 mM for phytoene {ECO:0000269|PubMed:29176862};
CC KM=66.8 mM for phytofluene {ECO:0000269|PubMed:29176862};
CC Vmax=28 nmol/min/mg enzyme with decylplastoquinone (DPQ) as substrate
CC {ECO:0000269|PubMed:29176862};
CC Vmax=46.3 nmol/min/mg enzyme with phytoene as substrate
CC {ECO:0000269|PubMed:29176862};
CC Vmax=48.4 nmol/min/mg enzyme with phytofluene as substrate
CC {ECO:0000269|PubMed:29176862};
CC pH dependence:
CC Optimum pH is 6.0. {ECO:0000269|PubMed:29176862};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius.
CC {ECO:0000269|PubMed:29176862};
CC -!- PATHWAY: Carotenoid biosynthesis; lycopene biosynthesis.
CC -!- SUBUNIT: Homotetramer (PubMed:26147209, PubMed:28669634). Homotetramer
CC is the active form of the enzyme (PubMed:26147209).
CC {ECO:0000269|PubMed:26147209, ECO:0000269|PubMed:28669634}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000250|UniProtKB:Q40406}. Plastid, chromoplast
CC {ECO:0000250|UniProtKB:Q40406}. Membrane {ECO:0000269|PubMed:26147209};
CC Peripheral membrane protein {ECO:0000269|PubMed:26147209}.
CC -!- SIMILARITY: Belongs to the carotenoid/retinoid oxidoreductase family.
CC {ECO:0000305}.
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DR EMBL; CM000128; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AF049356; AAD02489.1; -; mRNA.
DR PDB; 5MOG; X-ray; 2.77 A; A/B/C/D/E=88-578.
DR PDBsum; 5MOG; -.
DR AlphaFoldDB; A2XDA1; -.
DR SMR; A2XDA1; -.
DR STRING; 39946.A2XDA1; -.
DR BRENDA; 1.3.5.5; 11590.
DR UniPathway; UPA00803; -.
DR Proteomes; UP000007015; Chromosome 3.
DR GO; GO:0009507; C:chloroplast; ISS:UniProtKB.
DR GO; GO:0009509; C:chromoplast; ISS:UniProtKB.
DR GO; GO:0035452; C:extrinsic component of plastid membrane; IDA:UniProtKB.
DR GO; GO:0071949; F:FAD binding; IDA:UniProtKB.
DR GO; GO:0016166; F:phytoene dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0016120; P:carotene biosynthetic process; IDA:UniProtKB.
DR GO; GO:0016117; P:carotenoid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0051289; P:protein homotetramerization; IDA:UniProtKB.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR002937; Amino_oxidase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR014102; Phytoene_desaturase.
DR Pfam; PF01593; Amino_oxidase; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR TIGRFAMs; TIGR02731; phytoene_desat; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carotenoid biosynthesis; Chloroplast; Chromoplast;
KW Direct protein sequencing; FAD; Flavoprotein; Membrane; Oxidoreductase;
KW Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..87
FT /note="Chloroplast and chromoplast"
FT /evidence="ECO:0000255"
FT CHAIN 88..578
FT /note="15-cis-phytoene desaturase,
FT chloroplastic/chromoplastic"
FT /id="PRO_0000295009"
FT BINDING 115
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 134..135
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 142
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 159..160
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 165
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 300
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 342
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 531
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 539
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT BINDING 541
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:28669634,
FT ECO:0007744|PDB:5MOG"
FT MUTAGEN 162
FT /note="F->V: Shows less than 5% activity of that of the
FT wild-type. Confers norflurazon (NFZ) resistance. Remains
FT flavinylated."
FT /evidence="ECO:0000269|PubMed:29176862"
FT MUTAGEN 300
FT /note="R->S: 15% of the zeta-carotene forming activity of
FT that of the wild-type. 3.5-fold increase in affinity, but
FT 23-fold decrease in reaction rate with decylplastoquinone
FT (DPQ) as substrate. 12-fold increase in affinity, but 46-
FT fold decrease in reaction rate with phytoene as substrate.
FT Incorporation of FAD into the enzyme is not affected. No
FT difference in membrane association compared to wild-type.
FT No effect on the oligomeric assembly or solubility of the
FT protein. 5-fold increased resistance to norflurazon (NFZ)
FT compared to wild-type."
FT /evidence="ECO:0000269|PubMed:29176862"
FT MUTAGEN 300
FT /note="R->T: 6% of the zeta-carotene forming activity of
FT that of the wild-type."
FT /evidence="ECO:0000269|PubMed:29176862"
FT MUTAGEN 506
FT /note="Y->F: 5% of the zeta-carotene forming activity of
FT that of the wild-type. Forms 9,15-di-cis-phytofluene and
FT 9,15,9'-tri-cis-zeta-carotene as the sole products normally
FT as does the wild-type."
FT /evidence="ECO:0000269|PubMed:29176862"
FT MUTAGEN 508
FT /note="T->V: 5% of the zeta-carotene forming activity of
FT that of the wild-type. Forms 9,15-di-cis-phytofluene and
FT 9,15,9'-tri-cis-zeta-carotene as the sole products normally
FT as does the wild-type."
FT /evidence="ECO:0000269|PubMed:29176862"
FT MUTAGEN 538
FT /note="L->F,R: Shows less than 5% activity of that of the
FT wild-type. Confers norflurazon (NFZ) resistance. Remains
FT flavinylated."
FT /evidence="ECO:0000269|PubMed:29176862"
FT CONFLICT 15..16
FT /note="SQ -> AS (in Ref. 2; AAD02489)"
FT /evidence="ECO:0000305"
FT CONFLICT 19
FT /note="S -> Y (in Ref. 2; AAD02489)"
FT /evidence="ECO:0000305"
FT CONFLICT 40
FT /note="S -> G (in Ref. 2; AAD02489)"
FT /evidence="ECO:0000305"
FT CONFLICT 199
FT /note="F -> S (in Ref. 2; AAD02489)"
FT /evidence="ECO:0000305"
FT CONFLICT 446
FT /note="N -> S (in Ref. 2; AAD02489)"
FT /evidence="ECO:0000305"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 114..125
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 129..133
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 141..143
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 153..157
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 166..174
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 178..180
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 181..183
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 186..191
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 199..203
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 212..220
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 227..242
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 245..250
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 251..253
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 256..262
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 267..272
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 274..282
FT /evidence="ECO:0007829|PDB:5MOG"
FT TURN 286..288
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 291..302
FT /evidence="ECO:0007829|PDB:5MOG"
FT TURN 305..308
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 310..315
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 317..320
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 322..331
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 335..339
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 342..347
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 351..358
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 367..371
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 375..381
FT /evidence="ECO:0007829|PDB:5MOG"
FT TURN 384..388
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 390..393
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 394..396
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 403..412
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 427..434
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 435..438
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 449..454
FT /evidence="ECO:0007829|PDB:5MOG"
FT TURN 458..462
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 465..479
FT /evidence="ECO:0007829|PDB:5MOG"
FT TURN 481..483
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 488..491
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 493..501
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 513..515
FT /evidence="ECO:0007829|PDB:5MOG"
FT STRAND 526..528
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 541..557
FT /evidence="ECO:0007829|PDB:5MOG"
FT HELIX 559..566
FT /evidence="ECO:0007829|PDB:5MOG"
SQ SEQUENCE 578 AA; 64770 MW; 6561B0DE071282EF CRC64;
MDTGCLSSMN ITGTSQARSF AGQLPTHRCF ASSSIQALKS SQHVSFGVKS LVLRNKGKRF
RRRLGALQVV CQDFPRPPLE NTINFLEAGQ LSSFFRNSEQ PTKPLQVVIA GAGLAGLSTA
KYLADAGHKP ILLEARDVLG GKIAAWKDED GDWYETGLHI FFGAYPNIQN LFGELGINDR
LQWKEHSMIF AMPNKPGEFS RFDFPETLPA PLNGIWAILR NNEMLTWPEK VKFALGLLPA
MVGGQAYVEA QDGFTVSEWM KKQGVPDRVN DEVFIAMSKA LNFINPDELS MQCILIALNR
FLQEKHGSKM AFLDGNPPER LCMPIVDHVR SLGGEVRLNS RIQKIELNPD GTVKHFALTD
GTQITGDAYV FATPVDILKL LVPQEWKEIS YFKKLEKLVG VPVINVHIWF DRKLKNTYDH
LLFSRSSLLS VYADMSVTCK EYYDPNRSML ELVFAPAEEW VGRSDTEIIE ATMQELAKLF
PDEIAADQSK AKILKYHVVK TPRSVYKTIP DCEPCRPLQR SPIEGFYLAG DYTKQKYLAS
MEGAVLSGKL CAQSVVEDYK MLSRRSLKSL QSEVPVAS
