VDE_ARATH
ID VDE_ARATH Reviewed; 462 AA.
AC Q39249; Q9SJD9;
DT 23-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Violaxanthin de-epoxidase, chloroplastic {ECO:0000303|PubMed:9624110};
DE Short=AtVxDE;
DE EC=1.23.5.1 {ECO:0000305};
DE AltName: Full=Protein NON-PHOTOCHEMICAL QUENCHING 1;
DE Flags: Precursor;
GN Name=VDE1 {ECO:0000303|PubMed:9624110}; Synonyms=AVDE1, NPQ1, VXDE;
GN OrderedLocusNames=At1g08550 {ECO:0000312|Araport:AT1G08550};
GN ORFNames=F22O13.3 {ECO:0000312|EMBL:AAF99753.1},
GN T27G7.23 {ECO:0000312|EMBL:AAF22898.1};
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].
RC STRAIN=cv. Columbia;
RX PubMed=9624110; DOI=10.1074/jbc.273.25.15321;
RA Bugos R.C., Hieber A.D., Yamamoto H.Y.;
RT "Xanthophyll cycle enzymes are members of the lipocalin family, the first
RT identified from plants.";
RL J. Biol. Chem. 273:15321-15324(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [5]
RP PROTEIN SEQUENCE OF 114-143, AND SUBCELLULAR LOCATION.
RX PubMed=11719511; DOI=10.1074/jbc.m108575200;
RA Schubert M., Petersson U.A., Haas B.J., Funk C., Schroeder W.P.,
RA Kieselbach T.;
RT "Proteome map of the chloroplast lumen of Arabidopsis thaliana.";
RL J. Biol. Chem. 277:8354-8365(2002).
RN [6]
RP MUTAGENESIS OF CYS-185, AND FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=9668132; DOI=10.2307/3870716;
RA Niyogi K.K., Grossman A.R., Bjoerkman O.;
RT "Arabidopsis mutants define a central role for the xanthophyll cycle in the
RT regulation of photosynthetic energy conversion.";
RL Plant Cell 10:1121-1134(1998).
RN [7]
RP FUNCTION.
RX PubMed=10982442; DOI=10.1104/pp.124.1.273;
RA Havaux M., Bonfils J.-P., Luetz C., Niyogi K.K.;
RT "Photodamage of the photosynthetic apparatus and its dependence on the leaf
RT developmental stage in the npq1 Arabidopsis mutant deficient in the
RT xanthophyll cycle enzyme violaxanthin de-epoxidase.";
RL Plant Physiol. 124:273-284(2000).
RN [8]
RP DOMAIN, AND FUNCTION.
RX PubMed=11855651; DOI=10.1007/s00425-001-0704-2;
RA Hieber A.D., Bugos R.C., Verhoeven A.S., Yamamoto H.Y.;
RT "Overexpression of violaxanthin de-epoxidase: properties of C-terminal
RT deletions on activity and pH-dependent lipid binding.";
RL Planta 214:476-483(2002).
RN [9]
RP ACTIVITY REGULATION.
RX PubMed=11891252; DOI=10.1104/pp.010924;
RA Mueller-Moule P., Conklin P.L., Niyogi K.K.;
RT "Ascorbate deficiency can limit violaxanthin de-epoxidase activity in
RT vivo.";
RL Plant Physiol. 128:970-977(2002).
RN [10]
RP ACTIVITY REGULATION.
RX PubMed=14749490; DOI=10.1093/pcp/pch010;
RA Hieber A.D., Kawabata O., Yamamoto H.Y.;
RT "Significance of the lipid phase in the dynamics and functions of the
RT xanthophyll cycle as revealed by PsbS overexpression in tobacco and in-
RT vitro de-epoxidation in monogalactosyldiacylglycerol micelles.";
RL Plant Cell Physiol. 45:92-102(2004).
RN [11]
RP ACTIVITY REGULATION.
RX PubMed=16532316; DOI=10.1007/s00425-006-0257-5;
RA Yamamoto H.Y.;
RT "Functional roles of the major chloroplast lipids in the violaxanthin
RT cycle.";
RL Planta 224:719-724(2006).
RN [12]
RP ACTIVITY REGULATION.
RX PubMed=20049866; DOI=10.1002/pmic.200900654;
RA Hall M., Mata-Cabana A., Akerlund H.E., Florencio F.J., Schroeder W.P.,
RA Lindahl M., Kieselbach T.;
RT "Thioredoxin targets of the plant chloroplast lumen and their implications
RT for plastid function.";
RL Proteomics 10:987-1001(2010).
RN [13]
RP INTERACTION WITH LTO1.
RX PubMed=25412899; DOI=10.2174/0929866521666141121153138;
RA Lu Y., Du J.J., Yu Z.B., Peng J.J., Xu J.N., Wang X.Y.;
RT "Identification of potential targets for thylakoid oxidoreductase
RT AtVKOR/LTO1 in chloroplasts.";
RL Protein Pept. Lett. 22:219-225(2014).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 191-366, AND DISULFIDE BOND.
RX PubMed=19638474; DOI=10.1105/tpc.109.068007;
RA Arnoux P., Morosinotto T., Saga G., Bassi R., Pignol D.;
RT "A structural basis for the pH-dependent xanthophyll cycle in Arabidopsis
RT thaliana.";
RL Plant Cell 21:2036-2044(2009).
CC -!- FUNCTION: Part of the xanthophyll (or violaxanthin) cycle for
CC controlling the concentration of zeaxanthin in chloroplasts. Catalyzes
CC the two-step mono de-epoxidation reaction. Stereospecific for all-trans
CC xanthophylls. Zeaxanthin induces the dissipation of excitation energy
CC in the chlorophyll of the light-harvesting protein complex of
CC photosystem II. {ECO:0000269|PubMed:10982442,
CC ECO:0000269|PubMed:11855651, ECO:0000269|PubMed:9668132}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=all-trans-violaxanthin + 2 L-ascorbate = all-trans-zeaxanthin
CC + 2 H2O + 2 L-dehydroascorbate; Xref=Rhea:RHEA:32371,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:27547, ChEBI:CHEBI:35288,
CC ChEBI:CHEBI:38290, ChEBI:CHEBI:58539; EC=1.23.5.1;
CC Evidence={ECO:0000305};
CC -!- ACTIVITY REGULATION: Activity limited by low ascorbate availability.
CC Feedback inhibition by zeaxanthin. Requires the presence of micelle-
CC forming lipids such as monogalactosyldiacylglyceride (MGDG). Low
CC concentration of bilayer forming lipids, such as
CC digalactosyldiacylglyceride (DGDG) or phosphatidylcholine, supports a
CC slower but nearly complete activity (PubMed:11891252, PubMed:14749490,
CC PubMed:16532316). 80% of the specific activity in lumenal chloroplast
CC fractions is lost in vitro in the presence of reduced thioredoxin
CC (PubMed:20049866). {ECO:0000269|PubMed:11891252,
CC ECO:0000269|PubMed:14749490, ECO:0000269|PubMed:16532316,
CC ECO:0000269|PubMed:20049866}.
CC -!- SUBUNIT: Interacts in vitro with LTO1. {ECO:0000269|PubMed:25412899}.
CC -!- INTERACTION:
CC Q39249; P0AA25: trxA; Xeno; NbExp=2; IntAct=EBI-2895666, EBI-368542;
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000269|PubMed:11719511}; Peripheral membrane protein
CC {ECO:0000269|PubMed:11719511}; Lumenal side
CC {ECO:0000269|PubMed:11719511}.
CC -!- DOMAIN: The cysteine rich N-terminal region is required for activity.
CC {ECO:0000269|PubMed:11855651}.
CC -!- MISCELLANEOUS: The amount of VDE in vivo is estimated to be 1 molecule
CC per 20-100 electron transport chains.
CC -!- SIMILARITY: Belongs to the calycin superfamily. Lipocalin family.
CC {ECO:0000305}.
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DR EMBL; U44133; AAC50032.1; -; mRNA.
DR EMBL; AC003981; AAF99753.1; -; Genomic_DNA.
DR EMBL; AC006932; AAF22898.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28304.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE28305.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58901.1; -; Genomic_DNA.
DR EMBL; AY063067; AAL34241.1; -; mRNA.
DR EMBL; AF370251; AAK44066.1; -; mRNA.
DR PIR; T00708; T00708.
DR RefSeq; NP_001031000.1; NM_001035923.3.
DR RefSeq; NP_001321301.1; NM_001331777.1.
DR RefSeq; NP_172331.1; NM_100728.4.
DR PDB; 3CQN; X-ray; 2.00 A; A/B=191-366.
DR PDB; 3CQR; X-ray; 2.00 A; A/B=191-366.
DR PDBsum; 3CQN; -.
DR PDBsum; 3CQR; -.
DR AlphaFoldDB; Q39249; -.
DR SMR; Q39249; -.
DR BioGRID; 22618; 2.
DR IntAct; Q39249; 2.
DR STRING; 3702.AT1G08550.1; -.
DR PaxDb; Q39249; -.
DR PRIDE; Q39249; -.
DR ProteomicsDB; 243228; -.
DR EnsemblPlants; AT1G08550.1; AT1G08550.1; AT1G08550.
DR EnsemblPlants; AT1G08550.2; AT1G08550.2; AT1G08550.
DR EnsemblPlants; AT1G08550.3; AT1G08550.3; AT1G08550.
DR GeneID; 837377; -.
DR Gramene; AT1G08550.1; AT1G08550.1; AT1G08550.
DR Gramene; AT1G08550.2; AT1G08550.2; AT1G08550.
DR Gramene; AT1G08550.3; AT1G08550.3; AT1G08550.
DR KEGG; ath:AT1G08550; -.
DR Araport; AT1G08550; -.
DR TAIR; locus:2025510; AT1G08550.
DR eggNOG; ENOG502QSFY; Eukaryota.
DR HOGENOM; CLU_038426_1_0_1; -.
DR InParanoid; Q39249; -.
DR OMA; DFNGKWY; -.
DR OrthoDB; 489088at2759; -.
DR PhylomeDB; Q39249; -.
DR BioCyc; ARA:AT1G08550-MON; -.
DR BioCyc; MetaCyc:AT1G08550-MON; -.
DR BRENDA; 1.23.5.1; 399.
DR EvolutionaryTrace; Q39249; -.
DR PRO; PR:Q39249; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q39249; baseline and differential.
DR Genevisible; Q39249; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009534; C:chloroplast thylakoid; HDA:TAIR.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005576; C:extracellular region; HDA:TAIR.
DR GO; GO:0031977; C:thylakoid lumen; HDA:TAIR.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0019904; F:protein domain specific binding; IPI:CAFA.
DR GO; GO:0046422; F:violaxanthin de-epoxidase activity; IMP:TAIR.
DR GO; GO:0015994; P:chlorophyll metabolic process; IGI:TAIR.
DR GO; GO:0006631; P:fatty acid metabolic process; IGI:TAIR.
DR GO; GO:0009408; P:response to heat; IMP:TAIR.
DR GO; GO:0010028; P:xanthophyll cycle; IMP:TAIR.
DR Gene3D; 2.40.128.20; -; 1.
DR InterPro; IPR012674; Calycin.
DR InterPro; IPR022272; Lipocalin_CS.
DR InterPro; IPR044682; VDE.
DR InterPro; IPR010788; VDE_dom.
DR PANTHER; PTHR33970; PTHR33970; 1.
DR Pfam; PF07137; VDE; 1.
DR SUPFAM; SSF50814; SSF50814; 1.
DR PROSITE; PS00213; LIPOCALIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chloroplast; Coiled coil; Direct protein sequencing;
KW Disulfide bond; Membrane; Oxidoreductase; Plastid; Reference proteome;
KW Thylakoid; Transit peptide.
FT TRANSIT 1..?
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT TRANSIT ?..113
FT /note="Thylakoid"
FT /evidence="ECO:0000269|PubMed:11719511"
FT CHAIN 114..462
FT /note="Violaxanthin de-epoxidase, chloroplastic"
FT /id="PRO_5000144817"
FT REGION 380..391
FT /note="Involved in the binding to the thylakoid membrane"
FT COILED 372..437
FT /evidence="ECO:0000255"
FT DISULFID 231..362
FT /evidence="ECO:0007744|PDB:3CQN, ECO:0007744|PDB:3CQR"
FT MUTAGEN 185
FT /note="C->Y: In npq1-1; loss of activity."
FT /evidence="ECO:0000269|PubMed:9668132"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:3CQN"
FT HELIX 209..212
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 214..222
FT /evidence="ECO:0007829|PDB:3CQN"
FT TURN 224..226
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 233..239
FT /evidence="ECO:0007829|PDB:3CQN"
FT TURN 240..242
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 243..253
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 259..270
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 277..280
FT /evidence="ECO:0007829|PDB:3CQN"
FT HELIX 284..286
FT /evidence="ECO:0007829|PDB:3CQR"
FT STRAND 291..298
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 300..302
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 306..316
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 319..332
FT /evidence="ECO:0007829|PDB:3CQN"
FT HELIX 335..337
FT /evidence="ECO:0007829|PDB:3CQN"
FT HELIX 338..347
FT /evidence="ECO:0007829|PDB:3CQN"
FT HELIX 352..354
FT /evidence="ECO:0007829|PDB:3CQN"
FT STRAND 355..357
FT /evidence="ECO:0007829|PDB:3CQN"
SQ SEQUENCE 462 AA; 52017 MW; 58E37B2C12D4426B CRC64;
MAVATHCFTS PCHDRIRFFS SDDGIGRLGI TRKRINGTFL LKILPPIQSA DLRTTGGRSS
RPLSAFRSGF SKGIFDIVPL PSKNELKELT APLLLKLVGV LACAFLIVPS ADAVDALKTC
ACLLKGCRIE LAKCIANPAC AANVACLQTC NNRPDETECQ IKCGDLFENS VVDEFNECAV
SRKKCVPRKS DLGEFPAPDP SVLVQNFNIS DFNGKWYITS GLNPTFDAFD CQLHEFHTEG
DNKLVGNISW RIKTLDSGFF TRSAVQKFVQ DPNQPGVLYN HDNEYLHYQD DWYILSSKIE
NKPEDYIFVY YRGRNDAWDG YGGAVVYTRS SVLPNSIIPE LEKAAKSIGR DFSTFIRTDN
TCGPEPALVE RIEKTVEEGE RIIVKEVEEI EEEVEKEVEK VGRTEMTLFQ RLAEGFNELK
QDEENFVREL SKEEMEFLDE IKMEASEVEK LFGKALPIRK VR
