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Protein

Violaxanthin de-epoxidase, chloroplastic

Gene

VDE1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Part of the xanthophyll (or violaxanthin) cycle for controlling the concentration of zeaxanthin in chloroplasts. Catalyzes the two-step mono de-epoxidation reaction. Stereospecific for all-trans xanthophylls. Zeaxanthin induces the dissipation of excitation energy in the chlorophyll of the light-harvesting protein complex of photosystem II.3 Publications

Catalytic activityi

Violaxanthin + 2 L-ascorbate = antheraxanthin + 2 L-dehydroascorbate + H2O.Curated

Enzyme regulationi

Activity limited by low ascorbate availability. Feedback inhibition by zeaxanthin. Requires the presence of micelle-forming lipids such as monogalactosyldiacylglyceride (MGDG). Low concentration of bilayer forming lipids, such as digalactosyldiacylglyceride (DGDG) or phosphatidylcholine, supports a slower but nearly complete activity (PubMed:11891252, PubMed:14749490, PubMed:16532316). 80% of the specific activity in lumenal chloroplast fractions is lost in vitro in the presence of reduced thioredoxin (PubMed:20049866).4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei362 – 3621L-cysteine (covalent)Combined sources

GO - Molecular functioni

  • violaxanthin de-epoxidase activity Source: TAIR

GO - Biological processi

  • chlorophyll metabolic process Source: TAIR
  • fatty acid metabolic process Source: TAIR
  • response to heat Source: TAIR
  • xanthophyll cycle Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Enzyme and pathway databases

BioCyciARA:AT1G08550-MONOMER.
ARA:GQT-2385-MONOMER.
MetaCyc:AT1G08550-MONOMER.
BRENDAi1.10.99.3. 399.

Names & Taxonomyi

Protein namesi
Recommended name:
Violaxanthin de-epoxidase, chloroplastic1 Publication (EC:1.23.5.1Curated)
Short name:
AtVxDE
Alternative name(s):
Protein NON-PHOTOCHEMICAL QUENCHING 1
Gene namesi
Name:VDE11 Publication
Synonyms:AVDE1, NPQ1, VXDE
Ordered Locus Names:At1g08550Imported
ORF Names:F22O13.3Imported, T27G7.23Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G08550.

Subcellular locationi

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast thylakoid Source: TAIR
  • chloroplast thylakoid membrane Source: UniProtKB-SubCell
  • thylakoid lumen Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Membrane, Plastid, Thylakoid

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi185 – 1851C → Y in npq1-1; loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei? – 113Thylakoid1 Publication
Transit peptidei1 – ?ChloroplastSequence analysis
Chaini114 – 462349Violaxanthin de-epoxidase, chloroplasticPRO_5000144817Add
BLAST

Proteomic databases

PaxDbiQ39249.
PRIDEiQ39249.

Expressioni

Gene expression databases

ExpressionAtlasiQ39249. baseline and differential.
GenevisibleiQ39249. AT.

Interactioni

Subunit structurei

Interacts in vitro with LTO1.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
trxAP0AA252EBI-2895666,EBI-368542From a different organism.

Protein-protein interaction databases

BioGridi22618. 1 interaction.
IntActiQ39249. 2 interactions.
STRINGi3702.AT1G08550.1.

Structurei

Secondary structure

1
462
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi200 – 2023Combined sources
Helixi209 – 2124Combined sources
Beta strandi214 – 2229Combined sources
Turni224 – 2263Combined sources
Beta strandi233 – 2397Combined sources
Turni240 – 2423Combined sources
Beta strandi243 – 25311Combined sources
Beta strandi259 – 27012Combined sources
Beta strandi277 – 2804Combined sources
Helixi284 – 2863Combined sources
Beta strandi291 – 2988Combined sources
Beta strandi300 – 3023Combined sources
Beta strandi306 – 31611Combined sources
Beta strandi319 – 33214Combined sources
Helixi335 – 3373Combined sources
Helixi338 – 34710Combined sources
Helixi352 – 3543Combined sources
Beta strandi355 – 3573Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CQNX-ray2.00A/B191-366[»]
3CQRX-ray2.00A/B191-366[»]
ProteinModelPortaliQ39249.
SMRiQ39249. Positions 194-364.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ39249.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni380 – 39112Involved in the binding to the thylakoid membraneAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili372 – 43766Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi120 – 16344Cys-richAdd
BLAST

Domaini

The cysteine rich N-terminal region is required for activity.1 Publication

Sequence similaritiesi

Belongs to the calycin superfamily. Lipocalin family.Curated

Keywords - Domaini

Coiled coil, Transit peptide

Phylogenomic databases

eggNOGiENOG410IG0U. Eukaryota.
ENOG410XRAI. LUCA.
HOGENOMiHOG000265603.
InParanoidiQ39249.
KOiK09839.
OMAiDFNGKWY.
PhylomeDBiQ39249.

Family and domain databases

Gene3Di2.40.128.20. 1 hit.
InterProiIPR012674. Calycin.
IPR011038. Calycin-like.
IPR022272. Lipocalin_CS.
IPR010788. VDE.
[Graphical view]
PfamiPF07137. VDE. 1 hit.
[Graphical view]
SUPFAMiSSF50814. SSF50814. 1 hit.
PROSITEiPS00213. LIPOCALIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q39249-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVATHCFTS PCHDRIRFFS SDDGIGRLGI TRKRINGTFL LKILPPIQSA
60 70 80 90 100
DLRTTGGRSS RPLSAFRSGF SKGIFDIVPL PSKNELKELT APLLLKLVGV
110 120 130 140 150
LACAFLIVPS ADAVDALKTC ACLLKGCRIE LAKCIANPAC AANVACLQTC
160 170 180 190 200
NNRPDETECQ IKCGDLFENS VVDEFNECAV SRKKCVPRKS DLGEFPAPDP
210 220 230 240 250
SVLVQNFNIS DFNGKWYITS GLNPTFDAFD CQLHEFHTEG DNKLVGNISW
260 270 280 290 300
RIKTLDSGFF TRSAVQKFVQ DPNQPGVLYN HDNEYLHYQD DWYILSSKIE
310 320 330 340 350
NKPEDYIFVY YRGRNDAWDG YGGAVVYTRS SVLPNSIIPE LEKAAKSIGR
360 370 380 390 400
DFSTFIRTDN TCGPEPALVE RIEKTVEEGE RIIVKEVEEI EEEVEKEVEK
410 420 430 440 450
VGRTEMTLFQ RLAEGFNELK QDEENFVREL SKEEMEFLDE IKMEASEVEK
460
LFGKALPIRK VR
Length:462
Mass (Da):52,017
Last modified:November 1, 1996 - v1
Checksum:i58E37B2C12D4426B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U44133 mRNA. Translation: AAC50032.1.
AC003981 Genomic DNA. Translation: AAF99753.1.
AC006932 Genomic DNA. Translation: AAF22898.1.
CP002684 Genomic DNA. Translation: AEE28304.1.
CP002684 Genomic DNA. Translation: AEE28305.1.
AY063067 mRNA. Translation: AAL34241.1.
AF370251 mRNA. Translation: AAK44066.1.
PIRiT00708.
RefSeqiNP_001031000.1. NM_001035923.2.
NP_172331.1. NM_100728.3.
UniGeneiAt.20930.

Genome annotation databases

EnsemblPlantsiAT1G08550.1; AT1G08550.1; AT1G08550.
AT1G08550.2; AT1G08550.2; AT1G08550.
GeneIDi837377.
GrameneiAT1G08550.1; AT1G08550.1; AT1G08550.
AT1G08550.2; AT1G08550.2; AT1G08550.
KEGGiath:AT1G08550.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U44133 mRNA. Translation: AAC50032.1.
AC003981 Genomic DNA. Translation: AAF99753.1.
AC006932 Genomic DNA. Translation: AAF22898.1.
CP002684 Genomic DNA. Translation: AEE28304.1.
CP002684 Genomic DNA. Translation: AEE28305.1.
AY063067 mRNA. Translation: AAL34241.1.
AF370251 mRNA. Translation: AAK44066.1.
PIRiT00708.
RefSeqiNP_001031000.1. NM_001035923.2.
NP_172331.1. NM_100728.3.
UniGeneiAt.20930.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CQNX-ray2.00A/B191-366[»]
3CQRX-ray2.00A/B191-366[»]
ProteinModelPortaliQ39249.
SMRiQ39249. Positions 194-364.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi22618. 1 interaction.
IntActiQ39249. 2 interactions.
STRINGi3702.AT1G08550.1.

Proteomic databases

PaxDbiQ39249.
PRIDEiQ39249.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G08550.1; AT1G08550.1; AT1G08550.
AT1G08550.2; AT1G08550.2; AT1G08550.
GeneIDi837377.
GrameneiAT1G08550.1; AT1G08550.1; AT1G08550.
AT1G08550.2; AT1G08550.2; AT1G08550.
KEGGiath:AT1G08550.

Organism-specific databases

TAIRiAT1G08550.

Phylogenomic databases

eggNOGiENOG410IG0U. Eukaryota.
ENOG410XRAI. LUCA.
HOGENOMiHOG000265603.
InParanoidiQ39249.
KOiK09839.
OMAiDFNGKWY.
PhylomeDBiQ39249.

Enzyme and pathway databases

BioCyciARA:AT1G08550-MONOMER.
ARA:GQT-2385-MONOMER.
MetaCyc:AT1G08550-MONOMER.
BRENDAi1.10.99.3. 399.

Miscellaneous databases

EvolutionaryTraceiQ39249.
PROiQ39249.

Gene expression databases

ExpressionAtlasiQ39249. baseline and differential.
GenevisibleiQ39249. AT.

Family and domain databases

Gene3Di2.40.128.20. 1 hit.
InterProiIPR012674. Calycin.
IPR011038. Calycin-like.
IPR022272. Lipocalin_CS.
IPR010788. VDE.
[Graphical view]
PfamiPF07137. VDE. 1 hit.
[Graphical view]
SUPFAMiSSF50814. SSF50814. 1 hit.
PROSITEiPS00213. LIPOCALIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Xanthophyll cycle enzymes are members of the lipocalin family, the first identified from plants."
    Bugos R.C., Hieber A.D., Yamamoto H.Y.
    J. Biol. Chem. 273:15321-15324(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
    Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
    , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
    Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    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.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. Cited for: PROTEIN SEQUENCE OF 114-143, SUBCELLULAR LOCATION.
  6. "Arabidopsis mutants define a central role for the xanthophyll cycle in the regulation of photosynthetic energy conversion."
    Niyogi K.K., Grossman A.R., Bjoerkman O.
    Plant Cell 10:1121-1134(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-185, FUNCTION.
    Strain: cv. Columbia.
  7. "Photodamage of the photosynthetic apparatus and its dependence on the leaf developmental stage in the npq1 Arabidopsis mutant deficient in the xanthophyll cycle enzyme violaxanthin de-epoxidase."
    Havaux M., Bonfils J.-P., Luetz C., Niyogi K.K.
    Plant Physiol. 124:273-284(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Overexpression of violaxanthin de-epoxidase: properties of C-terminal deletions on activity and pH-dependent lipid binding."
    Hieber A.D., Bugos R.C., Verhoeven A.S., Yamamoto H.Y.
    Planta 214:476-483(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAIN, FUNCTION.
  9. "Ascorbate deficiency can limit violaxanthin de-epoxidase activity in vivo."
    Mueller-Moule P., Conklin P.L., Niyogi K.K.
    Plant Physiol. 128:970-977(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  10. "Significance of the lipid phase in the dynamics and functions of the xanthophyll cycle as revealed by PsbS overexpression in tobacco and in-vitro de-epoxidation in monogalactosyldiacylglycerol micelles."
    Hieber A.D., Kawabata O., Yamamoto H.Y.
    Plant Cell Physiol. 45:92-102(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  11. "Functional roles of the major chloroplast lipids in the violaxanthin cycle."
    Yamamoto H.Y.
    Planta 224:719-724(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  12. "Thioredoxin targets of the plant chloroplast lumen and their implications for plastid function."
    Hall M., Mata-Cabana A., Akerlund H.E., Florencio F.J., Schroeder W.P., Lindahl M., Kieselbach T.
    Proteomics 10:987-1001(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  13. "Identification of potential targets for thylakoid oxidoreductase AtVKOR/LTO1 in chloroplasts."
    Lu Y., Du J.J., Yu Z.B., Peng J.J., Xu J.N., Wang X.Y.
    Protein Pept. Lett. 22:219-225(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH LTO1.
  14. "A structural basis for the pH-dependent xanthophyll cycle in Arabidopsis thaliana."
    Arnoux P., Morosinotto T., Saga G., Bassi R., Pignol D.
    Plant Cell 21:2036-2044(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 191-366 IN COMPLEX WITH L-CYSTEINE.

Entry informationi

Entry nameiVDE_ARATH
AccessioniPrimary (citable) accession number: Q39249
Secondary accession number(s): Q9SJD9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2007
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

The amount of VDE in vivo is estimated to be 1 molecule per 20-100 electron transport chains.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.