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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)DescriptionActionsGraphical viewLength
Binding sitei362L-cysteine (covalent)Combined sources1

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.
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)DescriptionActionsGraphical viewLength
Mutagenesisi185C → Y in npq1-1; loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei? – 113Thylakoid1 Publication
Transit peptidei1 – ?ChloroplastSequence analysis
ChainiPRO_5000144817114 – 462Violaxanthin de-epoxidase, chloroplasticAdd BLAST349

Proteomic databases

PaxDbiQ39249.

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 interactor.
IntActiQ39249. 2 interactors.
STRINGi3702.AT1G08550.1.

Structurei

Secondary structure

1462
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi200 – 202Combined sources3
Helixi209 – 212Combined sources4
Beta strandi214 – 222Combined sources9
Turni224 – 226Combined sources3
Beta strandi233 – 239Combined sources7
Turni240 – 242Combined sources3
Beta strandi243 – 253Combined sources11
Beta strandi259 – 270Combined sources12
Beta strandi277 – 280Combined sources4
Helixi284 – 286Combined sources3
Beta strandi291 – 298Combined sources8
Beta strandi300 – 302Combined sources3
Beta strandi306 – 316Combined sources11
Beta strandi319 – 332Combined sources14
Helixi335 – 337Combined sources3
Helixi338 – 347Combined sources10
Helixi352 – 354Combined sources3
Beta strandi355 – 357Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ39249.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni380 – 391Involved in the binding to the thylakoid membraneAdd BLAST12

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili372 – 437Sequence analysisAdd BLAST66

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi120 – 163Cys-richAdd BLAST44

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.
OrthoDBiEOG09360AMT.
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_001035923.3.
NP_172331.1. NM_100728.4.
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_001035923.3.
NP_172331.1. NM_100728.4.
UniGeneiAt.20930.

3D structure databases

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

Protein-protein interaction databases

BioGridi22618. 1 interactor.
IntActiQ39249. 2 interactors.
STRINGi3702.AT1G08550.1.

Proteomic databases

PaxDbiQ39249.

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.
OrthoDBiEOG09360AMT.
PhylomeDBiQ39249.

Enzyme and pathway databases

BioCyciARA:AT1G08550-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...

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: November 30, 2016
This is version 122 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.