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Reviewed, UniProtKB/Swiss-Prot Q39249 (VDE_ARATH)

Last modified February 9, 2010. Version 73. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    Violaxanthin de-epoxidase, chloroplastic
      Short name=AtVxDE
    EC=1.10.99.3
Alternative name(s):
    Protein NON-PHOTOCHEMICAL QUENCHING 1
Gene names
Name: VDE1
Synonyms: AVDE1, NPQ1, VXDE
Ordered Locus Names: At1g08550
ORF Names: F22O13.3, T27G7.23
OrganismArabidopsis thaliana (Mouse-ear cress) [Complete proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonscore eudicotyledonsrosidsmalvidsBrassicalesBrassicaceaeArabidopsis

Protein attributes

Sequence length462 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

General annotation (Comments)

Function

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. Ref.4 Ref.5 Ref.6

Catalytic activity

Violaxanthin + ascorbate = antheraxanthin + dehydroascorbate + H2O.

Antheraxanthin + ascorbate = zeaxanthin + dehydroascorbate + H2O.

Enzyme regulation

Activity limitted 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. Ref.7 Ref.8 Ref.9

Subcellular location

Plastidchloroplast thylakoid membrane; Peripheral membrane protein; Lumenal side By similarity.

Domain

The cysteine rich N-terminal region is required for activity. Ref.6

Miscellaneous

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

Sequence similarities

Belongs to the calycin superfamily. Lipocalin family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – ?Chloroplast Potential
Transit peptide? – 113Thylakoid
Chain114 – 462349Violaxanthin de-epoxidase, chloroplastic
PRO_5000144817

Regions

Region380 – 39112Involved in the binding to the thylakoid membrane
Coiled coil372 – 43766 Potential
Compositional bias120 – 16344Cys-rich

Experimental info

Mutagenesis1851C → Y in npq1-1; loss of activity. Ref.4

Secondary structure

.................................. 462
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q39249-1 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 58E37B2C12D4426B

FASTA46252,017
        10         20         30         40         50         60 
MAVATHCFTS PCHDRIRFFS SDDGIGRLGI TRKRINGTFL LKILPPIQSA DLRTTGGRSS 

        70         80         90        100        110        120 
RPLSAFRSGF SKGIFDIVPL PSKNELKELT APLLLKLVGV LACAFLIVPS ADAVDALKTC 

       130        140        150        160        170        180 
ACLLKGCRIE LAKCIANPAC AANVACLQTC NNRPDETECQ IKCGDLFENS VVDEFNECAV 

       190        200        210        220        230        240 
SRKKCVPRKS DLGEFPAPDP SVLVQNFNIS DFNGKWYITS GLNPTFDAFD CQLHEFHTEG 

       250        260        270        280        290        300 
DNKLVGNISW RIKTLDSGFF TRSAVQKFVQ DPNQPGVLYN HDNEYLHYQD DWYILSSKIE 

       310        320        330        340        350        360 
NKPEDYIFVY YRGRNDAWDG YGGAVVYTRS SVLPNSIIPE LEKAAKSIGR DFSTFIRTDN 

       370        380        390        400        410        420 
TCGPEPALVE RIEKTVEEGE RIIVKEVEEI EEEVEKEVEK VGRTEMTLFQ RLAEGFNELK 

       430        440        450        460 
QDEENFVREL SKEEMEFLDE IKMEASEVEK LFGKALPIRK VR 

« Hide

References

« Hide 'large scale' references
[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: 9624110] [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. expand/collapse author list , 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: 11130712] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[3]"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. expand/collapse author list , 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: 14593172] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[4]"Arabidopsis mutants define a central role for the xanthophyll cycle in the regulation of photosynthetic energy conversion."
Niyogi K.K., Grossman A.R., Bjorkman O.
Plant Cell 10:1121-1134(1998) [PubMed: 9668132] [Abstract]
Cited for: MUTAGENESIS OF CYS-185, FUNCTION.
Strain: cv. Columbia.
[5]"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: 10982442] [Abstract]
Cited for: FUNCTION.
[6]"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: 11855651] [Abstract]
Cited for: DOMAIN, FUNCTION.
[7]"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: 11891252] [Abstract]
Cited for: ENZYME REGULATION.
[8]"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: 14749490] [Abstract]
Cited for: ENZYME REGULATION.
[9]"Functional roles of the major chloroplast lipids in the violaxanthin cycle."
Yamamoto H.Y.
Planta 224:719-724(2006) [PubMed: 16532316] [Abstract]
Cited for: ENZYME REGULATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U44133 mRNA. Translation: AAC50032.1.
AC003981 Genomic DNA. Translation: AAF99753.1.
AC006932 Genomic DNA. Translation: AAF22898.1.
AY063067 mRNA. Translation: AAL34241.1.
AF370251 mRNA. Translation: AAK44066.1.
IPIIPI00535762.
PIRT00708.
RefSeqNP_001031000.1.
NP_172331.1.
UniGeneAt.20930
Rsa.22802

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3CQNX-ray2.00A/B191-366[»]
3CQRX-ray2.00A/B191-366[»]
ModBaseSearch...

Protein-protein interaction databases

STRINGQ39249.

Proteomic databases

PRIDEQ39249.

Genome annotation databases

GeneID837377.
GenomeReviewsGene locus AT1G08550 in contig CT485782_GR.
KEGGath:AT1G08550.
NMPDRfig|3702.1.peg.1063.

Organism-specific databases

TAIRAt1g08550.

Phylogenomic databases

HOGENOMHBG605576.
InParanoidQ39249.
OMALAKCIAN.

Enzyme and pathway databases

BRENDA1.10.99.3. 302.

Gene expression databases

ArrayExpressQ39249.
GenevestigatorQ39249.

Family and domain databases

InterProIPR012674. Calycin.
IPR011038. Calycin-like.
IPR002345. Lipocalin.
IPR010788. VDE.
[Graphical view]
Gene3DG3DSA:2.40.128.20. Calycin. 1 hit.
PfamPF07137. VDE. 1 hit.
[Graphical view]
PROSITEPS00213. LIPOCALIN. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameVDE_ARATH
AccessionPrimary (citable) accession number: Q39249
Secondary accession number(s): Q9SJD9
Entry history
Integrated into UniProtKB/Swiss-Prot: January 23, 2007
Last sequence update: November 1, 1996
Last modified: February 9, 2010
This is version 73 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectPPAP (Plant Proteome Annotation Project)

Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents