Reviewed, UniProtKB/Swiss-Prot Q39249 (VDE_ARATH)

Names and origin

Protein names

Recommended 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

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	462 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.
Catalytic activity	Violaxanthin + ascorbate = antheraxanthin + dehydroascorbate + H(2)O. Antheraxanthin + ascorbate = zeaxanthin + dehydroascorbate + H(2)O.
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.
Subcellular location	Plastid › chloroplast thylakoid membrane; Peripheral membrane protein; Lumenal sideBy similarity.
Domain	The cysteine rich N-terminal region is required for activity.
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.

Ontologies

Keywords
Cellular component	Chloroplast Membrane Plastid Thylakoid
Domain	Coiled coil Transit peptide
Molecular function	Oxidoreductase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW transport Inferred from electronic annotation. Source: InterPro
Cellular component	chloroplast Inferred from electronic annotation. Source: UniProtKB-KW membrane Inferred from electronic annotation. Source: UniProtKB-KW thylakoid lumen Inferred from direct assay. Source: TAIR
Molecular function	binding Inferred from electronic annotation. Source: InterPro transporter activity Inferred from electronic annotation. Source: InterPro violaxanthin de-epoxidase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – ?		Chloroplast Potential
	Transit peptide	? – 113		Thylakoid
	Chain	114 – 462	349	Violaxanthin de-epoxidase, chloroplastic		PRO_5000144817
Regions
	Region	380 – 391	12	Involved in the binding to the thylakoid membrane
	Coiled coil	372 – 437	66	Potential
	Compositional bias	120 – 163	44	Cys-rich
Experimental info
	Mutagenesis	185	1	C → Y in npq1-1; loss of activity

Sequences

	Sequence		Length	Mass (Da)
	Q39249-1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 58E37B2C12D4426B	FASTA	462	52,017
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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.

Cross-references

Sequence databases
EMBLGenBankDDBJ	U44133 mRNA. Translation: AAC50032.1. AE005172 Genomic DNA. Translation: AAF99753.1. AC006932 Genomic DNA. Translation: AAF22898.1. AY063067 mRNA. Translation: AAL34241.1. AF370251 mRNA. Translation: AAK44066.1.
PIR	T00708.
RefSeq	NP_001031000.1. NP_172331.1.
UniGene	At.20930
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	837377.
GenomeReviews	Gene locus AT1G08550 in contig CT485782_GR.
KEGG	ath:AT1G08550.
NMPDR	fig|3702.1.peg.1063.
Organism-specific databases
TAIR	At1g08550.
Gene expression databases
ArrayExpress	Q39249.
Family and domain databases
InterPro	IPR012674. Calycin. IPR002345. Lipocalin. IPR010788. VDE. [Graphical view]
Gene3D	G3DSA:2.40.128.20. Calycin. 1 hit.
Pfam	PF07137. VDE. 1 hit. [Graphical view]
PROSITE	PS00213. LIPOCALIN. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

VDE_ARATH

Accession

Primary (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:	November 25, 2008
This is version 59 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)