Q39249 (VDE_ARATH) Reviewed, UniProtKB/Swiss-Prot

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)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › 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. Ref.5 Ref.6 Ref.7
Catalytic activity	Violaxanthin + ascorbate = antheraxanthin + dehydroascorbate + H2O. Antheraxanthin + ascorbate = zeaxanthin + dehydroascorbate + H2O.
Enzyme regulation	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. Ref.8 Ref.9 Ref.10
Subcellular location	Plastid › chloroplast thylakoid membrane; Peripheral membrane protein; Lumenal side By similarity.
Domain	The cysteine rich N-terminal region is required for activity. Ref.7
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	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	chlorophyll metabolic process Inferred from genetic interaction. Source: TAIR fatty acid metabolic process Inferred from genetic interaction. Source: TAIR response to heat Inferred from mutant phenotype. Source: TAIR xanthophyll cycle Inferred from mutant phenotype. Source: TAIR
Cellular component	chloroplast thylakoid membrane Inferred from electronic annotation. Source: UniProtKB-SubCell thylakoid lumen Inferred from direct assay. Source: TAIR
Molecular function	protein binding Inferred from physical interaction. Source: IntAct violaxanthin de-epoxidase activity Inferred from mutant phenotype. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
trxA	P0AA25	2	EBI-2895666,EBI-368542	From a different organism.

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. Ref.5

Secondary structure

1

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462

Helix Strand Turn

Details...

Helix

200 – 202

3

Helix

209 – 212

4

Beta strand

216 – 220

5

Turn

224 – 226

3

Beta strand

233 – 239

7

Beta strand

243 – 245

3

Beta strand

247 – 252

6

Beta strand

260 – 264

5

Beta strand

268 – 270

3

Beta strand

278 – 280

3

Beta strand

291 – 298

8

Beta strand

300 – 303

4

Beta strand

306 – 312

7

Beta strand

325 – 332

8

Helix

335 – 337

3

Helix

338 – 347

10

Helix

352 – 354

3

Sequences

	Sequence		Length	Mass (Da)
	Q39249 [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]	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: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"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: 9668132] [Abstract] Cited for: MUTAGENESIS OF CYS-185, FUNCTION. Strain: cv. Columbia.
[6]	"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.
[7]	"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.
[8]	"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.
[9]	"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.
[10]	"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.
CP002684 Genomic DNA. Translation: AEE28304.1.
CP002684 Genomic DNA. Translation: AEE28305.1.
AY063067 mRNA. Translation: AAL34241.1.
AF370251 mRNA. Translation: AAK44066.1.

IPI

IPI00535762.

PIR

T00708.

RefSeq

NP_001031000.1. NM_001035923.2.
NP_172331.1. NM_100728.3.

UniGene

At.20930.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3CQN	X-ray	2.00	A/B	191-366	[»]
3CQR	X-ray	2.00	A/B	191-366	[»]

ProteinModelPortal

Q39249.

SMR

Q39249. Positions 194-364.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q39249. 2 interactions.

STRING

Q39249.

Proteomic databases

PRIDE

Q39249.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT1G08550.1; AT1G08550.1; AT1G08550.
AT1G08550.2; AT1G08550.2; AT1G08550.

GeneID

837377.

GenomeReviews

Gene locus AT1G08550 in contig CT485782_GR.

KEGG

ath:AT1G08550.

NMPDR

fig|3702.1.peg.1063.

Organism-specific databases

TAIR

At1g08550.

Phylogenomic databases

GeneTree

EPGT00070000030968.

HOGENOM

HBG605576.

InParanoid

Q39249.

OMA

LAKCIAN.

PhylomeDB

Q39249.

ProtClustDB

PLN02372.

Enzyme and pathway databases

BioCyc

MetaCyc:AT1G08550-MONOMER.

BRENDA

1.10.99.3. 399.

Gene expression databases

ArrayExpress

Q39249.

Genevestigator

Q39249.

Family and domain databases

InterPro

IPR012674. Calycin.
IPR011038. Calycin-like.
IPR022272. Lipocalin_CS.
IPR010788. VDE.
[Graphical view]

Gene3D

G3DSA:2.40.128.20. Calycin. 1 hit.

KO

K09839.

Pfam

PF07137. VDE. 1 hit.
[Graphical view]

SUPFAM

SSF50814. Calycin. 1 hit.

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:	December 14, 2011
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program