Reviewed, UniProtKB/Swiss-Prot Q9SM43 (VDE_SPIOL)

Names and origin

Protein names

Recommended name:
    Violaxanthin de-epoxidase, chloroplastic
    EC=1.10.99.3

Gene names

Name:	VDE1
Synonyms:	SVDE1

Organism

Spinacia oleracea (Spinach)

Taxonomic identifier

3562 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › Caryophyllales › Amaranthaceae › Spinacia

Protein attributes

Sequence length	472 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 + H2O. Antheraxanthin + ascorbate = zeaxanthin + dehydroascorbate + H2O.
Enzyme regulation	Irreversibly inhibited by DTT and iodoacetamide at pH 5.7 or pH 5.2, but not at pH 7.2. Regulated through Ca2+ gating of H+ flux at the CFoH+ channel. Requires the presence of lipids forming reverse hexagonal structures such as monogalactosyldiacylglyceride (MGDG) or phosphatidylethanolamine. Ref.3 Ref.5 Ref.6 Ref.7
Subcellular location	Plastid › chloroplast thylakoid membrane; Peripheral membrane protein; Lumenal side. Note: Binds to the thylakoid membrane at pH 5.2 and is released in the lumen at pH 7.2. Ref.3 Ref.4
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.
biophysicochemical properties	Kinetic parameters: KM for ascorbate increased when H-245, H-248, H-291 or H-297 are mutated. KM=10 mM for ascorbate at pH 6.0 KM=2.5 mM for ascorbate at pH 5.5 KM=1 mM for ascorbate at pH 5.0 KM=0.3 mM for ascorbate at pH 4.5 pH dependence: Optimum pH is 5.0.

Ontologies

Keywords
Cellular component	Chloroplast Membrane Plastid Thylakoid
Domain	Coiled coil Transit peptide
Molecular function	Oxidoreductase
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chloroplast thylakoid membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	binding Inferred from electronic annotation. Source: InterPro violaxanthin de-epoxidase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – ?		Chloroplast
	Transit peptide	? – 124		Thylakoid Ref.2
	Chain	125 – 472	348	Violaxanthin de-epoxidase, chloroplastic		PRO_0000273251
Regions
	Coiled coil	379 – 462	84	Potential
	Compositional bias	131 – 174	44	Cys-rich
Experimental info
	Mutagenesis	245	1	H → A: 55% loss of activity; when associated with A-248. Total loss of activity; when associated with A-248; A-291 and R-297. Ref.1
	Mutagenesis	245	1	H → R: Total loss of activity; when associated with R-248. Total loss of activity; when associated with R-248; R-291 and R-297. Ref.1
	Mutagenesis	248	1	H → A: 40% loss of activity. 55% loss of activity; when associated with A-245. Total loss of activity; when associated with A-245; A-291 and R-297. Ref.1
	Mutagenesis	248	1	H → R: No effect. Total loss of activity; when associated with R-245. Total loss of activity; when associated with R-245; R-291 and R-297. Ref.1
	Mutagenesis	291	1	H → A: 99% loss of activity. Total loss of activity; when associated with A-245; A-248 and A-297. Ref.1
	Mutagenesis	291	1	H → R: 55% loss of activity; when associated with R-297. Total loss of activity; when associated with R-245; R-248 and R-297. Ref.1
	Mutagenesis	297	1	H → R: 55% loss of activity; when associated with R-291. Total loss of activity; when associated with R-245; R-248 and R-291. Total loss of activity; when associated with A-245; A-248 and A-291. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9SM43-1 [UniParc]. Last modified March 1, 2002. Version 2. Checksum: 03C48EDE108BEEDB	FASTA	472	53,667
	10 20 30 40 50 60 MALVARSICV SYDEIAGICN NVSHRNFKKW VQWKNPFLFQ DDARRNIRFN DRKLSCTKFI 70 80 90 100 110 120 GASEKLQHSK SPKSGLISCG WEVNSSKVVS NAVIPKKWNL LKLKVVEVTA IVACTFFVMS 130 140 150 160 170 180 SAQAVDALKT CTCLLKECRI ELAKCIANPS CAANVACLQT CNNRPDETEC QIKCGDLFAN 190 200 210 220 230 240 KVVDEFNECA VSRKKCVPQK SDVGEFPVPD PSVLVKSFNM ADFNGKWFIS SGLNPTFDAF 250 260 270 280 290 300 DCQLHEFHLE DGKLVGNLSW RIKTPDGGFF TRTAVQKFAQ DPSQPGMLYN HDNAYLHYQD 310 320 330 340 350 360 DWYILSSKIE NQPDDYVFVY YRGRNDAWDG YGGAFLYTRS ATVPENIVPE LNRAAQSVGK 370 380 390 400 410 420 DFNKFIRTDN TCGPEPPLVE RLEKTVEEGE RTIIKEVEQL EGEIEGDLEK VGKTEMTLFQ 430 440 450 460 470 RLLEGFQELQ KDEEYFLKEL NKEERELLED LKMEAGEVEK LFGRALPIRK LR

References

[1]	"Chemical and mutational modification of histidines in violaxanthinde-epoxidase from Spinacia oleracea." Emanuelsson A.K., Eskling M., Aakerlund H.-E. Physiol. Plantarum 119:97-104(2003) Cited for: NUCLEOTIDE SEQUENCE [MRNA], MUTAGENESIS OF HIS-245; HIS-248; HIS-291 AND HIS-297. Tissue: Leaf.
[2]	"Purification and identification of the violaxanthin deepoxidase as a 43 kDa protein." Arvidsson P.-O., Bratt C.E., Carlsson M., Aakerlund H.-E. Photosyn. Res. 49:119-129(1996) Cited for: PROTEIN SEQUENCE OF 125-144.
[3]	"Localization of the xanthophyll-cycle enzyme violaxanthin de-epoxidase within the thylakoid lumen and abolition of its mobility by a (light-dependent) pH decrease." Hager A., Holocher K. Planta 192:581-589(1994) Cited for: SUBCELLULAR LOCATION, ENZYME REGULATION.
[4]	"Regulation of violaxanthin de-epoxidase activity by pH and ascorbate concentration." Bratt C.E., Arvidsson P.-O., Carlsson M., Aakerlund H.-E. Photosyn. Res. 45:169-175(1995) Cited for: SUBCELLULAR LOCATION AND BIOPHYSICOCHEMICAL PROPERTIES.
[5]	"Violaxanthin accessibility and temperature dependency for de-epoxidation in spinach thylakoid membranes." Arvidsson P.-O., Carlsson M., Stefansson H., Albertsson P.-A., Aakerlund H.-E. Photosyn. Res. 52:39-48(1997) Cited for: ENZYME REGULATION.
[6]	"Influence of Ca(2+) on the thylakoid lumen violaxanthin de-epoxidase activity through Ca(2+) gating of H(+) flux at the CF(o) H(+) channel." Pan R.-S., Dilley R.A. Photosyn. Res. 65:141-154(2000) [PubMed: 16228481] [Abstract] Cited for: ENZYME REGULATION.
[7]	"Violaxanthin de-epoxidase, the xanthophyll cycle enzyme, requires lipid inverted hexagonal structures for its activity." Latowski D., Aakerlund H.-E., Strzalka K. Biochemistry 43:4417-4420(2004) [PubMed: 15078086] [Abstract] Cited for: ENZYME REGULATION.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AJ250433 mRNA. Translation: CAB59211.2.
3D structure databases
ModBase	Search...
Enzyme and pathway databases
BRENDA	1.10.99.3. 286.
Family and domain databases
InterPro	IPR012674. Calycin. IPR010788. VDE. [Graphical view]
Gene3D	G3DSA:2.40.128.20. Calycin. 1 hit.
Pfam	PF07137. VDE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

VDE_SPIOL

Accession

Primary (citable) accession number: Q9SM43

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 23, 2007
Last sequence update:	March 1, 2002
Last modified:	June 16, 2009
This is version 38 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)