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Entry version 76 (02 Jun 2021)
Sequence version 2 (01 Mar 2002)
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Protein

Violaxanthin de-epoxidase, chloroplastic

Gene

VDE1

Organism
Spinacia oleracea (Spinach)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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.

Miscellaneous

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Irreversibly inhibited by DTT and iodoacetamide at pH 5.7 or pH 5.2, but not at pH 7.2 (Ref. 5, Ref. 3). Regulated through Ca2+ gating of H+ flux at the CFoH+ channel (PubMed:16228481). Requires the presence of lipids forming reverse hexagonal structures such as monogalactosyldiacylglyceride (MGDG) or phosphatidylethanolamine (PubMed:15078086). A negative curvature elastic stress in the thylakoid lipid bilayer is required for VDE1 activity (PubMed:17618598).5 Publications

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

KM for ascorbate increased when H-245, H-248, H-291 or H-297 are mutated.1 Publication
  1. KM=10 mM for ascorbate at pH 6.01 Publication
  2. KM=2.5 mM for ascorbate at pH 5.51 Publication
  3. KM=1 mM for ascorbate at pH 5.01 Publication
  4. KM=0.3 mM for ascorbate at pH 4.51 Publication

    pH dependencei

    Optimum pH is 5.0.1 Publication

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionOxidoreductase

    Enzyme and pathway databases

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    1.23.5.1, 5812

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Violaxanthin de-epoxidase, chloroplastic1 Publication (EC:1.23.5.12 Publications)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:VDE11 Publication
    Synonyms:SVDE1
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSpinacia oleracea (Spinach)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri3562 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaeCaryophyllalesChenopodiaceaeChenopodioideaeAnserineaeSpinacia

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    Keywords - Cellular componenti

    Chloroplast, Membrane, Plastid, Thylakoid

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi131C → S: No effect on activity. 1 Publication1
    Mutagenesisi133C → S: Loss of activity. 1 Publication1
    Mutagenesisi138C → S: Loss of activity. 1 Publication1
    Mutagenesisi145C → S: Loss of activity. 1 Publication1
    Mutagenesisi151C → S: Loss of activity. 1 Publication1
    Mutagenesisi157C → S: Loss of activity. 1 Publication1
    Mutagenesisi161C → S: Loss of activity. 1 Publication1
    Mutagenesisi170C → S: Loss of activity. 1 Publication1
    Mutagenesisi174C → S: Loss of activity. 1 Publication1
    Mutagenesisi189C → S: Loss of activity. 1 Publication1
    Mutagenesisi196C → S: Loss of activity. 1 Publication1
    Mutagenesisi242C → S: Loss of activity. 1 Publication1
    Mutagenesisi245H → A: 55% loss of activity; when associated with A-248. Total loss of activity; when associated with A-248; A-291 and R-297. 1 Publication1
    Mutagenesisi245H → R: Total loss of activity; when associated with R-248. Total loss of activity; when associated with R-248; R-291 and R-297. 1 Publication1
    Mutagenesisi248H → 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. 1 Publication1
    Mutagenesisi248H → 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. 1 Publication1
    Mutagenesisi291H → A: 99% loss of activity. Total loss of activity; when associated with A-245; A-248 and A-297. 1 Publication1
    Mutagenesisi291H → R: 55% loss of activity; when associated with R-297. Total loss of activity; when associated with R-245; R-248 and R-297. 1 Publication1
    Mutagenesisi297H → 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. 1 Publication1
    Mutagenesisi372C → S: Loss of activity. 1 Publication1

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a transit peptide.<p><a href='/help/transit' target='_top'>More...</a></p>Transit peptidei1 – ?Chloroplast
    Transit peptidei? – 124Thylakoid1 Publication
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_0000273251125 – 472Violaxanthin de-epoxidase, chloroplasticAdd BLAST348

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the PTM / Processing":/help/ptm_processing_section section describes the positions of cysteine residues participating in disulfide bonds.<p><a href='/help/disulfid' target='_top'>More...</a></p>Disulfide bondi133 ↔ 1511 Publication
    Disulfide bondi138 ↔ 1451 Publication
    Disulfide bondi157 ↔ 1741 Publication
    Disulfide bondi161 ↔ 1701 Publication
    Disulfide bondi189 ↔ 1961 Publication
    Disulfide bondi242 ↔ 3721 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

    Disulfide bonds. Reduction of the disulfides results in loss of a rigid structure, a decrease in thermal stability of 15 degrees Celsius and a loss of activity.1 Publication

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PRoteomics IDEntifications database

    More...
    PRIDEi
    Q9SM43

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    Q9SM43

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Coiled coil

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili379 – 462Sequence analysisAdd BLAST84

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the calycin superfamily. Lipocalin family.Curated

    Keywords - Domaini

    Coiled coil, Transit peptide

    Phylogenomic databases

    Database of Orthologous Groups

    More...
    OrthoDBi
    489088at2759

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    2.40.128.20, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR012674, Calycin
    IPR044682, VDE
    IPR010788, VDE_dom

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR33970, PTHR33970, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF07137, VDE, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF50814, SSF50814, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9SM43-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MALVARSICV SYDEIAGICN NVSHRNFKKW VQWKNPFLFQ DDARRNIRFN
    60 70 80 90 100
    DRKLSCTKFI GASEKLQHSK SPKSGLISCG WEVNSSKVVS NAVIPKKWNL
    110 120 130 140 150
    LKLKVVEVTA IVACTFFVMS SAQAVDALKT CTCLLKECRI ELAKCIANPS
    160 170 180 190 200
    CAANVACLQT CNNRPDETEC QIKCGDLFAN KVVDEFNECA VSRKKCVPQK
    210 220 230 240 250
    SDVGEFPVPD PSVLVKSFNM ADFNGKWFIS SGLNPTFDAF DCQLHEFHLE
    260 270 280 290 300
    DGKLVGNLSW RIKTPDGGFF TRTAVQKFAQ DPSQPGMLYN HDNAYLHYQD
    310 320 330 340 350
    DWYILSSKIE NQPDDYVFVY YRGRNDAWDG YGGAFLYTRS ATVPENIVPE
    360 370 380 390 400
    LNRAAQSVGK DFNKFIRTDN TCGPEPPLVE RLEKTVEEGE RTIIKEVEQL
    410 420 430 440 450
    EGEIEGDLEK VGKTEMTLFQ RLLEGFQELQ KDEEYFLKEL NKEERELLED
    460 470
    LKMEAGEVEK LFGRALPIRK LR
    Length:472
    Mass (Da):53,667
    Last modified:March 1, 2002 - v2
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i03C48EDE108BEEDB
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    AJ250433 mRNA Translation: CAB59211.2

    Genome annotation databases

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ag:CAB59211

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AJ250433 mRNA Translation: CAB59211.2

    3D structure databases

    SMRiQ9SM43
    ModBaseiSearch...

    Proteomic databases

    PRIDEiQ9SM43

    Genome annotation databases

    KEGGiag:CAB59211

    Phylogenomic databases

    OrthoDBi489088at2759

    Enzyme and pathway databases

    BRENDAi1.23.5.1, 5812

    Family and domain databases

    Gene3Di2.40.128.20, 1 hit
    InterProiView protein in InterPro
    IPR012674, Calycin
    IPR044682, VDE
    IPR010788, VDE_dom
    PANTHERiPTHR33970, PTHR33970, 1 hit
    PfamiView protein in Pfam
    PF07137, VDE, 1 hit
    SUPFAMiSSF50814, SSF50814, 1 hit

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiVDE_SPIOL
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q9SM43
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 23, 2007
    Last sequence update: March 1, 2002
    Last modified: June 2, 2021
    This is version 76 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    Direct protein sequencing

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
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