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Protein

Probable pyridoxal 5'-phosphate synthase subunit PDX2

Gene

PDX2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PDX1. Involved in the indirect resistance to singlet oxygen-generating photosensitizers.2 Publications

Miscellaneous

In plants, synthesis of vitamin B6 does not involve deoxyxylulose 5-phosphate but utilizes intermediates from the pentose phosphate pathway and from glycolysis.
Vitamin B6 is an essential quencher of singlet oxygen in plants, that can protect cellular membranes from lipid peroxidation.

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.1 Publication
L-glutamine + H2O = L-glutamate + NH3.1 Publication

Kineticsi

kcat is 0.023 min(-1) for L-glutamine.1 Publication
  1. KM=1.92 mM for L-glutamine1 Publication

    Pathwayi: pyridoxal 5'-phosphate biosynthesis

    This protein is involved in the pathway pyridoxal 5'-phosphate biosynthesis, which is part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the pathway pyridoxal 5'-phosphate biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei78NucleophileBy similarity1
    Binding sitei108L-glutamineBy similarity1
    Active sitei202Charge relay systemBy similarity1
    Active sitei204Charge relay systemBy similarity1

    GO - Molecular functioni

    • glutaminase activity Source: TAIR
    • protein heterodimerization activity Source: TAIR
    • pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity Source: UniProtKB-EC

    GO - Biological processi

    Keywordsi

    Molecular functionHydrolase, Lyase
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BioCyciARA:AT5G60540-MONOMER
    MetaCyc:AT5G60540-MONOMER
    UniPathwayiUPA00245

    Protein family/group databases

    MEROPSiC26.A32

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Probable pyridoxal 5'-phosphate synthase subunit PDX2 (EC:4.3.3.61 Publication)
    Short name:
    AtPDX2
    Alternative name(s):
    Protein EMBRYO DEFECTIVE 2407
    Pyridoxal 5'-phosphate synthase glutaminase subunit (EC:3.5.1.21 Publication)
    Gene namesi
    Name:PDX2
    Synonyms:EMB2407
    Ordered Locus Names:At5g60540
    ORF Names:muf9.190
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 5

    Organism-specific databases

    AraportiAT5G60540
    TAIRilocus:2175083 AT5G60540

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Embryonic lethality when homozygous.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002706261 – 255Probable pyridoxal 5'-phosphate synthase subunit PDX2Add BLAST255

    Proteomic databases

    PaxDbiQ8LAD0
    PRIDEiQ8LAD0

    Expressioni

    Tissue specificityi

    Strongly expressed in roots, stems, leaves and flowers.1 Publication

    Gene expression databases

    ExpressionAtlasiQ8LAD0 baseline and differential
    GenevisibleiQ8LAD0 AT

    Interactioni

    Subunit structurei

    Interacts with PDX1.1 or PDX1.3, but not with PDX1.2. Binds to RPA2A.2 Publications

    GO - Molecular functioni

    • protein heterodimerization activity Source: TAIR

    Protein-protein interaction databases

    BioGridi21419, 6 interactors
    IntActiQ8LAD0, 5 interactors
    STRINGi3702.AT5G60540.1

    Structurei

    3D structure databases

    ProteinModelPortaliQ8LAD0
    SMRiQ8LAD0
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni46 – 48L-glutamine bindingBy similarity3
    Regioni142 – 143L-glutamine bindingBy similarity2

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi227 – 231Poly-Ser5

    Sequence similaritiesi

    Belongs to the glutaminase PdxT/SNO family.Curated

    Keywords - Domaini

    Glutamine amidotransferase

    Phylogenomic databases

    eggNOGiKOG3210 Eukaryota
    COG0311 LUCA
    HOGENOMiHOG000039949
    InParanoidiQ8LAD0
    KOiK08681
    OMAiVFIRAPI
    OrthoDBiEOG09360JS7
    PhylomeDBiQ8LAD0

    Family and domain databases

    CDDicd01749 GATase1_PB, 1 hit
    Gene3Di3.40.50.880, 1 hit
    HAMAPiMF_01615 PdxT, 1 hit
    InterProiView protein in InterPro
    IPR029062 Class_I_gatase-like
    IPR002161 PdxT/SNO
    IPR021196 PdxT/SNO_CS
    PANTHERiPTHR31559 PTHR31559, 1 hit
    PfamiView protein in Pfam
    PF01174 SNO, 1 hit
    PIRSFiPIRSF005639 Glut_amidoT_SNO, 1 hit
    SUPFAMiSSF52317 SSF52317, 1 hit
    TIGRFAMsiTIGR03800 PLP_synth_Pdx2, 1 hit
    PROSITEiView protein in PROSITE
    PS01236 PDXT_SNO_1, 1 hit
    PS51130 PDXT_SNO_2, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Q8LAD0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTVGVLALQG SFNEHIAALR RLGVQGVEIR KADQLLTVSS LIIPGGESTT
    60 70 80 90 100
    MAKLAEYHNL FPALREFVKM GKPVWGTCAG LIFLADRAVG QKEGGQELVG
    110 120 130 140 150
    GLDCTVHRNF FGSQIQSFEA DILVPQLTSQ EGGPETYRGV FIRAPAVLDV
    160 170 180 190 200
    GPDVEVLADY PVPSNKVLYS SSTVQIQEED ALPETKVIVA VKQGNLLATA
    210 220 230 240 250
    FHPELTADTR WHSYFIKMTK EIEQGASSSS SKTIVSVGET SAGPEPAKPD

    LPIFQ
    Length:255
    Mass (Da):27,438
    Last modified:October 1, 2002 - v1
    Checksum:i2B6447833990A677
    GO

    Sequence cautioni

    The sequence BAB08237 differs from that shown. Reason: Erroneous gene model prediction.Curated
    The sequence BAD94363 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti212H → P in BAD94363 (Ref. 6) Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB011483 Genomic DNA Translation: BAB08237.1 Sequence problems.
    CP002688 Genomic DNA Translation: AED97341.1
    AK117313 mRNA Translation: BAC41984.1
    BT005266 mRNA Translation: AAO63330.1
    AY087902 mRNA Translation: AAM65453.1
    AK220914 mRNA Translation: BAD94363.1 Different initiation.
    RefSeqiNP_568922.1, NM_125447.2
    UniGeneiAt.29154

    Genome annotation databases

    EnsemblPlantsiAT5G60540.1; AT5G60540.1; AT5G60540
    GeneIDi836175
    GrameneiAT5G60540.1; AT5G60540.1; AT5G60540
    KEGGiath:AT5G60540

    Similar proteinsi

    Entry informationi

    Entry nameiPDX2_ARATH
    AccessioniPrimary (citable) accession number: Q8LAD0
    Secondary accession number(s): Q56ZP9, Q9FKJ3
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 9, 2007
    Last sequence update: October 1, 2002
    Last modified: April 25, 2018
    This is version 100 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

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