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Protein

Probable pyridoxal 5'-phosphate synthase subunit PDX2

Gene

PDX2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

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

Manual assertion based on experiment ini

  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

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Lyase

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciARA:AT5G60540-MONOMER.
    MetaCyc:AT5G60540-MONOMER.
    UniPathwayiUPA00245.

    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

    TAIRiAT5G60540.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: TAIR
    • glutaminase complex Source: GO_Central
    Complete GO annotation...

    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

    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.
    MINTiMINT-8063085.
    STRINGi3702.AT5G60540.1.

    Structurei

    3D structure databases

    ProteinModelPortaliQ8LAD0.
    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.
    OMAiVYGTCAG.
    OrthoDBiEOG09360JS7.
    PhylomeDBiQ8LAD0.

    Family and domain databases

    CDDicd01749. GATase1_PB. 1 hit.
    Gene3Di3.40.50.880. 1 hit.
    HAMAPiMF_01615. PdxT. 1 hit.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002161. PdxT/SNO.
    IPR021196. PdxT/SNO_CS.
    [Graphical view]
    PANTHERiPTHR31559:SF0. PTHR31559:SF0. 1 hit.
    PfamiPF01174. SNO. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
    PROSITEiPS01236. PDXT_SNO_1. 1 hit.
    PS51130. PDXT_SNO_2. 1 hit.
    [Graphical view]

    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.

    Cross-referencesi

    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.

    3D structure databases

    ProteinModelPortaliQ8LAD0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi21419. 6 interactors.
    IntActiQ8LAD0. 5 interactors.
    MINTiMINT-8063085.
    STRINGi3702.AT5G60540.1.

    Proteomic databases

    PaxDbiQ8LAD0.
    PRIDEiQ8LAD0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    TAIRiAT5G60540.

    Phylogenomic databases

    eggNOGiKOG3210. Eukaryota.
    COG0311. LUCA.
    HOGENOMiHOG000039949.
    InParanoidiQ8LAD0.
    KOiK08681.
    OMAiVYGTCAG.
    OrthoDBiEOG09360JS7.
    PhylomeDBiQ8LAD0.

    Enzyme and pathway databases

    UniPathwayiUPA00245.
    BioCyciARA:AT5G60540-MONOMER.
    MetaCyc:AT5G60540-MONOMER.

    Miscellaneous databases

    PROiQ8LAD0.

    Gene expression databases

    GenevisibleiQ8LAD0. AT.

    Family and domain databases

    CDDicd01749. GATase1_PB. 1 hit.
    Gene3Di3.40.50.880. 1 hit.
    HAMAPiMF_01615. PdxT. 1 hit.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002161. PdxT/SNO.
    IPR021196. PdxT/SNO_CS.
    [Graphical view]
    PANTHERiPTHR31559:SF0. PTHR31559:SF0. 1 hit.
    PfamiPF01174. SNO. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
    PROSITEiPS01236. PDXT_SNO_1. 1 hit.
    PS51130. PDXT_SNO_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPDX2_ARATH
    AccessioniPrimary (citable) accession number: Q8LAD0
    Secondary accession number(s): Q56ZP9, Q9FKJ3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 9, 2007
    Last sequence update: October 1, 2002
    Last modified: November 2, 2016
    This is version 93 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    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.

    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.