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Protein

Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic

Gene

EMB3004

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

3-dehydroquinate = 3-dehydroshikimate + H2O.
Shikimate + NADP+ = 3-dehydroshikimate + NADPH.

Kineticsi

  1. KM=685 µM for shikimate1 Publication
  2. KM=131 µM for NADP1 Publication

    Pathwayi: chorismate biosynthesis

    This protein is involved in step 3 and 4 of the subpathway that synthesizes chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate.
    Proteins known to be involved in the 7 steps of the subpathway in this organism are:
    1. Phospho-2-dehydro-3-deoxyheptonate aldolase, Phospho-2-dehydro-3-deoxyheptonate aldolase, Phospho-2-dehydro-3-deoxyheptonate aldolase (DHS2), Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic (DHS2), Phospho-2-dehydro-3-deoxyheptonate aldolase (At4g33510), Phospho-2-dehydro-3-deoxyheptonate aldolase (At4g33510), Phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic (DHS1), Phospho-2-dehydro-3-deoxyheptonate aldolase (F12K8.24)
    2. 3-dehydroquinate synthase, chloroplastic (DHQS)
    3. Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic (EMB3004)
    4. Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic (EMB3004)
    5. Shikimate kinase 1, chloroplastic (SK1), Shikimate kinase 2, chloroplastic (SK2)
    6. 3-phosphoshikimate 1-carboxyvinyltransferase (F27K7.11), 3-phosphoshikimate 1-carboxyvinyltransferase, 3-phosphoshikimate 1-carboxyvinyltransferase, chloroplastic (At2g45300)
    7. Chorismate synthase (At1g48850), Chorismate synthase (EMB1144), Chorismate synthase (EMB1144), Chorismate synthase, chloroplastic (EMB1144)
    This subpathway is part of the pathway chorismate biosynthesis, which is itself part of Metabolic intermediate biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate, the pathway chorismate biosynthesis and in Metabolic intermediate biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei214 – 2141Proton acceptor; for 3-dehydroquinate dehydratase activity
    Active sitei241 – 2411Schiff-base intermediate with substrate; for 3-dehydroquinate dehydratase activity
    Binding sitei279 – 2791Substrate; for 3-dehydroquinate dehydratase activity
    Binding sitei336 – 3361Substrate; for shikimate dehydrogenase activity
    Binding sitei338 – 3381Substrate; for shikimate dehydrogenase activity
    Active sitei385 – 3851For shikimate dehydrogenase activity
    Binding sitei406 – 4061Substrate; for shikimate dehydrogenase activity
    Active sitei423 – 4231For shikimate dehydrogenase activity
    Binding sitei550 – 5501Substrate; for shikimate dehydrogenase activity
    Binding sitei578 – 5781Substrate; for shikimate dehydrogenase activity
    Binding sitei582 – 5821Substrate; for shikimate dehydrogenase activity

    GO - Molecular functioni

    GO - Biological processi

    • aromatic amino acid family biosynthetic process Source: UniProtKB-KW
    • chorismate biosynthetic process Source: UniProtKB-UniPathway
    • embryo development ending in seed dormancy Source: TAIR
    • shikimate metabolic process Source: TAIR

    Keywords - Molecular functioni

    Lyase, Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Aromatic amino acid biosynthesis

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciARA:AT3G06350-MONOMER.
    MetaCyc:AT3G06350-MONOMER.
    BRENDAi4.2.1.10. 399.
    SABIO-RKQ9SQT8.
    UniPathwayiUPA00053; UER00086.
    UPA00053; UER00087.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic
    Short name:
    DHQ-SDH protein
    Alternative name(s):
    DHQase-SORase
    Protein EMBRYO DEFECTIVE 3004
    Including the following 2 domains:
    Dehydroquinate dehydratase (EC:4.2.1.10)
    Short name:
    DHQ
    Shikimate dehydrogenase (EC:1.1.1.25)
    Short name:
    SDH
    Gene namesi
    Name:EMB3004
    Ordered Locus Names:At3g06350
    ORF Names:F24P17.18
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 3

    Organism-specific databases

    TAIRiAT3G06350.

    Subcellular locationi

    GO - Cellular componenti

    • chloroplast Source: TAIR
    • chloroplast stroma Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Plastid

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi336 – 3361S → A: 13-fold decrease in substrate affinity but almost no change in activity. 1 Publication
    Mutagenesisi338 – 3381S → A: 10-fold decrease in activity, and 9-fold decrease in substrate affinity. 1 Publication
    Mutagenesisi385 – 3851K → A: Strongly reduced shikimate dehydrogenase activity, but minor change in substrate affinity. 1 Publication
    Mutagenesisi385 – 3851K → N: Strongly reduced shikimate dehydrogenase activity, but no change in substrate affinity. 1 Publication
    Mutagenesisi423 – 4231D → A: Loss of shikimate dehydrogenase activity. 1 Publication
    Mutagenesisi423 – 4231D → N: Reduced shikimate dehydrogenase activity, but no change in substrate affinity. 1 Publication
    Mutagenesisi550 – 5501Y → F or A: 100-fold decrease in activity, and 2-fold decrease in substrate affinity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6666ChloroplastSequence analysisAdd
    BLAST
    Chaini67 – 603537Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplasticPRO_0000250645Add
    BLAST

    Proteomic databases

    PaxDbiQ9SQT8.
    PRIDEiQ9SQT8.

    PTM databases

    iPTMnetiQ9SQT8.

    Expressioni

    Gene expression databases

    GenevisibleiQ9SQT8. AT.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    STRINGi3702.AT3G06350.1.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi95 – 1006Combined sources
    Helixi105 – 11814Combined sources
    Beta strandi121 – 1266Combined sources
    Helixi127 – 1293Combined sources
    Helixi135 – 14511Combined sources
    Beta strandi150 – 1534Combined sources
    Helixi157 – 1593Combined sources
    Beta strandi161 – 1633Combined sources
    Helixi167 – 18014Combined sources
    Beta strandi183 – 1886Combined sources
    Helixi189 – 19810Combined sources
    Turni199 – 2013Combined sources
    Beta strandi208 – 2147Combined sources
    Helixi222 – 23312Combined sources
    Turni234 – 2363Combined sources
    Beta strandi238 – 2458Combined sources
    Helixi249 – 2513Combined sources
    Helixi252 – 26110Combined sources
    Beta strandi266 – 2727Combined sources
    Helixi273 – 2764Combined sources
    Helixi277 – 2804Combined sources
    Turni282 – 2865Combined sources
    Beta strandi288 – 2914Combined sources
    Beta strandi293 – 2953Combined sources
    Helixi307 – 3126Combined sources
    Helixi316 – 3183Combined sources
    Beta strandi324 – 3329Combined sources
    Helixi338 – 34811Combined sources
    Beta strandi352 – 3598Combined sources
    Helixi363 – 3697Combined sources
    Beta strandi375 – 3806Combined sources
    Helixi385 – 3917Combined sources
    Beta strandi393 – 3953Combined sources
    Helixi397 – 4026Combined sources
    Beta strandi406 – 4105Combined sources
    Turni412 – 4143Combined sources
    Beta strandi417 – 4204Combined sources
    Helixi423 – 43412Combined sources
    Beta strandi456 – 4594Combined sources
    Helixi463 – 47513Combined sources
    Beta strandi480 – 4856Combined sources
    Helixi486 – 49510Combined sources
    Beta strandi499 – 5024Combined sources
    Turni503 – 5086Combined sources
    Beta strandi514 – 5196Combined sources
    Turni536 – 5383Combined sources
    Helixi539 – 5413Combined sources
    Beta strandi542 – 5476Combined sources
    Beta strandi551 – 5544Combined sources
    Helixi556 – 5627Combined sources
    Turni563 – 5653Combined sources
    Beta strandi567 – 5693Combined sources
    Helixi571 – 58717Combined sources
    Helixi593 – 60311Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GPTX-ray1.95A90-603[»]
    2O7QX-ray2.20A90-603[»]
    2O7SX-ray1.78A90-603[»]
    ProteinModelPortaliQ9SQT8.
    SMRiQ9SQT8. Positions 90-603.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9SQT8.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni96 – 3132183-dehydroquinate dehydrataseAdd
    BLAST
    Regioni328 – 558231Shikimate dehydrogenaseAdd
    BLAST

    Sequence similaritiesi

    In the N-terminal section; belongs to the type-I 3-dehydroquinase family.Curated
    In the C-terminal section; belongs to the shikimate dehydrogenase family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG0692. Eukaryota.
    COG0169. LUCA.
    COG0710. LUCA.
    HOGENOMiHOG000237875.
    InParanoidiQ9SQT8.
    KOiK13832.
    OMAiGYEMFIE.
    OrthoDBiEOG093606TB.
    PhylomeDBiQ9SQT8.

    Family and domain databases

    CDDicd00502. DHQase_I. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    3.40.50.720. 1 hit.
    HAMAPiMF_00214. AroD. 1 hit.
    MF_00222. Shikimate_DH_AroE. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR001381. DHquinase_I.
    IPR016040. NAD(P)-bd_dom.
    IPR011342. Shikimate_DH.
    IPR013708. Shikimate_DH-bd_N.
    IPR022893. Shikimate_DH_fam.
    IPR006151. Shikm_DH/Glu-tRNA_Rdtase.
    [Graphical view]
    PfamiPF01487. DHquinase_I. 1 hit.
    PF01488. Shikimate_DH. 1 hit.
    PF08501. Shikimate_dh_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01093. aroD. 1 hit.
    TIGR00507. aroE. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9SQT8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAASSTNARL TNPPRLLSKP RLSPTSVANL RFPAADFSTR FFADSSSPRL
    60 70 80 90 100
    RSVPFPVVFS DQRRRRSMEP SNVYVASNST EMEIGSHDIV KNPSLICAPV
    110 120 130 140 150
    MADSIDKMVI ETSKAHELGA DLVEIRLDWL KDFNPLEDLK TIIKKSPLPT
    160 170 180 190 200
    LFTYRPKWEG GQYEGDENER RDVLRLAMEL GADYIDVELQ VASEFIKSID
    210 220 230 240 250
    GKKPGKFKVI VSSHNYQNTP SVEDLDGLVA RIQQTGADIV KIATTAVDIA
    260 270 280 290 300
    DVARMFHITS KAQVPTIGLV MGERGLMSRI LCSKFGGYLT FGTLDSSKVS
    310 320 330 340 350
    APGQPTIKDL LDLYNFRRIG PDTKVYGIIG KPVSHSKSPI VHNQAFKSVD
    360 370 380 390 400
    FNGVYVHLLV DNLVSFLQAY SSSDFAGFSC TIPHKEAALQ CCDEVDPLAK
    410 420 430 440 450
    SIGAVNTILR RKSDGKLLGY NTDCIGSISA IEDGLRSSGD PSSVPSSSSP
    460 470 480 490 500
    LASKTVVVIG AGGAGKALAY GAKEKGAKVV IANRTYERAL ELAEAIGGKA
    510 520 530 540 550
    LSLTDLDNYH PEDGMVLANT TSMGMQPNVE ETPISKDALK HYALVFDAVY
    560 570 580 590 600
    TPRITRLLRE AEESGAITVS GSEMFVRQAY EQFEIFTGLP APKELYWQIM

    SKY
    Length:603
    Mass (Da):65,796
    Last modified:May 1, 2000 - v1
    Checksum:i4DAAB35F594E7CB6
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti491 – 4911E → K in BAD94599 (Ref. 5) Curated
    Sequence conflicti557 – 5571L → Q in AAS76684 (Ref. 3) Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AC011623 Genomic DNA. Translation: AAF08579.1.
    CP002686 Genomic DNA. Translation: AEE74381.1.
    BT012197 mRNA. Translation: AAS76684.1.
    AY736474 mRNA. Translation: AAW63134.1.
    AK220988 mRNA. Translation: BAD94599.1.
    RefSeqiNP_187286.1. NM_111510.3.
    UniGeneiAt.43031.

    Genome annotation databases

    EnsemblPlantsiAT3G06350.1; AT3G06350.1; AT3G06350.
    GeneIDi819809.
    GrameneiAT3G06350.1; AT3G06350.1; AT3G06350.
    KEGGiath:AT3G06350.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AC011623 Genomic DNA. Translation: AAF08579.1.
    CP002686 Genomic DNA. Translation: AEE74381.1.
    BT012197 mRNA. Translation: AAS76684.1.
    AY736474 mRNA. Translation: AAW63134.1.
    AK220988 mRNA. Translation: BAD94599.1.
    RefSeqiNP_187286.1. NM_111510.3.
    UniGeneiAt.43031.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GPTX-ray1.95A90-603[»]
    2O7QX-ray2.20A90-603[»]
    2O7SX-ray1.78A90-603[»]
    ProteinModelPortaliQ9SQT8.
    SMRiQ9SQT8. Positions 90-603.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi3702.AT3G06350.1.

    PTM databases

    iPTMnetiQ9SQT8.

    Proteomic databases

    PaxDbiQ9SQT8.
    PRIDEiQ9SQT8.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT3G06350.1; AT3G06350.1; AT3G06350.
    GeneIDi819809.
    GrameneiAT3G06350.1; AT3G06350.1; AT3G06350.
    KEGGiath:AT3G06350.

    Organism-specific databases

    TAIRiAT3G06350.

    Phylogenomic databases

    eggNOGiKOG0692. Eukaryota.
    COG0169. LUCA.
    COG0710. LUCA.
    HOGENOMiHOG000237875.
    InParanoidiQ9SQT8.
    KOiK13832.
    OMAiGYEMFIE.
    OrthoDBiEOG093606TB.
    PhylomeDBiQ9SQT8.

    Enzyme and pathway databases

    UniPathwayiUPA00053; UER00086.
    UPA00053; UER00087.
    BioCyciARA:AT3G06350-MONOMER.
    MetaCyc:AT3G06350-MONOMER.
    BRENDAi4.2.1.10. 399.
    SABIO-RKQ9SQT8.

    Miscellaneous databases

    EvolutionaryTraceiQ9SQT8.
    PROiQ9SQT8.

    Gene expression databases

    GenevisibleiQ9SQT8. AT.

    Family and domain databases

    CDDicd00502. DHQase_I. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    3.40.50.720. 1 hit.
    HAMAPiMF_00214. AroD. 1 hit.
    MF_00222. Shikimate_DH_AroE. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR001381. DHquinase_I.
    IPR016040. NAD(P)-bd_dom.
    IPR011342. Shikimate_DH.
    IPR013708. Shikimate_DH-bd_N.
    IPR022893. Shikimate_DH_fam.
    IPR006151. Shikm_DH/Glu-tRNA_Rdtase.
    [Graphical view]
    PfamiPF01487. DHquinase_I. 1 hit.
    PF01488. Shikimate_DH. 1 hit.
    PF08501. Shikimate_dh_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01093. aroD. 1 hit.
    TIGR00507. aroE. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDHQSD_ARATH
    AccessioniPrimary (citable) accession number: Q9SQT8
    Secondary accession number(s): Q3ZLP7, Q56ZH7, Q6NLY1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 3, 2006
    Last sequence update: May 1, 2000
    Last modified: September 7, 2016
    This is version 112 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.