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Protein

3-dehydroquinate dehydratase

Gene

aroD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the third step of the chorismate pathway, which leads to the biosynthesis of aromatic amino acids. Catalyzes the cis-dehydration of 3-dehydroquinate (DHQ) and introduces the first double bond of the aromatic ring to yield 3-dehydroshikimate. The reaction involves the formation of an imine intermediate between the keto group of 3-dehydroquinate and the epsylon-amino group of a lys-170 at the active site.UniRule annotation4 Publications

Catalytic activityi

3-dehydroquinate = 3-dehydroshikimate + H2O.UniRule annotation4 Publications

Enzyme regulationi

Inhibited by (2R)-2-methyl-3-dehydroquinic acid.1 Publication

Kineticsi

Kcat is 210 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius). Kcat is 255 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.2 and 25 degrees Celsius). Kcat is 310 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius).4 Publications

Manual assertion based on experiment ini

  1. KM=18 µM for 3-dehydroquinate (at pH 7.2 and 25 degrees Celsius)1 Publication
  2. KM=21 µM for 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius)1 Publication
  3. KM=53 µM for 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius)1 Publication

    Pathwayi: chorismate biosynthesis

    This protein is involved in step 3 of the subpathway that synthesizes chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate.UniRule annotation
    Proteins known to be involved in the 7 steps of the subpathway in this organism are:
    1. Phospho-2-dehydro-3-deoxyheptonate aldolase, Tyr-sensitive (aroF), Phospho-2-dehydro-3-deoxyheptonate aldolase, Trp-sensitive (aroH), Phospho-2-dehydro-3-deoxyheptonate aldolase (aroG)
    2. 3-dehydroquinate synthase (aroB)
    3. 3-dehydroquinate dehydratase (aroD)
    4. Quinate/shikimate dehydrogenase (ydiB), Shikimate dehydrogenase (NADP(+)) (aroE)
    5. Shikimate kinase 2 (aroL), Shikimate kinase 1 (aroK)
    6. 3-phosphoshikimate 1-carboxyvinyltransferase (aroA)
    7. Chorismate synthase (aroC)
    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)DescriptionActionsGraphical viewLength
    Binding sitei213-dehydroquinateUniRule annotation4 Publications1
    Binding sitei823-dehydroquinateUniRule annotation6 Publications1
    Active sitei143Proton donor/acceptorUniRule annotation5 Publications1
    Active sitei170Schiff-base intermediate with substrateUniRule annotation5 Publications1
    Binding sitei2133-dehydroquinateUniRule annotation5 Publications1
    Binding sitei2323-dehydroquinateUniRule annotation3 Publications1
    Binding sitei2363-dehydroquinateUniRule annotation5 Publications1

    GO - Molecular functioni

    • 3-dehydroquinate dehydratase activity Source: UniProtKB
    • NADP binding Source: GO_Central

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Amino-acid biosynthesis, Aromatic amino acid biosynthesis

    Keywords - Ligandi

    Schiff base

    Enzyme and pathway databases

    BRENDAi4.2.1.10. 2169.
    UniPathwayiUPA00053; UER00086.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-dehydroquinate dehydrataseUniRule annotation (EC:4.2.1.10UniRule annotation4 Publications)
    Short name:
    3-dehydroquinaseUniRule annotation
    Short name:
    DHQD1 Publication
    Alternative name(s):
    Type I DHQaseUniRule annotation
    Type I dehydroquinaseUniRule annotation
    Short name:
    DHQ1UniRule annotation
    Gene namesi
    Name:aroDUniRule annotation
    Ordered Locus Names:STM1358
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi86E → A: Very strong reduction of the catalytic efficiency and almost the same affinity for 3-dehydroquinate. 1 Publication1
    Mutagenesisi86E → Q: Strong reduction of the catalytic efficiency and slight increase of the affinity for 3-dehydroquinate. 1 Publication1
    Mutagenesisi170K → M: Abolishes enzyme activity and 1.5-fold reduction of the affinity for 3-dehydroquinate. 2 Publications1
    Mutagenesisi232S → A: Reduces enzyme activity 50-fold. 1 Publication1
    Mutagenesisi236Q → A: Nearly abolishes enzyme activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001388061 – 2523-dehydroquinate dehydrataseAdd BLAST252

    Proteomic databases

    PaxDbiP58687.
    PRIDEiP58687.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation7 Publications

    Protein-protein interaction databases

    STRINGi99287.STM1358.

    Structurei

    Secondary structure

    1252
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 6Combined sources3
    Beta strandi9 – 11Combined sources3
    Beta strandi13 – 15Combined sources3
    Beta strandi17 – 22Combined sources6
    Helixi27 – 37Combined sources11
    Beta strandi43 – 48Combined sources6
    Helixi49 – 51Combined sources3
    Turni53 – 56Combined sources4
    Helixi58 – 71Combined sources14
    Beta strandi77 – 80Combined sources4
    Helixi84 – 86Combined sources3
    Helixi94 – 107Combined sources14
    Beta strandi111 – 116Combined sources6
    Helixi117 – 119Combined sources3
    Helixi121 – 133Combined sources13
    Beta strandi137 – 146Combined sources10
    Helixi151 – 163Combined sources13
    Beta strandi167 – 173Combined sources7
    Helixi178 – 194Combined sources17
    Beta strandi201 – 204Combined sources4
    Helixi207 – 210Combined sources4
    Helixi211 – 214Combined sources4
    Helixi216 – 219Combined sources4
    Beta strandi223 – 225Combined sources3
    Beta strandi227 – 229Combined sources3
    Helixi239 – 251Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3L2IX-ray1.85A/B1-252[»]
    3LB0X-ray1.65A/B1-252[»]
    3M7WX-ray1.95A/B/C/D/E/F1-252[»]
    3NNTX-ray1.60A/B1-252[»]
    3O1NX-ray1.03A/B1-252[»]
    3OEXX-ray1.90A/B/C/D1-252[»]
    3S42X-ray1.45A/B1-252[»]
    4GFSX-ray1.80A/B1-252[»]
    4GUFX-ray1.50A/B1-252[»]
    4GUGX-ray1.62A/B1-252[»]
    4GUHX-ray1.95A/B1-252[»]
    4GUIX-ray1.78A/B1-252[»]
    4GUJX-ray1.50A/B1-252[»]
    4IUOX-ray1.80A/B1-252[»]
    ProteinModelPortaliP58687.
    SMRiP58687.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP58687.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni46 – 483-dehydroquinate bindingUniRule annotation5 Publications3

    Sequence similaritiesi

    Belongs to the type-I 3-dehydroquinase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105FF2. Bacteria.
    COG0710. LUCA.
    HOGENOMiHOG000105514.
    KOiK03785.
    OMAiLFTFRSK.
    PhylomeDBiP58687.

    Family and domain databases

    CDDicd00502. DHQase_I. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00214. AroD. 1 hit.
    InterProiIPR018508. 3-dehydroquinate_DH_AS.
    IPR013785. Aldolase_TIM.
    IPR001381. DHquinase_I.
    [Graphical view]
    PfamiPF01487. DHquinase_I. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01093. aroD. 1 hit.
    PROSITEiPS01028. DEHYDROQUINASE_I. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P58687-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKTVTVRDLV VGEGAPKIIV SLMGKTITDV KSEALAYREA DFDILEWRVD
    60 70 80 90 100
    HFANVTTAES VLEAAGAIRE IITDKPLLFT FRSAKEGGEQ ALTTGQYIDL
    110 120 130 140 150
    NRAAVDSGLV DMIDLELFTG DDEVKATVGY AHQHNVAVIM SNHDFHKTPA
    160 170 180 190 200
    AEEIVQRLRK MQELGADIPK IAVMPQTKAD VLTLLTATVE MQERYADRPI
    210 220 230 240 250
    ITMSMSKTGV ISRLAGEVFG SAATFGAVKK ASAPGQISVA DLRTVLTILH

    QA
    Length:252
    Mass (Da):27,325
    Last modified:January 31, 2002 - v1
    Checksum:i10BB561E38EA0A75
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL20283.1.
    RefSeqiNP_460324.1. NC_003197.1.
    WP_000860225.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL20283; AAL20283; STM1358.
    GeneIDi1252876.
    KEGGistm:STM1358.
    PATRICi32381199. VBISalEnt20916_1442.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL20283.1.
    RefSeqiNP_460324.1. NC_003197.1.
    WP_000860225.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3L2IX-ray1.85A/B1-252[»]
    3LB0X-ray1.65A/B1-252[»]
    3M7WX-ray1.95A/B/C/D/E/F1-252[»]
    3NNTX-ray1.60A/B1-252[»]
    3O1NX-ray1.03A/B1-252[»]
    3OEXX-ray1.90A/B/C/D1-252[»]
    3S42X-ray1.45A/B1-252[»]
    4GFSX-ray1.80A/B1-252[»]
    4GUFX-ray1.50A/B1-252[»]
    4GUGX-ray1.62A/B1-252[»]
    4GUHX-ray1.95A/B1-252[»]
    4GUIX-ray1.78A/B1-252[»]
    4GUJX-ray1.50A/B1-252[»]
    4IUOX-ray1.80A/B1-252[»]
    ProteinModelPortaliP58687.
    SMRiP58687.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM1358.

    Proteomic databases

    PaxDbiP58687.
    PRIDEiP58687.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL20283; AAL20283; STM1358.
    GeneIDi1252876.
    KEGGistm:STM1358.
    PATRICi32381199. VBISalEnt20916_1442.

    Phylogenomic databases

    eggNOGiENOG4105FF2. Bacteria.
    COG0710. LUCA.
    HOGENOMiHOG000105514.
    KOiK03785.
    OMAiLFTFRSK.
    PhylomeDBiP58687.

    Enzyme and pathway databases

    UniPathwayiUPA00053; UER00086.
    BRENDAi4.2.1.10. 2169.

    Miscellaneous databases

    EvolutionaryTraceiP58687.

    Family and domain databases

    CDDicd00502. DHQase_I. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00214. AroD. 1 hit.
    InterProiIPR018508. 3-dehydroquinate_DH_AS.
    IPR013785. Aldolase_TIM.
    IPR001381. DHquinase_I.
    [Graphical view]
    PfamiPF01487. DHquinase_I. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01093. aroD. 1 hit.
    PROSITEiPS01028. DEHYDROQUINASE_I. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiAROD_SALTY
    AccessioniPrimary (citable) accession number: P58687
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 31, 2002
    Last sequence update: January 31, 2002
    Last modified: November 30, 2016
    This is version 103 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.