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Protein

3-dehydroquinate dehydratase

Gene

aroD

Organism
Peptoclostridium difficile (strain 630) (Clostridium difficile)
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 Lys-170 at the active site.UniRule annotation1 Publication

Catalytic activityi

3-dehydroquinate = 3-dehydroshikimate + H2O.UniRule annotation1 Publication

Kineticsi

Kcat is 125 sec(-1) for dehydratase activity with 3-dehydroquinate (at pH 7.5 and 37 degrees Celsius).1 Publication

  1. KM=36 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. no protein annotated in this organism
    2. 3-dehydroquinate synthase (aroB)
    3. 3-dehydroquinate dehydratase (aroD)
    4. Shikimate dehydrogenase (NADP(+)) (aroE1), Shikimate dehydrogenase (NADP(+)) (aroE2)
    5. Shikimate kinase (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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei83 – 8313-dehydroquinateUniRule annotation2 Publications
    Active sitei144 – 1441Proton donor/acceptorUniRule annotation1 Publication
    Active sitei171 – 1711Schiff-base intermediate with substrateUniRule annotation2 Publications
    Binding sitei214 – 21413-dehydroquinateUniRule annotation2 Publications
    Binding sitei233 – 23313-dehydroquinateUniRule annotation1 Publication
    Binding sitei237 – 23713-dehydroquinateUniRule annotation2 Publications

    GO - Molecular functioni

    • 3-dehydroquinate dehydratase activity Source: UniProtKB

    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

    UniPathwayiUPA00053; UER00086.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-dehydroquinate dehydratase1 PublicationUniRule annotation (EC:4.2.1.101 PublicationUniRule annotation)
    Short name:
    3-dehydroquinase1 PublicationUniRule annotation
    Alternative name(s):
    Type I DHQaseUniRule annotation
    Type I dehydroquinaseUniRule annotation
    Short name:
    DHQ1UniRule annotation
    Gene namesi
    Name:aroDUniRule annotation
    Ordered Locus Names:CD630_22170
    OrganismiPeptoclostridium difficile (strain 630) (Clostridium difficile)
    Taxonomic identifieri272563 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaePeptoclostridium
    Proteomesi
    • UP000001978 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2552553-dehydroquinate dehydratasePRO_0000325520Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer or homotetramer.UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi272563.CD2217.

    Structurei

    Secondary structure

    1
    255
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 73Combined sources
    Beta strandi10 – 123Combined sources
    Beta strandi14 – 163Combined sources
    Beta strandi18 – 236Combined sources
    Helixi28 – 3811Combined sources
    Beta strandi44 – 496Combined sources
    Helixi50 – 523Combined sources
    Turni54 – 574Combined sources
    Helixi59 – 7214Combined sources
    Beta strandi78 – 814Combined sources
    Helixi85 – 873Combined sources
    Helixi95 – 10713Combined sources
    Beta strandi112 – 1176Combined sources
    Helixi118 – 1203Combined sources
    Helixi122 – 13413Combined sources
    Beta strandi138 – 14710Combined sources
    Helixi152 – 16413Combined sources
    Beta strandi168 – 1747Combined sources
    Helixi179 – 19517Combined sources
    Beta strandi201 – 2055Combined sources
    Helixi208 – 2147Combined sources
    Helixi217 – 2204Combined sources
    Beta strandi224 – 2263Combined sources
    Beta strandi228 – 2314Combined sources
    Helixi240 – 25213Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3JS3X-ray2.20A/B/C/D1-255[»]
    4H3DX-ray1.95A/B/C/D1-255[»]
    ProteinModelPortaliQ186A6.
    SMRiQ186A6. Positions 3-253.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ186A6.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni47 – 4933-dehydroquinate bindingUniRule annotation1 Publication

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105FF2. Bacteria.
    COG0710. LUCA.
    HOGENOMiHOG000105514.
    KOiK03785.
    OMAiCTFGAGE.
    OrthoDBiEOG6P33BK.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00214. AroD.
    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.

    Q186A6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKRKVQVKNI TIGEGRPKIC VPIIGKNKKD IIKEAKELKD ACLDIIEWRV
    60 70 80 90 100
    DFFENVENIK EVKEVLYELR SYIHDIPLLF TFRSVVEGGE KLISRDYYTT
    110 120 130 140 150
    LNKEISNTGL VDLIDVELFM GDEVIDEVVN FAHKKEVKVI ISNHDFNKTP
    160 170 180 190 200
    KKEEIVSRLC RMQELGADLP KIAVMPQNEK DVLVLLEATN EMFKIYADRP
    210 220 230 240 250
    IITMSMSGMG VISRLCGEIF GSALTFGAAK SVSAPGQISF KELNSVLNLL

    HKSIN
    Length:255
    Mass (Da):28,876
    Last modified:March 18, 2008 - v2
    Checksum:i60B9943466E5C9AD
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AM180355 Genomic DNA. Translation: CAJ69102.2.
    RefSeqiWP_009897376.1. NZ_CP010905.1.
    YP_001088731.2. NC_009089.1.

    Genome annotation databases

    EnsemblBacteriaiCAJ69102; CAJ69102; CD630_22170.
    GeneIDi4914552.
    KEGGicdf:CD630_22170.
    pdc:CDIF630_02450.
    PATRICi19442893. VBICloDif38397_2333.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AM180355 Genomic DNA. Translation: CAJ69102.2.
    RefSeqiWP_009897376.1. NZ_CP010905.1.
    YP_001088731.2. NC_009089.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3JS3X-ray2.20A/B/C/D1-255[»]
    4H3DX-ray1.95A/B/C/D1-255[»]
    ProteinModelPortaliQ186A6.
    SMRiQ186A6. Positions 3-253.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi272563.CD2217.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAJ69102; CAJ69102; CD630_22170.
    GeneIDi4914552.
    KEGGicdf:CD630_22170.
    pdc:CDIF630_02450.
    PATRICi19442893. VBICloDif38397_2333.

    Phylogenomic databases

    eggNOGiENOG4105FF2. Bacteria.
    COG0710. LUCA.
    HOGENOMiHOG000105514.
    KOiK03785.
    OMAiCTFGAGE.
    OrthoDBiEOG6P33BK.

    Enzyme and pathway databases

    UniPathwayiUPA00053; UER00086.

    Miscellaneous databases

    EvolutionaryTraceiQ186A6.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00214. AroD.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 630.
    2. "Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates."
      Light S.H., Minasov G., Shuvalova L., Duban M.E., Caffrey M., Anderson W.F., Lavie A.
      J. Biol. Chem. 286:3531-3539(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH 3-DEHYDROSHIKIMATE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, REACTION MECHANISM.
      Strain: 630.
    3. "1.95 Angstrom crystal structure of of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent modified comenic acid."
      Center for Structural Genomics of Infectious Diseases (CSGID)
      Minasov G., Light S.H., Shuvalova L., Duban M.E., Dubrovska I., Winsor J., Papazisi L., Anderson W.F.
      Submitted (SEP-2012) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, ACTIVE SITE, SUBUNIT.

    Entry informationi

    Entry nameiAROD_PEPD6
    AccessioniPrimary (citable) accession number: Q186A6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 18, 2008
    Last sequence update: March 18, 2008
    Last modified: December 9, 2015
    This is version 63 of the entry and version 2 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.