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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

  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

    Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei21 – 2113-dehydroquinateUniRule annotation4 Publications
    Binding sitei82 – 8213-dehydroquinateUniRule annotation6 Publications
    Active sitei143 – 1431Proton donor/acceptorUniRule annotation5 Publications
    Active sitei170 – 1701Schiff-base intermediate with substrateUniRule annotation5 Publications
    Binding sitei213 – 21313-dehydroquinateUniRule annotation5 Publications
    Binding sitei232 – 23213-dehydroquinateUniRule annotation3 Publications
    Binding sitei236 – 23613-dehydroquinateUniRule annotation5 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

    BioCyciSENT99287:GCTI-1368-MONOMER.
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi86 – 861E → A: Very strong reduction of the catalytic efficiency and almost the same affinity for 3-dehydroquinate. 1 Publication
    Mutagenesisi86 – 861E → Q: Strong reduction of the catalytic efficiency and slight increase of the affinity for 3-dehydroquinate. 1 Publication
    Mutagenesisi170 – 1701K → M: Abolishes enzyme activity and 1.5-fold reduction of the affinity for 3-dehydroquinate. 2 Publications
    Mutagenesisi232 – 2321S → A: Reduces enzyme activity 50-fold. 1 Publication
    Mutagenesisi236 – 2361Q → A: Nearly abolishes enzyme activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2522523-dehydroquinate dehydratasePRO_0000138806Add
    BLAST

    Proteomic databases

    PRIDEiP58687.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation7 Publications

    Protein-protein interaction databases

    STRINGi99287.STM1358.

    Structurei

    Secondary structure

    1
    252
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 63Combined sources
    Beta strandi9 – 113Combined sources
    Beta strandi13 – 153Combined sources
    Beta strandi17 – 226Combined sources
    Helixi27 – 3711Combined sources
    Beta strandi43 – 486Combined sources
    Helixi49 – 513Combined sources
    Turni53 – 564Combined sources
    Helixi58 – 7114Combined sources
    Beta strandi77 – 804Combined sources
    Helixi84 – 863Combined sources
    Helixi94 – 10714Combined sources
    Beta strandi111 – 1166Combined sources
    Helixi117 – 1193Combined sources
    Helixi121 – 13313Combined sources
    Beta strandi137 – 14610Combined sources
    Helixi151 – 16313Combined sources
    Beta strandi167 – 1737Combined sources
    Helixi178 – 19417Combined sources
    Beta strandi201 – 2044Combined sources
    Helixi207 – 2104Combined sources
    Helixi211 – 2144Combined sources
    Helixi216 – 2194Combined sources
    Beta strandi223 – 2253Combined sources
    Beta strandi227 – 2293Combined sources
    Helixi239 – 25113Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-252.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP58687.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni46 – 4833-dehydroquinate bindingUniRule annotation5 Publications

    Sequence similaritiesi

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

    Phylogenomic databases

    HOGENOMiHOG000105514.
    KOiK03785.
    OMAiLFTFRSK.
    OrthoDBiEOG6P33BK.
    PhylomeDBiP58687.

    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.

    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
    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. Positions 1-252.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM1358.

    Proteomic databases

    PRIDEiP58687.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    HOGENOMiHOG000105514.
    KOiK03785.
    OMAiLFTFRSK.
    OrthoDBiEOG6P33BK.
    PhylomeDBiP58687.

    Enzyme and pathway databases

    UniPathwayiUPA00053; UER00086.
    BioCyciSENT99287:GCTI-1368-MONOMER.
    BRENDAi4.2.1.10. 2169.

    Miscellaneous databases

    EvolutionaryTraceiP58687.

    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: LT2 / SGSC1412 / ATCC 700720.
    2. "New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study."
      Yao Y., Li Z.S.
      Org. Biomol. Chem. 10:7037-7044(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE.
    3. "Insights into substrate binding and catalysis in bacterial type I dehydroquinase."
      Maneiro M., Peon A., Lence E., Otero J.M., Van Raaij M.J., Thompson P., Hawkins A.R., Gonzalez-Bello C.
      Biochem. J. 462:415-424(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
    4. "Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with citrate bound to the active Site."
      Minasov G., Light S.H., Shuvalova L., Papazisi L., Anderson W.F.
      Submitted (JAN-2010) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.
      Strain: LT2 / SGSC1412 / ATCC 700720.
    5. "A conserved surface loop in type I dehydroquinate dehydratases positions an active site arginine and functions in substrate binding."
      Light S.H., Minasov G., Shuvalova L., Peterson S.N., Caffrey M., Anderson W.F., Lavie A.
      Biochemistry 50:2357-2363(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.03 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-236, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF SER-232 AND GLN-236, REACTION MECHANISM.
    6. "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 (1.60 ANGSTROMS) OF WILD-TYPE AND MUTANT MET-170 IN COMPLEX WITH 3-DEHYDROQUINIC ACID, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, SUBUNIT, MUTAGENESIS OF LYS-170, REACTION MECHANISM.
      Strain: LT2 / SGSC1412 / ATCC 700720.
    7. "Crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella enterica typhimurium LT2 with malonate and boric acid at the active site."
      Light S.H., Minasov G., Duban M.-E., Halavaty A.S., Krishna S.N., Shuvalova L., Kwon K., Anderson W.F.
      Submitted (MAY-2011) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBUNIT.
    8. "1.8 angstrom crystal structure of the 3-dehydroquinate dehydratase (aroD) from Salmonella typhimurium LT2 with nickel bound at active site."
      Light S.H., Minasov G., Krishna S.N., Shuvalova L., Kwon K., Lavie A., Anderson W.F.
      Submitted (AUG-2012) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG, SUBUNIT.
    9. "Reassessing the type I dehydroquinate dehydratase catalytic triad: kinetic and structural studies of Glu86 mutants."
      Light S.H., Anderson W.F., Lavie A.
      Protein Sci. 22:418-424(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF MUTANT ALA-86 IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLU-86, ACTIVE SITE, SUBUNIT, REACTION MECHANISM.
    10. "Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation."
      Light S.H., Antanasijevic A., Krishna S.N., Caffrey M., Anderson W.F., Lavie A.
      Biochemistry 53:872-880(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) WILD-TYPE AND MUTANT MET-170 IN COMPLEX WITH SUBSTRATE ANALOGS, MUTAGENESIS OF LYS-170, SUBUNIT.

    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: May 27, 2015
    This is version 95 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

    External Data

    Dasty 3

    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 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.