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Protein

Quinate/shikimate dehydrogenase

Gene

ydiB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The actual biological function of YdiB remains unclear, nor is it known whether 3-dehydroshikimate or quinate represents the natural substrate. Catalyzes the reversible NAD-dependent reduction of both 3-dehydroshikimate (DHSA) and 3-dehydroquinate to yield shikimate (SA) and quinate, respectively. It can use both NAD or NADP for catalysis, however it has higher catalytic efficiency with NAD.UniRule annotation3 Publications

Catalytic activityi

L-quinate + NAD(P)+ = 3-dehydroquinate + NAD(P)H.UniRule annotation2 Publications
Shikimate + NAD(P)+ = 3-dehydroshikimate + NAD(P)H.UniRule annotation2 Publications

Kineticsi

Kcat is 91 sec(-1) for dehydrogenase activity with shikimate (at pH 9 and 20 degrees Celsius). Kcat is 113 sec(-1) for dehydrogenase activity with quinate (at pH 9 and 20 degrees Celsius). Kcat is 105 sec(-1) for dehydrogenase activity with NAD (with shikinate at pH 9 and 20 degrees Celsius). Kcat is 142 sec(-1) for dehydrogenase activity with NAD (with quinate at pH 9 and 20 degrees Celsius).

  1. KM=2.9 µM for shikimate (at pH 9 and 20 degrees Celsius)1 Publication
  2. KM=9.1 µM for quinate (at pH 9 and 20 degrees Celsius)1 Publication
  3. KM=12.2 µM for NAD (with shikimate at pH 9 and 20 degrees Celsius)1 Publication
  4. KM=18.4 µM for NAD (with quinate at pH 9 and 20 degrees Celsius)1 Publication
  5. KM=20 µM for shikimate (with NAD at pH 9 and 20 degrees Celsius)1 Publication
  6. KM=41 µM for quinate (with NAD at pH 9 and 20 degrees Celsius)1 Publication
  7. KM=87 µM for NAD (with shikimate at pH 9 and 20 degrees Celsius)1 Publication
  8. KM=100 µM for NADP (with shikimate at pH 9 and 20 degrees Celsius)1 Publication
  9. KM=116 µM for NAD (with quinate at pH 9 and 20 degrees Celsius)1 Publication
  10. KM=120 µM for shikimate (with NADP at pH 9 and 20 degrees Celsius)1 Publication
  11. KM=500 µM for NADP (with quinate at pH 9 and 20 degrees Celsius)1 Publication
  12. KM=555 µM for quinate (with NADP at pH 9 and 20 degrees Celsius)1 Publication

    Pathwayi: chorismate biosynthesis

    This protein is involved in step 4 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, Phe-sensitive (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 sitei71 – 711SubstrateUniRule annotation
    Binding sitei107 – 1071SubstrateUniRule annotation
    Binding sitei205 – 2051NAD; via amide nitrogenUniRule annotation3 Publications
    Binding sitei255 – 2551NAD; via carbonyl oxygenUniRule annotation3 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi132 – 1354NADUniRule annotation3 Publications
    Nucleotide bindingi155 – 1584NADUniRule annotation3 Publications
    Nucleotide bindingi232 – 2354NADUniRule annotation3 Publications

    GO - Molecular functioni

    • NAD binding Source: EcoCyc
    • NADP binding Source: EcoCyc
    • nucleotide binding Source: EcoCyc
    • quinate 3-dehydrogenase (NAD+) activity Source: EcoCyc
    • quinate 3-dehydrogenase (NADP+) activity Source: UniProtKB-EC
    • shikimate 3-dehydrogenase (NAD+) activity Source: EcoCyc
    • shikimate 3-dehydrogenase (NADP+) activity Source: EcoCyc

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Aromatic amino acid biosynthesis

    Keywords - Ligandi

    NAD, NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11234-MONOMER.
    ECOL316407:JW1682-MONOMER.
    MetaCyc:EG11234-MONOMER.
    BRENDAi1.1.1.282. 2026.
    SABIO-RKP0A6D5.
    UniPathwayiUPA00053; UER00087.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Quinate/shikimate dehydrogenase1 PublicationUniRule annotation (EC:1.1.1.282UniRule annotation2 Publications)
    Alternative name(s):
    NAD-dependent shikimate 5-dehydrogenase1 PublicationUniRule annotation
    Gene namesi
    Name:ydiB1 PublicationUniRule annotation
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11234. ydiB.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi22 – 221S → A: Kinetically unchanged as compared with the wild-type. 1 Publication
    Mutagenesisi39 – 391Y → F: Kinetically unchanged as compared with the wild-type. 1 Publication
    Mutagenesisi67 – 671S → A: Reduces activity towards quinate about 6-fold, but has a little effect on shikimate conversion. 1 Publication
    Mutagenesisi71 – 711K → A: 3200-fold decrease in the affinity for quinate. 170-fold decrease in the affinity for shikimate. 1 Publication
    Mutagenesisi71 – 711K → G: 10-fold greater reduction in catalytic efficiency is observed with quinate than with shikimate. 1 Publication
    Mutagenesisi92 – 921N → A: Alters protein structure. Loss of activity for both substrates. 1 Publication
    Mutagenesisi106 – 1061T → A: 2000-fold decrease in the affinity for quinate. 70-fold decrease in the affinity for shikimate. 10-fold greater reduction in catalytic efficiency is observed with quinate than with shikimate. 1 Publication
    Mutagenesisi107 – 1071D → A: Loss of activity towards quinate. 20000-fold decrease in the affinity for shikimate. 1 Publication
    Mutagenesisi262 – 2621Q → A: 3-fold reduction in catalytic efficiency for both substrates. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 288287Quinate/shikimate dehydrogenasePRO_0000136069Add
    BLAST

    Proteomic databases

    PaxDbiP0A6D5.
    PRIDEiP0A6D5.

    Expressioni

    Inductioni

    Induced under carbon limitation but not under phosphate limitation.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation4 Publications

    Protein-protein interaction databases

    BioGridi4263505. 7 interactions.
    DIPiDIP-47967N.
    IntActiP0A6D5. 3 interactions.
    MINTiMINT-1283305.
    STRINGi511145.b1692.

    Structurei

    Secondary structure

    1
    288
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 158Combined sources
    Helixi22 – 3211Combined sources
    Beta strandi36 – 438Combined sources
    Turni46 – 483Combined sources
    Helixi49 – 5810Combined sources
    Beta strandi63 – 664Combined sources
    Helixi73 – 775Combined sources
    Beta strandi79 – 813Combined sources
    Helixi83 – 886Combined sources
    Beta strandi92 – 976Combined sources
    Beta strandi100 – 1045Combined sources
    Helixi106 – 11712Combined sources
    Beta strandi126 – 1305Combined sources
    Helixi134 – 14512Combined sources
    Beta strandi149 – 1557Combined sources
    Helixi161 – 17414Combined sources
    Beta strandi178 – 1836Combined sources
    Helixi187 – 1959Combined sources
    Beta strandi198 – 2025Combined sources
    Helixi220 – 2223Combined sources
    Beta strandi228 – 2314Combined sources
    Beta strandi235 – 2384Combined sources
    Helixi240 – 2467Combined sources
    Turni247 – 2493Combined sources
    Beta strandi251 – 2533Combined sources
    Helixi255 – 27117Combined sources
    Helixi277 – 2848Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NPDX-ray2.30A/B1-288[»]
    1O9BX-ray2.50A/B1-288[»]
    1VI2X-ray2.10A/B2-288[»]
    ProteinModelPortaliP0A6D5.
    SMRiP0A6D5. Positions 5-288.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6D5.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the shikimate dehydrogenase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105E2X. Bacteria.
    COG0169. LUCA.
    HOGENOMiHOG000237875.
    InParanoidiP0A6D5.
    KOiK05887.
    OMAiPFIHNSA.
    OrthoDBiEOG64R67G.
    PhylomeDBiP0A6D5.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    HAMAPiMF_00222. Shikimate_DH_AroE.
    MF_01578. Shikimate_DH_YdiB.
    InterProiIPR016040. NAD(P)-bd_dom.
    IPR022872. Quinate/Shikimate_DH.
    IPR013708. Shikimate_DH-bd_N.
    IPR022893. Shikimate_DH_fam.
    [Graphical view]
    PfamiPF08501. Shikimate_dh_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P0A6D5-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDVTAKYELI GLMAYPIRHS LSPEMQNKAL EKAGLPFTYM AFEVDNDSFP
    60 70 80 90 100
    GAIEGLKALK MRGTGVSMPN KQLACEYVDE LTPAAKLVGA INTIVNDDGY
    110 120 130 140 150
    LRGYNTDGTG HIRAIKESGF DIKGKTMVLL GAGGASTAIG AQGAIEGLKE
    160 170 180 190 200
    IKLFNRRDEF FDKALAFAQR VNENTDCVVT VTDLADQQAF AEALASADIL
    210 220 230 240 250
    TNGTKVGMKP LENESLVNDI SLLHPGLLVT ECVYNPHMTK LLQQAQQAGC
    260 270 280
    KTIDGYGMLL WQGAEQFTLW TGKDFPLEYV KQVMGFGA
    Length:288
    Mass (Da):31,228
    Last modified:June 7, 2005 - v1
    Checksum:iC3D1415E03820A5A
    GO

    Sequence cautioni

    The sequence CAA27848.1 differs from that shown. Reason: Frameshift at positions 170, 200 and 212. Curated

    Mass spectrometryi

    Molecular mass is 31361 Da from positions 1 - 288. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74762.1.
    AP009048 Genomic DNA. Translation: BAA15449.1.
    X04306 Genomic DNA. Translation: CAA27848.1. Frameshift.
    PIRiD64927.
    RefSeqiNP_416207.1. NC_000913.3.
    WP_000383469.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74762; AAC74762; b1692.
    BAA15449; BAA15449; BAA15449.
    GeneIDi946200.
    KEGGiecj:JW1682.
    eco:b1692.
    PATRICi32118690. VBIEscCol129921_1763.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74762.1.
    AP009048 Genomic DNA. Translation: BAA15449.1.
    X04306 Genomic DNA. Translation: CAA27848.1. Frameshift.
    PIRiD64927.
    RefSeqiNP_416207.1. NC_000913.3.
    WP_000383469.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NPDX-ray2.30A/B1-288[»]
    1O9BX-ray2.50A/B1-288[»]
    1VI2X-ray2.10A/B2-288[»]
    ProteinModelPortaliP0A6D5.
    SMRiP0A6D5. Positions 5-288.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263505. 7 interactions.
    DIPiDIP-47967N.
    IntActiP0A6D5. 3 interactions.
    MINTiMINT-1283305.
    STRINGi511145.b1692.

    Proteomic databases

    PaxDbiP0A6D5.
    PRIDEiP0A6D5.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74762; AAC74762; b1692.
    BAA15449; BAA15449; BAA15449.
    GeneIDi946200.
    KEGGiecj:JW1682.
    eco:b1692.
    PATRICi32118690. VBIEscCol129921_1763.

    Organism-specific databases

    EchoBASEiEB1216.
    EcoGeneiEG11234. ydiB.

    Phylogenomic databases

    eggNOGiENOG4105E2X. Bacteria.
    COG0169. LUCA.
    HOGENOMiHOG000237875.
    InParanoidiP0A6D5.
    KOiK05887.
    OMAiPFIHNSA.
    OrthoDBiEOG64R67G.
    PhylomeDBiP0A6D5.

    Enzyme and pathway databases

    UniPathwayiUPA00053; UER00087.
    BioCyciEcoCyc:EG11234-MONOMER.
    ECOL316407:JW1682-MONOMER.
    MetaCyc:EG11234-MONOMER.
    BRENDAi1.1.1.282. 2026.
    SABIO-RKP0A6D5.

    Miscellaneous databases

    EvolutionaryTraceiP0A6D5.
    PROiP0A6D5.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    HAMAPiMF_00222. Shikimate_DH_AroE.
    MF_01578. Shikimate_DH_YdiB.
    InterProiIPR016040. NAD(P)-bd_dom.
    IPR022872. Quinate/Shikimate_DH.
    IPR013708. Shikimate_DH-bd_N.
    IPR022893. Shikimate_DH_fam.
    [Graphical view]
    PfamiPF08501. Shikimate_dh_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF51735. SSF51735. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "The overexpression and complete amino acid sequence of Escherichia coli 3-dehydroquinase."
      Duncan K., Chaudhuri S., Campbell M.S., Coggins J.R.
      Biochem. J. 238:475-483(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 67-288, FUNCTION, SUBUNIT.
      Strain: K12.
    5. "Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli."
      Lindner H.A., Nadeau G., Matte A., Michel G., Menard R., Cygler M.
      J. Biol. Chem. 280:7162-7169(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF SER-22; TYR-39; SER-67; LYS-71; ASN-92; THR-106; ASP-107 AND GLN-262, MASS SPECTROMETRY, SUBSTRATE SPECIFICITY.
    6. "Transcriptome analysis of a shikimic acid producing strain of Escherichia coli W3110 grown under carbon- and phosphate-limited conditions."
      Johansson L., Liden G.
      J. Biotechnol. 126:528-545(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. "The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase."
      Benach J., Lee I., Edstrom W., Kuzin A.P., Chiang Y., Acton T.B., Montelione G.T., Hunt J.F.
      J. Biol. Chem. 278:19176-19182(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NAD, FUNCTION, SUBUNIT.
    8. "Structures of shikimate dehydrogenase AroE and its paralog YdiB. A common structural framework for different activities."
      Michel G., Roszak A.W., Sauve V., Maclean J., Matte A., Coggins J.R., Cygler M., Lapthorn A.J.
      J. Biol. Chem. 278:19463-19472(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH NAD, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, SUBSTRATE SPECIFICITY.
    9. Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-288 IN COMPLEX WITH NAD, SUBUNIT.

    Entry informationi

    Entry nameiYDIB_ECOLI
    AccessioniPrimary (citable) accession number: P0A6D5
    Secondary accession number(s): P28244, P77647
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: July 6, 2016
    This is version 100 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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.