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P0A955

- ALKH_ECOLI

UniProt

P0A955 - ALKH_ECOLI

Protein

KHG/KDPG aldolase

Gene

eda

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 81 (01 Oct 2014)
      Sequence version 1 (19 Jul 2005)
      Previous versions | rss
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    Functioni

    Involved in the degradation of glucose via the Entner-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-Keto-3-deoxy-6-phosphogluconate (KDPG) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with si-facial selectivity. It accepts some nucleophiles other than pyruvate, including 2-oxobutanoate, phenylpyruvate, and fluorobutanoate. It has a preference for the S-configuration at C2 of the electrophile.2 Publications

    Catalytic activityi

    4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate.1 Publication
    2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate.1 Publication

    Kineticsi

    Kcat is 80 sec(-1) for KDPG, 0.012 sec(-1) for pyruvate and 0.0004 sec(-1) for 2-oxobutyrate.

    1. KM=0.1 mM for KDPG2 Publications
    2. KM=9 mM for 2-oxobutyrate2 Publications
    3. KM=10 mM for pyruvate2 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei45 – 451Proton acceptor
    Active sitei49 – 491
    Binding sitei49 – 491Substrate1 Publication
    Binding sitei73 – 731Substrate1 Publication
    Active sitei133 – 1331Schiff-base intermediate with substrate
    Binding sitei133 – 1331Substrate (covalent)1 Publication
    Binding sitei161 – 1611Substrate1 Publication
    Sitei161 – 1611Plays a major role in determining the stereoselectivity
    Binding sitei163 – 1631Substrate; via amide nitrogen1 Publication
    Binding sitei184 – 1841Substrate1 Publication

    GO - Molecular functioni

    1. 2-dehydro-3-deoxy-phosphogluconate aldolase activity Source: EcoliWiki
    2. 4-hydroxy-2-oxoglutarate aldolase activity Source: UniProtKB
    3. identical protein binding Source: IntAct

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Schiff base

    Enzyme and pathway databases

    BioCyciEcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
    ECOL316407:JW1839-MONOMER.
    MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
    UniPathwayiUPA00227.
    UPA00856; UER00829.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    KHG/KDPG aldolase
    Including the following 2 domains:
    4-hydroxy-2-oxoglutarate aldolase (EC:4.1.3.16)
    Alternative name(s):
    2-keto-4-hydroxyglutarate aldolase
    Short name:
    KHG-aldolase
    2-dehydro-3-deoxy-phosphogluconate aldolase (EC:4.1.2.14)
    Alternative name(s):
    2-keto-3-deoxy-6-phosphogluconate aldolase
    Short name:
    KDPG-aldolase
    Phospho-2-dehydro-3-deoxygluconate aldolase
    Phospho-2-keto-3-deoxygluconate aldolase
    Gene namesi
    Name:eda
    Synonyms:hga, kdgA
    Ordered Locus Names:b1850, JW1839
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10256. eda.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytosol Source: UniProtKB
    2. membrane Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene lose KHG aldolase activity.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi45 – 451E → N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity. 2 Publications
    Mutagenesisi133 – 1331K → Q: Absence of aldolase activity. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha-ketobutyrate; when associated with k-161. 1 Publication
    Mutagenesisi161 – 1611T → K: Shows activity significantly greater than wild-type. Shows a markedly altered substrate specificity relative to the wild-type, with an enhanced activity against pyridine carboxaldehyde, benzaldehyde, and alpha-ketobutyrate; when associated with Q-133. 2 Publications
    Mutagenesisi161 – 1611T → V: Little stereoselectivity, accepting KDPG and KDPGal as substrate with roughly equal efficacy. It strongly diminishes the activity against KDPG and slightly increases activity against KDPGal. 2 Publications
    Mutagenesisi168 – 1681N → S: Shows activity significantly greater than wild-type. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 213213KHG/KDPG aldolasePRO_0000201037Add
    BLAST

    Proteomic databases

    PaxDbiP0A955.
    PRIDEiP0A955.

    2D gel databases

    SWISS-2DPAGEP0A955.

    Expressioni

    Inductioni

    Constitutive, three-fold induction occurs for growth on gluconate and two-fold for growth on hexuronic acids.1 Publication

    Gene expression databases

    GenevestigatoriP0A955.

    Interactioni

    Subunit structurei

    Homotrimer.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-558114,EBI-558114

    Protein-protein interaction databases

    DIPiDIP-36196N.
    IntActiP0A955. 9 interactions.
    STRINGi511145.b1850.

    Structurei

    Secondary structure

    1
    213
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi8 – 136
    Beta strandi16 – 216
    Helixi26 – 283
    Helixi29 – 3810
    Beta strandi43 – 486
    Helixi53 – 6311
    Beta strandi67 – 737
    Helixi77 – 8610
    Beta strandi91 – 955
    Helixi98 – 1069
    Beta strandi107 – 1093
    Beta strandi111 – 1177
    Helixi118 – 1269
    Beta strandi131 – 1344
    Turni135 – 1417
    Helixi142 – 1509
    Beta strandi157 – 1637
    Turni166 – 1683
    Helixi169 – 1735
    Beta strandi181 – 1833
    Helixi184 – 1863
    Helixi189 – 1946
    Helixi197 – 21014

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EUAX-ray1.95A/B/C1-213[»]
    1EUNX-ray2.00A/B/C1-213[»]
    1FQ0X-ray2.10A/B/C1-213[»]
    1FWRX-ray2.70A/B/C1-213[»]
    1WAUX-ray2.80A1-213[»]
    1WBHX-ray1.55A/B/C1-213[»]
    2C0AX-ray1.55A/B/C1-213[»]
    ProteinModelPortaliP0A955.
    SMRiP0A955. Positions 1-213.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A955.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni8 – 92Substrate binding

    Sequence similaritiesi

    Belongs to the KHG/KDPG aldolase family.Curated

    Phylogenomic databases

    eggNOGiCOG0800.
    HOGENOMiHOG000233114.
    KOiK01625.
    OMAiSWLVPND.
    OrthoDBiEOG67DPKT.
    PhylomeDBiP0A955.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR000887. Aldlse_KDPG_KHG.
    IPR013785. Aldolase_TIM.
    [Graphical view]
    PfamiPF01081. Aldolase. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR01182. eda. 1 hit.
    PROSITEiPS00159. ALDOLASE_KDPG_KHG_1. 1 hit.
    PS00160. ALDOLASE_KDPG_KHG_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A955-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKNWKTSAES ILTTGPVVPV IVVKKLEHAV PMAKALVAGG VRVLEVTLRT    50
    ECAVDAIRAI AKEVPEAIVG AGTVLNPQQL AEVTEAGAQF AISPGLTEPL 100
    LKAATEGTIP LIPGISTVSE LMLGMDYGLK EFKFFPAEAN GGVKALQAIA 150
    GPFSQVRFCP TGGISPANYR DYLALKSVLC IGGSWLVPAD ALEAGDYDRI 200
    TKLAREAVEG AKL 213
    Length:213
    Mass (Da):22,284
    Last modified:July 19, 2005 - v1
    Checksum:iCC8D51B50480D0B7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X68871 Genomic DNA. Translation: CAA48732.1.
    M87458 Genomic DNA. Translation: AAA23723.1.
    L20897 Genomic DNA. Translation: AAA23862.1.
    X63694 Genomic DNA. Translation: CAA45222.1.
    U00096 Genomic DNA. Translation: AAC74920.1.
    AP009048 Genomic DNA. Translation: BAA15658.1.
    PIRiB42986. ADECOG.
    RefSeqiNP_416364.1. NC_000913.3.
    YP_490112.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74920; AAC74920; b1850.
    BAA15658; BAA15658; BAA15658.
    GeneIDi12930159.
    946367.
    KEGGiecj:Y75_p1826.
    eco:b1850.
    PATRICi32119021. VBIEscCol129921_1928.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X68871 Genomic DNA. Translation: CAA48732.1 .
    M87458 Genomic DNA. Translation: AAA23723.1 .
    L20897 Genomic DNA. Translation: AAA23862.1 .
    X63694 Genomic DNA. Translation: CAA45222.1 .
    U00096 Genomic DNA. Translation: AAC74920.1 .
    AP009048 Genomic DNA. Translation: BAA15658.1 .
    PIRi B42986. ADECOG.
    RefSeqi NP_416364.1. NC_000913.3.
    YP_490112.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EUA X-ray 1.95 A/B/C 1-213 [» ]
    1EUN X-ray 2.00 A/B/C 1-213 [» ]
    1FQ0 X-ray 2.10 A/B/C 1-213 [» ]
    1FWR X-ray 2.70 A/B/C 1-213 [» ]
    1WAU X-ray 2.80 A 1-213 [» ]
    1WBH X-ray 1.55 A/B/C 1-213 [» ]
    2C0A X-ray 1.55 A/B/C 1-213 [» ]
    ProteinModelPortali P0A955.
    SMRi P0A955. Positions 1-213.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-36196N.
    IntActi P0A955. 9 interactions.
    STRINGi 511145.b1850.

    2D gel databases

    SWISS-2DPAGE P0A955.

    Proteomic databases

    PaxDbi P0A955.
    PRIDEi P0A955.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74920 ; AAC74920 ; b1850 .
    BAA15658 ; BAA15658 ; BAA15658 .
    GeneIDi 12930159.
    946367.
    KEGGi ecj:Y75_p1826.
    eco:b1850.
    PATRICi 32119021. VBIEscCol129921_1928.

    Organism-specific databases

    EchoBASEi EB0252.
    EcoGenei EG10256. eda.

    Phylogenomic databases

    eggNOGi COG0800.
    HOGENOMi HOG000233114.
    KOi K01625.
    OMAi SWLVPND.
    OrthoDBi EOG67DPKT.
    PhylomeDBi P0A955.

    Enzyme and pathway databases

    UniPathwayi UPA00227 .
    UPA00856 ; UER00829 .
    BioCyci EcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
    ECOL316407:JW1839-MONOMER.
    MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0A955.
    PROi P0A955.

    Gene expression databases

    Genevestigatori P0A955.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    InterProi IPR000887. Aldlse_KDPG_KHG.
    IPR013785. Aldolase_TIM.
    [Graphical view ]
    Pfami PF01081. Aldolase. 1 hit.
    [Graphical view ]
    TIGRFAMsi TIGR01182. eda. 1 hit.
    PROSITEi PS00159. ALDOLASE_KDPG_KHG_1. 1 hit.
    PS00160. ALDOLASE_KDPG_KHG_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The complete amino acid sequence and identification of the active-site arginine peptide of Escherichia coli 2-keto-4-hydroxyglutarate aldolase."
      Vlahos C.J., Dekker E.E.
      J. Biol. Chem. 263:11683-11691(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE, ACTIVE SITE.
      Strain: K12.
    2. "Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene."
      Patil R.V., Dekker E.E.
      J. Bacteriol. 174:102-107(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION AS A KHG-ALDOLASE, DISRUPTION PHENOTYPE.
    3. "Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon."
      Egan S.E., Fliege R., Tong S., Shibata A., Wolf R.E. Jr., Conway T.
      J. Bacteriol. 174:4638-4646(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. "Purine and one-carbon metabolism in Escherichia coli K12: DNA sequence of a second GAR transformylase."
      Smith J.M., Nygaard P.
      Submitted (JUL-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    5. "Sequence of the Escherichia coli K-12 edd and eda genes of the Entner-Doudoroff pathway."
      Carter A.T., Pearson B.M., Dickinson J.R., Lancashire W.E.
      Gene 130:155-156(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    8. "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.
    9. "Active-site residues of 2-keto-4-hydroxyglutarate aldolase from Escherichia coli. Bromopyruvate inactivation and labeling of glutamate 45."
      Vlahos C.J., Dekker E.E.
      J. Biol. Chem. 265:20384-20389(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACTIVE SITE.
    10. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    11. "Characterization and crystal structure of Escherichia coli KDPGal aldolase."
      Walters M.J., Srikannathasan V., McEwan A.R., Naismith J.H., Fierke C.A., Toone E.J.
      Bioorg. Med. Chem. 16:710-720(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A KDPG-ALDOLASE, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-45 AND THR-161, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, INDUCTION.
    12. "Covalent intermediate trapped in 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase structure at 1.95-A resolution."
      Allard J., Grochulski P., Sygusch J.
      Proc. Natl. Acad. Sci. U.S.A. 98:3679-3684(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH SUSBTRATE, REACTION MECHANISM, SUBUNIT.
    13. "Directed evolution of a new catalytic site in 2-keto-3-deoxy-6-phosphogluconate aldolase from Escherichia coli."
      Wymer N., Buchanan L.V., Henderson D., Mehta N., Botting C.H., Pocivavsek L., Fierke C.A., Toone E.J., Naismith J.H.
      Structure 9:1-9(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF WILD-TYPE AND DOUBLE MUTANT IN COMPLEX WITH SUSBTRATE, MUTAGENESIS OF LYS-133; THR-161 AND ASN-168, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    14. Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF WILD-TYPE AND MUTANT IN COMPLEX WITH SUBSTRATE, MUTAGENESIS OF GLU-45, REACTION MECHANISM, SUBUNIT.

    Entry informationi

    Entry nameiALKH_ECOLI
    AccessioniPrimary (citable) accession number: P0A955
    Secondary accession number(s): P10177
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 19, 2005
    Last sequence update: July 19, 2005
    Last modified: October 1, 2014
    This is version 81 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, Direct protein sequencing, Multifunctional enzyme, 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

    External Data

    Dasty 3