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Protein

KHG/KDPG aldolase

Gene

eda

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

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: 2-dehydro-3-deoxy-D-gluconate degradation

    This protein is involved in step 2 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. 2-dehydro-3-deoxygluconokinase (kdgK)
    2. KHG/KDPG aldolase (eda)
    This subpathway is part of the pathway 2-dehydro-3-deoxy-D-gluconate degradation, which is itself part of Carbohydrate acid metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-gluconate, the pathway 2-dehydro-3-deoxy-D-gluconate degradation and in Carbohydrate acid metabolism.

    Pathwayi: glyoxylate and dicarboxylate metabolism

    This protein is involved in the pathway glyoxylate and dicarboxylate metabolism, which is part of Carbohydrate metabolism.
    View all proteins of this organism that are known to be involved in the pathway glyoxylate and dicarboxylate metabolism and in Carbohydrate metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei45Proton acceptor1
    Active sitei491
    Binding sitei49Substrate1 Publication1
    Binding sitei73Substrate1 Publication1
    Active sitei133Schiff-base intermediate with substrate1
    Binding sitei133Substrate (covalent)1 Publication1
    Binding sitei161Substrate1 Publication1
    Sitei161Plays a major role in determining the stereoselectivity1
    Binding sitei163Substrate; via amide nitrogen1 Publication1
    Binding sitei184Substrate1 Publication1

    GO - Molecular functioni

    • 2-dehydro-3-deoxy-phosphogluconate aldolase activity Source: EcoliWiki
    • 4-hydroxy-2-oxoglutarate aldolase activity Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Schiff base

    Enzyme and pathway databases

    BioCyciEcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
    ECOL316407:JW1839-MONOMER.
    MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
    BRENDAi4.1.2.14. 2026.
    4.1.3.42. 2026.
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10256. eda.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: UniProtKB
    • membrane Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene lose KHG aldolase activity.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi45E → N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity. 2 Publications1
    Mutagenesisi133K → 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 Publication1
    Mutagenesisi161T → 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 Publications1
    Mutagenesisi161T → 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 Publications1
    Mutagenesisi168N → S: Shows activity significantly greater than wild-type. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002010371 – 213KHG/KDPG aldolaseAdd BLAST213

    Proteomic databases

    EPDiP0A955.
    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

    Interactioni

    Subunit structurei

    Homotrimer.3 Publications

    Binary interactionsi

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

    Protein-protein interaction databases

    BioGridi4259153. 13 interactors.
    DIPiDIP-36196N.
    IntActiP0A955. 9 interactors.
    STRINGi511145.b1850.

    Structurei

    Secondary structure

    1213
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi8 – 13Combined sources6
    Beta strandi16 – 21Combined sources6
    Helixi26 – 28Combined sources3
    Helixi29 – 38Combined sources10
    Beta strandi43 – 48Combined sources6
    Helixi53 – 63Combined sources11
    Beta strandi67 – 73Combined sources7
    Helixi77 – 86Combined sources10
    Beta strandi91 – 95Combined sources5
    Helixi98 – 106Combined sources9
    Beta strandi107 – 109Combined sources3
    Beta strandi111 – 117Combined sources7
    Helixi118 – 126Combined sources9
    Beta strandi131 – 134Combined sources4
    Turni135 – 141Combined sources7
    Helixi142 – 150Combined sources9
    Beta strandi157 – 163Combined sources7
    Turni166 – 168Combined sources3
    Helixi169 – 173Combined sources5
    Beta strandi181 – 183Combined sources3
    Helixi184 – 186Combined sources3
    Helixi189 – 194Combined sources6
    Helixi197 – 210Combined sources14

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A955.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni8 – 9Substrate binding2

    Sequence similaritiesi

    Belongs to the KHG/KDPG aldolase family.Curated

    Phylogenomic databases

    eggNOGiENOG4108UHU. Bacteria.
    COG0800. LUCA.
    HOGENOMiHOG000233114.
    InParanoidiP0A955.
    KOiK01625.
    OMAiFLISPGL.
    PhylomeDBiP0A955.

    Family and domain databases

    CDDicd00452. KDPG_aldolase. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR000887. Aldlse_KDPG_KHG.
    IPR013785. Aldolase_TIM.
    IPR031337. KDPG/KHG_AS_1.
    IPR031338. KDPG/KHG_AS_2.
    [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

            10         20         30         40         50
    MKNWKTSAES ILTTGPVVPV IVVKKLEHAV PMAKALVAGG VRVLEVTLRT
    60 70 80 90 100
    ECAVDAIRAI AKEVPEAIVG AGTVLNPQQL AEVTEAGAQF AISPGLTEPL
    110 120 130 140 150
    LKAATEGTIP LIPGISTVSE LMLGMDYGLK EFKFFPAEAN GGVKALQAIA
    160 170 180 190 200
    GPFSQVRFCP TGGISPANYR DYLALKSVLC IGGSWLVPAD ALEAGDYDRI
    210
    TKLAREAVEG AKL
    Length:213
    Mass (Da):22,284
    Last modified:July 19, 2005 - v1
    Checksum:iCC8D51B50480D0B7
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.
    WP_000800512.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74920; AAC74920; b1850.
    BAA15658; BAA15658; BAA15658.
    GeneIDi946367.
    KEGGiecj:JW1839.
    eco:b1850.
    PATRICi32119021. VBIEscCol129921_1928.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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.
    WP_000800512.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259153. 13 interactors.
    DIPiDIP-36196N.
    IntActiP0A955. 9 interactors.
    STRINGi511145.b1850.

    2D gel databases

    SWISS-2DPAGEP0A955.

    Proteomic databases

    EPDiP0A955.
    PaxDbiP0A955.
    PRIDEiP0A955.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74920; AAC74920; b1850.
    BAA15658; BAA15658; BAA15658.
    GeneIDi946367.
    KEGGiecj:JW1839.
    eco:b1850.
    PATRICi32119021. VBIEscCol129921_1928.

    Organism-specific databases

    EchoBASEiEB0252.
    EcoGeneiEG10256. eda.

    Phylogenomic databases

    eggNOGiENOG4108UHU. Bacteria.
    COG0800. LUCA.
    HOGENOMiHOG000233114.
    InParanoidiP0A955.
    KOiK01625.
    OMAiFLISPGL.
    PhylomeDBiP0A955.

    Enzyme and pathway databases

    UniPathwayiUPA00227.
    UPA00856; UER00829.
    BioCyciEcoCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
    ECOL316407:JW1839-MONOMER.
    MetaCyc:KDPGALDOL-4OH2OXOGLUTARALDOL-MONOMER.
    BRENDAi4.1.2.14. 2026.
    4.1.3.42. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0A955.
    PROiP0A955.

    Family and domain databases

    CDDicd00452. KDPG_aldolase. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR000887. Aldlse_KDPG_KHG.
    IPR013785. Aldolase_TIM.
    IPR031337. KDPG/KHG_AS_1.
    IPR031338. KDPG/KHG_AS_2.
    [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]
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 96 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

    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.