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Protein

2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Gene

dgoA

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 galactose via the DeLey-Doudoroff pathway. Catalyzes the reversible, stereospecific retro-aldol cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) to pyruvate and D-glyceraldehyde-3-phosphate. In the synthetic direction, it catalyzes the addition of pyruvate to electrophilic aldehydes with re-facial selectivity. It can use a limited number of aldehyde substrates, including D-glyceraldehyde-3-phosphate (natural substrate), D-glyceraldehyde, glycolaldehyde, 2-pyridinecarboxaldehyde, D-ribose, D-erythrose and D-threose. It efficiently catalyzes aldol addition only using pyruvate as the nucleophilic component and accepts both stereochemical configurations at C2 of the electrophile.2 Publications

Catalytic activityi

2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate.1 Publication

Kineticsi

Kcat is 4 sec(-1) for KDPGal.

  1. KM=0.2 mM for KDPGal1 Publication

    Pathwayi: D-galactonate degradation

    This protein is involved in step 3 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate.
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. D-galactonate dehydratase (dgoD)
    2. 2-dehydro-3-deoxygalactonokinase (dgoK)
    3. 2-dehydro-3-deoxy-6-phosphogalactonate aldolase (dgoA)
    This subpathway is part of the pathway D-galactonate 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 D-galactonate, the pathway D-galactonate degradation and in Carbohydrate acid metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei14 – 141Substrate1 Publication
    Sitei14 – 141Orients the nucleophilic substrate
    Active sitei37 – 371Proton donor/acceptor1 Publication
    Binding sitei66 – 661Substrate1 Publication
    Active sitei126 – 1261Schiff-base intermediate with substrate1 Publication
    Binding sitei126 – 1261Substrate (covalent)1 Publication
    Sitei154 – 1541Plays a major role in determining the stereoselectivity
    Binding sitei156 – 1561Substrate; via amide nitrogenBy similarity

    GO - Molecular functioni

    • 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity Source: EcoCyc

    GO - Biological processi

    • D-galactonate catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Enzyme and pathway databases

    BioCyciEcoCyc:DEHYDDEOXPHOSGALACT-ALDOL-MONOMER.
    ECOL316407:JW5628-MONOMER.
    MetaCyc:DEHYDDEOXPHOSGALACT-ALDOL-MONOMER.
    RETL1328306-WGS:GSTH-866-MONOMER.
    UniPathwayiUPA00081; UER00520.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-dehydro-3-deoxy-6-phosphogalactonate aldolase (EC:4.1.2.21)
    Alternative name(s):
    2-oxo-3-deoxygalactonate 6-phosphate aldolase
    6-phospho-2-dehydro-3-deoxygalactonate aldolase
    6-phospho-2-keto-3-deoxygalactonate aldolase
    Short name:
    KDPGal
    Gene namesi
    Name:dgoA
    Synonyms:yidU
    Ordered Locus Names:b4477, JW5628
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11716. dgoA.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi37 – 371E → N: 50-fold decrease in catalytic efficiency and 6-fold decrease of binding affinity. 1 Publication
    Mutagenesisi154 – 1541V → T: Little stereoselectivity, accepting KDPG and KDPGal as substrate with roughly equal efficacy. Reduced the preference for KDPGal. It diminishes the activity against KDPGal and increases activity against KDPG. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2052052-dehydro-3-deoxy-6-phosphogalactonate aldolasePRO_0000079880Add
    BLAST

    Proteomic databases

    PaxDbiQ6BF16.

    Expressioni

    Inductioni

    By galactonate and galactose.1 Publication

    Interactioni

    Subunit structurei

    Homotrimer.1 Publication

    Protein-protein interaction databases

    BioGridi4260839. 13 interactions.
    STRINGi511145.b4477.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 73Combined sources
    Beta strandi9 – 124Combined sources
    Helixi18 – 3114Combined sources
    Beta strandi35 – 395Combined sources
    Helixi45 – 5612Combined sources
    Turni57 – 593Combined sources
    Beta strandi60 – 656Combined sources
    Helixi70 – 789Combined sources
    Beta strandi83 – 853Combined sources
    Helixi91 – 999Combined sources
    Beta strandi103 – 1053Combined sources
    Beta strandi107 – 1104Combined sources
    Helixi111 – 1199Combined sources
    Beta strandi123 – 1275Combined sources
    Helixi130 – 1334Combined sources
    Helixi135 – 1428Combined sources
    Beta strandi150 – 1567Combined sources
    Turni159 – 1613Combined sources
    Helixi162 – 1687Combined sources
    Beta strandi171 – 1755Combined sources
    Turni177 – 1793Combined sources
    Helixi186 – 20520Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2V81X-ray2.40A1-205[»]
    2V82X-ray2.10A1-205[»]
    4QCCX-ray7.08A/B1-203[»]
    ProteinModelPortaliQ6BF16.
    SMRiQ6BF16. Positions 1-205.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ6BF16.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni176 – 1772Substrate binding

    Sequence similaritiesi

    Belongs to the KHG/KDPG aldolase family.Curated

    Phylogenomic databases

    eggNOGiENOG4108RTU. Bacteria.
    COG0800. LUCA.
    HOGENOMiHOG000233112.
    InParanoidiQ6BF16.
    KOiK01631.
    OMAiRQFVEKI.
    OrthoDBiEOG6C2WFG.
    PhylomeDBiQ6BF16.

    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]

    Sequencei

    Sequence statusi: Complete.

    Q6BF16-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQWQTKLPLI AILRGITPDE ALAHVGAVID AGFDAVEIPL NSPQWEQSIP
    60 70 80 90 100
    AIVDAYGDKA LIGAGTVLKP EQVDALARMG CQLIVTPNIH SEVIRRAVGY
    110 120 130 140 150
    GMTVCPGCAT ATEAFTALEA GAQALKIFPS SAFGPQYIKA LKAVLPSDIA
    160 170 180 190 200
    VFAVGGVTPE NLAQWIDAGC AGAGLGSDLY RAGQSVERTA QQAAAFVKAY

    REAVQ
    Length:205
    Mass (Da):21,391
    Last modified:August 16, 2004 - v1
    Checksum:iFC59B92BAAA41CE4
    GO

    Sequence cautioni

    The sequence AAA62044.1 differs from that shown. Reason: Frameshift at positions 124, 160 and 204. The frameshift in position 204 caused the prediction of an ORF that fused dgoA and dgoD.Curated

    Mass spectrometryi

    Molecular mass is 21383 Da from positions 1 - 205. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10328 Genomic DNA. Translation: AAA62044.1. Frameshift.
    U00096 Genomic DNA. Translation: AAT48198.1.
    AP009048 Genomic DNA. Translation: BAE77601.1.
    PIRiE65171.
    RefSeqiWP_001198722.1. NZ_LN832404.1.
    YP_026238.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAT48198; AAT48198; b4477.
    BAE77601; BAE77601; BAE77601.
    GeneIDi2847766.
    KEGGiecj:JW5628.
    eco:b4477.
    PATRICi32122881. VBIEscCol129921_3816.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10328 Genomic DNA. Translation: AAA62044.1. Frameshift.
    U00096 Genomic DNA. Translation: AAT48198.1.
    AP009048 Genomic DNA. Translation: BAE77601.1.
    PIRiE65171.
    RefSeqiWP_001198722.1. NZ_LN832404.1.
    YP_026238.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2V81X-ray2.40A1-205[»]
    2V82X-ray2.10A1-205[»]
    4QCCX-ray7.08A/B1-203[»]
    ProteinModelPortaliQ6BF16.
    SMRiQ6BF16. Positions 1-205.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260839. 13 interactions.
    STRINGi511145.b4477.

    Proteomic databases

    PaxDbiQ6BF16.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAT48198; AAT48198; b4477.
    BAE77601; BAE77601; BAE77601.
    GeneIDi2847766.
    KEGGiecj:JW5628.
    eco:b4477.
    PATRICi32122881. VBIEscCol129921_3816.

    Organism-specific databases

    EchoBASEiEB1667.
    EcoGeneiEG11716. dgoA.

    Phylogenomic databases

    eggNOGiENOG4108RTU. Bacteria.
    COG0800. LUCA.
    HOGENOMiHOG000233112.
    InParanoidiQ6BF16.
    KOiK01631.
    OMAiRQFVEKI.
    OrthoDBiEOG6C2WFG.
    PhylomeDBiQ6BF16.

    Enzyme and pathway databases

    UniPathwayiUPA00081; UER00520.
    BioCyciEcoCyc:DEHYDDEOXPHOSGALACT-ALDOL-MONOMER.
    ECOL316407:JW5628-MONOMER.
    MetaCyc:DEHYDDEOXPHOSGALACT-ALDOL-MONOMER.
    RETL1328306-WGS:GSTH-866-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ6BF16.
    PROiQ6BF16.

    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]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
      Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
      Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: SEQUENCE REVISION.
    4. "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.
    5. "D-galactonate utilisation by enteric bacteria. The catabolic pathway in Escherichia coli."
      Deacon J., Cooper R.A.
      FEBS Lett. 77:201-205(1977) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INDUCTION.
    6. "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: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-37 AND VAL-154, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, MASS SPECTROMETRY, SUBSTRATE SPECIFICITY, SUBUNIT.

    Entry informationi

    Entry nameiDGOA_ECOLI
    AccessioniPrimary (citable) accession number: Q6BF16
    Secondary accession number(s): P31458, Q2M805
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 23, 2004
    Last sequence update: August 16, 2004
    Last modified: January 20, 2016
    This is version 92 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.