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Protein

5-keto-4-deoxy-D-glucarate aldolase

Gene

garL

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

Functioni

Catalyzes the reversible retro-aldol cleavage of both 5-keto-4-deoxy-D-glucarate and 2-keto-3-deoxy-D-glucarate to pyruvate and tartronic semialdehyde.2 Publications

Catalytic activityi

5-dehydro-4-deoxy-D-glucarate = pyruvate + tartronate semialdehyde.1 Publication
2-dehydro-3-deoxy-D-glucarate = pyruvate + tartronate semialdehyde.1 Publication

Cofactori

Mg2+1 Publication, Co2+1 Publication, Fe2+1 Publication, Mn2+1 PublicationNote: Binds 1 Mg(2+) ion per subunit. Can also use, although less efficiently, Co(2+), Fe(2+) and Mn2+.1 Publication

Enzyme regulationi

Inhibited by acetate, chloride and bromide ions, nitrate, fluoride, cyanide, EDTA and pyrophosphate.1 Publication

Kineticsi

  1. KM=65 µM for 5-keto-4-deoxy-D-glucarate1 Publication

    pH dependencei

    Optimum pH is 7.4-8.6. Stable from pH 6 to 7.5.1 Publication

    Pathway: galactarate degradation

    This protein is involved in step 2 of the subpathway that synthesizes D-glycerate from galactarate.
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. D-galactarate dehydratase (garD)
    2. 5-keto-4-deoxy-D-glucarate aldolase (garL), 5-keto-4-deoxy-D-glucarate aldolase (garL)
    3. 2-hydroxy-3-oxopropionate reductase (garR)
    This subpathway is part of the pathway galactarate 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-glycerate from galactarate, the pathway galactarate degradation and in Carbohydrate acid metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei50 – 501Proton acceptorBy similarity
    Sitei75 – 751Transition state stabilizerBy similarity
    Sitei89 – 891Increases basicity of active site HisBy similarity
    Binding sitei151 – 1511Substrate
    Metal bindingi153 – 1531Magnesium
    Binding sitei178 – 1781Substrate; via amide nitrogen
    Metal bindingi179 – 1791Magnesium
    Binding sitei179 – 1791Substrate

    GO - Molecular functioni

    • 2-dehydro-3-deoxyglucarate aldolase activity Source: EcoliWiki
    • carbon-carbon lyase activity Source: EcoliWiki
    • magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    • D-glucarate catabolic process Source: EcoCyc
    • galactarate catabolic process Source: EcoCyc
    • glucarate catabolic process Source: EcoliWiki
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Cobalt, Iron, Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:KDGALDOL-MONOMER.
    ECOL316407:JW3095-MONOMER.
    MetaCyc:KDGALDOL-MONOMER.
    BRENDAi4.1.2.20. 2026.
    UniPathwayiUPA00565; UER00630.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    5-keto-4-deoxy-D-glucarate aldolase (EC:4.1.2.20)
    Short name:
    KDGluc aldolase
    Short name:
    KDGlucA
    Alternative name(s):
    2-dehydro-3-deoxy-D-glucarate aldolase
    2-keto-3-deoxy-D-glucarate aldolase
    5-dehydro-4-deoxy-D-glucarate aldolase
    Alpha-keto-beta-deoxy-D-glucarate aldolase
    Gene namesi
    Name:garL
    Synonyms:yhaF
    Ordered Locus Names:b3126, JW3095
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10016. garL.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: EcoliWiki
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2562565-keto-4-deoxy-D-glucarate aldolasePRO_0000207093Add
    BLAST

    Proteomic databases

    PaxDbiP23522.
    PRIDEiP23522.

    Interactioni

    Subunit structurei

    Homohexamer; trimer of dimers.1 Publication

    Protein-protein interaction databases

    DIPiDIP-9740N.
    IntActiP23522. 9 interactions.
    STRINGi511145.b3126.

    Structurei

    Secondary structure

    1
    256
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 157Combined sources
    Beta strandi20 – 256Combined sources
    Helixi30 – 367Combined sources
    Beta strandi42 – 5211Combined sources
    Helixi55 – 6410Combined sources
    Turni65 – 673Combined sources
    Beta strandi69 – 757Combined sources
    Beta strandi77 – 793Combined sources
    Helixi81 – 899Combined sources
    Beta strandi94 – 985Combined sources
    Helixi103 – 1119Combined sources
    Turni116 – 1183Combined sources
    Beta strandi125 – 1273Combined sources
    Helixi128 – 1303Combined sources
    Turni131 – 1344Combined sources
    Helixi138 – 1425Combined sources
    Beta strandi147 – 1526Combined sources
    Helixi155 – 1595Combined sources
    Helixi161 – 1655Combined sources
    Beta strandi172 – 1754Combined sources
    Helixi177 – 1837Combined sources
    Helixi193 – 20816Combined sources
    Beta strandi213 – 2164Combined sources
    Helixi220 – 2289Combined sources
    Beta strandi233 – 2386Combined sources
    Helixi239 – 25416Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DXEX-ray1.80A/B1-256[»]
    1DXFX-ray2.60A/B1-256[»]
    ProteinModelPortaliP23522.
    SMRiP23522. Positions 4-256.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP23522.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG3836.
    HOGENOMiHOG000179750.
    InParanoidiP23522.
    KOiK01630.
    OMAiVRPPCNE.
    OrthoDBiEOG6NPM5P.
    PhylomeDBiP23522.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01291. KDGluc_aldolase.
    InterProiIPR005000. Aldolase/citrate-lyase_domain.
    IPR017648. Dehyd-dGlucarate-aldolase_GarL.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PfamiPF03328. HpcH_HpaI. 1 hit.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    TIGRFAMsiTIGR03239. GarL. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P23522-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNNDVFPNKF KAALAAKQVQ IGCWSALSNP ISTEVLGLAG FDWLVLDGEH
    60 70 80 90 100
    APNDISTFIP QLMALKGSAS APVVRVPTNE PVIIKRLLDI GFYNFLIPFV
    110 120 130 140 150
    ETKEEAELAV ASTRYPPEGI RGVSVSHRAN MFGTVADYFA QSNKNITILV
    160 170 180 190 200
    QIESQQGVDN VDAIAATEGV DGIFVGPSDL AAALGHLGNA SHPDVQKAIQ
    210 220 230 240 250
    HIFNRASAHG KPSGILAPVE ADARRYLEWG ATFVAVGSDL GVFRSATQKL

    ADTFKK
    Length:256
    Mass (Da):27,384
    Last modified:November 1, 1995 - v2
    Checksum:i8E6345EE3F1CFCDB
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA57929.1.
    U00096 Genomic DNA. Translation: AAC76160.1.
    AP009048 Genomic DNA. Translation: BAE77173.1.
    D90212 Genomic DNA. Translation: BAA14237.1.
    PIRiB65102.
    RefSeqiNP_417595.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC76160; AAC76160; b3126.
    BAE77173; BAE77173; BAE77173.
    GeneIDi947630.
    KEGGiecj:Y75_p3048.
    eco:b3126.
    PATRICi32121666. VBIEscCol129921_3219.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA57929.1.
    U00096 Genomic DNA. Translation: AAC76160.1.
    AP009048 Genomic DNA. Translation: BAE77173.1.
    D90212 Genomic DNA. Translation: BAA14237.1.
    PIRiB65102.
    RefSeqiNP_417595.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DXEX-ray1.80A/B1-256[»]
    1DXFX-ray2.60A/B1-256[»]
    ProteinModelPortaliP23522.
    SMRiP23522. Positions 4-256.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-9740N.
    IntActiP23522. 9 interactions.
    STRINGi511145.b3126.

    Proteomic databases

    PaxDbiP23522.
    PRIDEiP23522.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76160; AAC76160; b3126.
    BAE77173; BAE77173; BAE77173.
    GeneIDi947630.
    KEGGiecj:Y75_p3048.
    eco:b3126.
    PATRICi32121666. VBIEscCol129921_3219.

    Organism-specific databases

    EchoBASEiEB0016.
    EcoGeneiEG10016. garL.

    Phylogenomic databases

    eggNOGiCOG3836.
    HOGENOMiHOG000179750.
    InParanoidiP23522.
    KOiK01630.
    OMAiVRPPCNE.
    OrthoDBiEOG6NPM5P.
    PhylomeDBiP23522.

    Enzyme and pathway databases

    UniPathwayiUPA00565; UER00630.
    BioCyciEcoCyc:KDGALDOL-MONOMER.
    ECOL316407:JW3095-MONOMER.
    MetaCyc:KDGALDOL-MONOMER.
    BRENDAi4.1.2.20. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP23522.
    PROiP23522.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01291. KDGluc_aldolase.
    InterProiIPR005000. Aldolase/citrate-lyase_domain.
    IPR017648. Dehyd-dGlucarate-aldolase_GarL.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PfamiPF03328. HpcH_HpaI. 1 hit.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    TIGRFAMsiTIGR03239. GarL. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. "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.
    3. "Precise mapping of the rnpB gene encoding the RNA component of RNase P in Escherichia coli K-12."
      Komine Y., Inokuchi H.
      J. Bacteriol. 173:1813-1816(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 89-256.
      Strain: K12.
    4. "Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli."
      Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A.
      Biochemistry 37:14369-14375(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-16, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
      Strain: K12 / MG1655 / ATCC 47076.
    5. "2-keto-3-deoxy-D-glucarate aldolase."
      Fish D.C., Blumenthal H.J.
      Methods Enzymol. 9:529-534(1966)
      Cited for: FUNCTION, CHARACTERIZATION, SUBSTRATE SPECIFICITY, COFACTOR, ENZYME REGULATION, PH DEPENDENCE.
      Strain: K12 / CR63.
    6. "A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli."
      Monterrubio R., Baldoma L., Obradors N., Aguilar J., Badia J.
      J. Bacteriol. 182:2672-2674(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE NAME.
    7. "Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism."
      Izard T., Blackwell N.C.
      EMBO J. 19:3849-3856(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND PYRUVATE, SUBUNIT.

    Entry informationi

    Entry nameiGARL_ECOLI
    AccessioniPrimary (citable) accession number: P23522
    Secondary accession number(s): Q2M983
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1991
    Last sequence update: November 1, 1995
    Last modified: June 24, 2015
    This is version 128 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The catalytic mechanism was originally thought to use a phosphate as the catalytic acid, but this was subsequently disputed (PubMed:15996099, PubMed:17881002 and PubMed:18754683).1 Publication

    Caution

    Was wrongly named 2-dehydro-3-deoxygalactarate aldolase (DDG aldolase or DDGA) in PubMed:10921867. 2-dehydro-3-deoxygalactarate is the enantiomer of 5-dehydro-4-deoxy-D-glucarate, but is not an isomer obtained in the degradation pathway of D-glucarate/galactarate and the enzyme has not been shown to be active on it.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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

    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.