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P23522

- GARL_ECOLI

UniProt

P23522 - GARL_ECOLI

Protein

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

Gene

garL

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 121 (01 Oct 2014)
      Sequence version 2 (01 Nov 1995)
      Previous versions | rss
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    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

    Binds 1 magnesium ion per subunit. Can also use, although less efficiently, Co2+, Fe2+ 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

    Pathwayi

    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

    1. 2-dehydro-3-deoxyglucarate aldolase activity Source: EcoliWiki
    2. carbon-carbon lyase activity Source: EcoliWiki
    3. magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. cellular aromatic compound metabolic process Source: InterPro
    2. D-glucarate catabolic process Source: EcoCyc
    3. galactarate catabolic process Source: EcoCyc
    4. glucarate catabolic process Source: EcoliWiki

    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.
    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10016. garL.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    PTM / Processingi

    Molecule processing

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

    Proteomic databases

    PaxDbiP23522.
    PRIDEiP23522.

    PTM databases

    PhosSiteiP0809389.

    Expressioni

    Gene expression databases

    GenevestigatoriP23522.

    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 – 157
    Beta strandi20 – 256
    Helixi30 – 367
    Beta strandi42 – 5211
    Helixi55 – 6410
    Turni65 – 673
    Beta strandi69 – 757
    Beta strandi77 – 793
    Helixi81 – 899
    Beta strandi94 – 985
    Helixi103 – 1119
    Turni116 – 1183
    Beta strandi125 – 1273
    Helixi128 – 1303
    Turni131 – 1344
    Helixi138 – 1425
    Beta strandi147 – 1526
    Helixi155 – 1595
    Helixi161 – 1655
    Beta strandi172 – 1754
    Helixi177 – 1837
    Helixi193 – 20816
    Beta strandi213 – 2164
    Helixi220 – 2289
    Beta strandi233 – 2386
    Helixi239 – 25416

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK01630.
    OMAiHAPNDIT.
    OrthoDBiEOG6NPM5P.
    PhylomeDBiP23522.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01291. KDGluc_aldolase.
    InterProiIPR005000. Aldehyde-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

    MNNDVFPNKF KAALAAKQVQ IGCWSALSNP ISTEVLGLAG FDWLVLDGEH    50
    APNDISTFIP QLMALKGSAS APVVRVPTNE PVIIKRLLDI GFYNFLIPFV 100
    ETKEEAELAV ASTRYPPEGI RGVSVSHRAN MFGTVADYFA QSNKNITILV 150
    QIESQQGVDN VDAIAATEGV DGIFVGPSDL AAALGHLGNA SHPDVQKAIQ 200
    HIFNRASAHG KPSGILAPVE ADARRYLEWG ATFVAVGSDL GVFRSATQKL 250
    ADTFKK 256
    Length:256
    Mass (Da):27,384
    Last modified:November 1, 1995 - v2
    Checksum:i8E6345EE3F1CFCDB
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_491314.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76160; AAC76160; b3126.
    BAE77173; BAE77173; BAE77173.
    GeneIDi12930493.
    947630.
    KEGGiecj:Y75_p3048.
    eco:b3126.
    PATRICi32121666. VBIEscCol129921_3219.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi B65102.
    RefSeqi NP_417595.1. NC_000913.3.
    YP_491314.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1DXE X-ray 1.80 A/B 1-256 [» ]
    1DXF X-ray 2.60 A/B 1-256 [» ]
    ProteinModelPortali P23522.
    SMRi P23522. Positions 4-256.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9740N.
    IntActi P23522. 9 interactions.
    STRINGi 511145.b3126.

    PTM databases

    PhosSitei P0809389.

    Proteomic databases

    PaxDbi P23522.
    PRIDEi P23522.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76160 ; AAC76160 ; b3126 .
    BAE77173 ; BAE77173 ; BAE77173 .
    GeneIDi 12930493.
    947630.
    KEGGi ecj:Y75_p3048.
    eco:b3126.
    PATRICi 32121666. VBIEscCol129921_3219.

    Organism-specific databases

    EchoBASEi EB0016.
    EcoGenei EG10016. garL.

    Phylogenomic databases

    eggNOGi COG3836.
    HOGENOMi HOG000179750.
    KOi K01630.
    OMAi HAPNDIT.
    OrthoDBi EOG6NPM5P.
    PhylomeDBi P23522.

    Enzyme and pathway databases

    UniPathwayi UPA00565 ; UER00630 .
    BioCyci EcoCyc:KDGALDOL-MONOMER.
    ECOL316407:JW3095-MONOMER.
    MetaCyc:KDGALDOL-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P23522.
    PROi P23522.

    Gene expression databases

    Genevestigatori P23522.

    Family and domain databases

    Gene3Di 3.20.20.60. 1 hit.
    HAMAPi MF_01291. KDGluc_aldolase.
    InterProi IPR005000. Aldehyde-lyase_domain.
    IPR017648. Dehyd-dGlucarate-aldolase_GarL.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view ]
    Pfami PF03328. HpcH_HpaI. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51621. SSF51621. 1 hit.
    TIGRFAMsi TIGR03239. GarL. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 121 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