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Protein

Glycerol dehydrogenase

Gene

gldA

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

Functioni

Catalyzes the NAD-dependent oxidation of glycerol to dihydroxyacetone (glycerone). Allows microorganisms to utilize glycerol as a source of carbon under anaerobic conditions. In E.coli, an important role of GldA is also likely to regulate the intracellular level of dihydroxyacetone by catalyzing the reverse reaction, i.e. the conversion of dihydroxyacetone into glycerol. Possesses a broad substrate specificity, since it is also able to oxidize 1,2-propanediol and to reduce glycolaldehyde, methylglyoxal and hydroxyacetone into ethylene glycol, lactaldehyde and 1,2-propanediol, respectively.4 Publications

Catalytic activityi

Glycerol + NAD+ = glycerone + NADH.1 Publication

Cofactori

Zn2+By similarityNote: Binds 1 zinc ion per subunit.By similarity

Enzyme regulationi

Inhibited by Cu2+.1 Publication

Kineticsi

The catalytic efficiency of the reverse reaction (dihydroxyacetone reduction) is more than 100-fold higher than that of the forward direction (glycerol oxidation).

  1. KM=0.30 mM for dihydroxyacetone (at 25 degrees Celsius and pH 7)1 Publication
  2. KM=0.85 mM for glycolaldehyde (at 25 degrees Celsius and pH 7)1 Publication
  3. KM=0.50 mM for methylglyoxal (at 25 degrees Celsius and pH 7)1 Publication
  4. KM=56 mM for glycerol (at 25 degrees Celsius and pH 7)1 Publication

    pH dependencei

    Optimum pH is 5.5-6.0 for dihydroxyacetone reduction and 9.5-10.0 for glycerol oxidation.1 Publication

    Pathwayi: glycerol fermentation

    This protein is involved in step 1 of the subpathway that synthesizes glycerone phosphate from glycerol (oxidative route).
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Glycerol dehydrogenase (gldA)
    2. no protein annotated in this organism
    This subpathway is part of the pathway glycerol fermentation, which is itself part of Polyol metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes glycerone phosphate from glycerol (oxidative route), the pathway glycerol fermentation and in Polyol metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei37 – 371NADBy similarity
    Binding sitei121 – 1211SubstrateBy similarity
    Binding sitei125 – 1251NADBy similarity
    Binding sitei127 – 1271NAD; via carbonyl oxygenBy similarity
    Binding sitei131 – 1311NADBy similarity
    Metal bindingi171 – 1711Zinc; catalyticBy similarity
    Binding sitei171 – 1711SubstrateBy similarity
    Metal bindingi254 – 2541Zinc; catalyticBy similarity
    Binding sitei254 – 2541SubstrateBy similarity
    Metal bindingi271 – 2711Zinc; catalyticBy similarity
    Binding sitei271 – 2711SubstrateBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi94 – 985NADBy similarity
    Nucleotide bindingi116 – 1194NADBy similarity

    GO - Molecular functioni

    • (R)-aminopropanol dehydrogenase activity Source: EcoCyc
    • glycerol dehydrogenase [NAD+] activity Source: EcoCyc
    • identical protein binding Source: EcoCyc
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    • anaerobic glycerol catabolic process Source: EcoCyc
    • methylglyoxal catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glycerol metabolism

    Keywords - Ligandi

    Metal-binding, NAD, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:GLYCDEH-MONOMER.
    ECOL316407:JW5556-MONOMER.
    MetaCyc:GLYCDEH-MONOMER.
    SABIO-RKP0A9S5.
    UniPathwayiUPA00617; UER00668.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycerol dehydrogenase (EC:1.1.1.6)
    Short name:
    GDH
    Short name:
    GLDH
    Gene namesi
    Name:gldA
    Ordered Locus Names:b3945, JW5556
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11904. gldA.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 367367Glycerol dehydrogenasePRO_0000087828Add
    BLAST

    Proteomic databases

    PaxDbiP0A9S5.
    PRIDEiP0A9S5.

    Expressioni

    Developmental stagei

    Expression is higher during stationary phase than during logarithmic growth.1 Publication

    Inductioni

    Full expression of gldA is achieved by induction with hydroxyacetone and stationary-phase growth conditions.1 Publication

    Interactioni

    Subunit structurei

    Homodimer and homooctamer.1 Publication

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

    BioGridi4262653. 12 interactions.
    852737. 1 interaction.
    DIPiDIP-47916N.
    IntActiP0A9S5. 1 interaction.
    STRINGi511145.b3945.

    Structurei

    3D structure databases

    ProteinModelPortaliP0A9S5.
    SMRiP0A9S5. Positions 1-365.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DCT. Bacteria.
    COG0371. LUCA.
    HOGENOMiHOG000031784.
    InParanoidiP0A9S5.
    KOiK00005.
    OMAiCERTLFA.
    PhylomeDBiP0A9S5.

    Family and domain databases

    InterProiIPR001670. ADH_Fe.
    IPR018211. ADH_Fe_CS.
    [Graphical view]
    PfamiPF00465. Fe-ADH. 1 hit.
    [Graphical view]
    PROSITEiPS00913. ADH_IRON_1. 1 hit.
    PS00060. ADH_IRON_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A9S5-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MDRIIQSPGK YIQGADVINR LGEYLKPLAE RWLVVGDKFV LGFAQSTVEK
    60 70 80 90 100
    SFKDAGLVVE IAPFGGECSQ NEIDRLRGIA ETAQCGAILG IGGGKTLDTA
    110 120 130 140 150
    KALAHFMGVP VAIAPTIAST DAPCSALSVI YTDEGEFDRY LLLPNNPNMV
    160 170 180 190 200
    IVDTKIVAGA PARLLAAGIG DALATWFEAR ACSRSGATTM AGGKCTQAAL
    210 220 230 240 250
    ALAELCYNTL LEEGEKAMLA AEQHVVTPAL ERVIEANTYL SGVGFESGGL
    260 270 280 290 300
    AAAHAVHNGL TAIPDAHHYY HGEKVAFGTL TQLVLENAPV EEIETVAALS
    310 320 330 340 350
    HAVGLPITLA QLDIKEDVPA KMRIVAEAAC AEGETIHNMP GGATPDQVYA
    360
    ALLVADQYGQ RFLQEWE
    Length:367
    Mass (Da):38,712
    Last modified:July 19, 2005 - v1
    Checksum:iF6F3F275B4091F28
    GO

    Sequence cautioni

    The sequence AAC43051 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00006 Genomic DNA. Translation: AAC43051.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76927.2.
    AP009048 Genomic DNA. Translation: BAE77365.1.
    PIRiD65201.
    RefSeqiNP_418380.4. NC_000913.3.
    WP_000374004.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76927; AAC76927; b3945.
    BAE77365; BAE77365; BAE77365.
    GeneIDi948440.
    KEGGiecj:JW5556.
    eco:b3945.
    PATRICi32123413. VBIEscCol129921_4067.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00006 Genomic DNA. Translation: AAC43051.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76927.2.
    AP009048 Genomic DNA. Translation: BAE77365.1.
    PIRiD65201.
    RefSeqiNP_418380.4. NC_000913.3.
    WP_000374004.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP0A9S5.
    SMRiP0A9S5. Positions 1-365.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262653. 12 interactions.
    852737. 1 interaction.
    DIPiDIP-47916N.
    IntActiP0A9S5. 1 interaction.
    STRINGi511145.b3945.

    Proteomic databases

    PaxDbiP0A9S5.
    PRIDEiP0A9S5.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76927; AAC76927; b3945.
    BAE77365; BAE77365; BAE77365.
    GeneIDi948440.
    KEGGiecj:JW5556.
    eco:b3945.
    PATRICi32123413. VBIEscCol129921_4067.

    Organism-specific databases

    EchoBASEiEB1849.
    EcoGeneiEG11904. gldA.

    Phylogenomic databases

    eggNOGiENOG4105DCT. Bacteria.
    COG0371. LUCA.
    HOGENOMiHOG000031784.
    InParanoidiP0A9S5.
    KOiK00005.
    OMAiCERTLFA.
    PhylomeDBiP0A9S5.

    Enzyme and pathway databases

    UniPathwayiUPA00617; UER00668.
    BioCyciEcoCyc:GLYCDEH-MONOMER.
    ECOL316407:JW5556-MONOMER.
    MetaCyc:GLYCDEH-MONOMER.
    SABIO-RKP0A9S5.

    Miscellaneous databases

    PROiP0A9S5.

    Family and domain databases

    InterProiIPR001670. ADH_Fe.
    IPR018211. ADH_Fe_CS.
    [Graphical view]
    PfamiPF00465. Fe-ADH. 1 hit.
    [Graphical view]
    PROSITEiPS00913. ADH_IRON_1. 1 hit.
    PS00060. ADH_IRON_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGLDA_ECOLI
    AccessioniPrimary (citable) accession number: P0A9S5
    Secondary accession number(s): P32665, P78132, Q2M8P1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 19, 2005
    Last sequence update: July 19, 2005
    Last modified: September 7, 2016
    This is version 95 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

    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. 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.