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Protein

Glycerol dehydrogenase

Gene

gldA

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
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. Is also able to use various diols as substrates, such as propan-1,2-diol, butan-2,3-diol, ethan-1,2-diol, and 3-mercapto-1,2-dihydroxypropane.1 Publication

Catalytic activityi

Glycerol + NAD+ = glycerone + NADH.

Cofactori

Zn2+2 PublicationsNote: Binds 1 zinc ion per subunit.2 Publications

Kineticsi

  1. KM=3.8 mM for glycerol1 Publication
  2. KM=121 µM for NAD+1 Publication

    pH dependencei

    Optimum pH is 6.0-8.5.1 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 sitei39 – 391NAD
    Binding sitei123 – 1231Substrate
    Binding sitei127 – 1271NAD
    Binding sitei129 – 1291NAD; via carbonyl oxygen
    Binding sitei133 – 1331NAD
    Metal bindingi173 – 1731Zinc; catalytic
    Binding sitei173 – 1731Substrate
    Metal bindingi256 – 2561Zinc; catalytic
    Binding sitei256 – 2561Substrate
    Metal bindingi274 – 2741Zinc; catalytic
    Binding sitei274 – 2741Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi96 – 1005NAD
    Nucleotide bindingi118 – 1214NAD

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Glycerol metabolism

    Keywords - Ligandi

    Metal-binding, NAD, Zinc

    Enzyme and pathway databases

    SABIO-RKP32816.
    UniPathwayiUPA00617; UER00668.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycerol dehydrogenase (EC:1.1.1.6)
    Short name:
    GDH
    Short name:
    GLDH
    Short name:
    GlyDH
    Gene namesi
    Name:gldA
    Synonyms:gld
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi97 – 971K → H: Loss of activity. 1 Publication
    Mutagenesisi305 – 3051S → C: No effect on affinity for substrates. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 370370Glycerol dehydrogenasePRO_0000087826Add
    BLAST

    Interactioni

    Subunit structurei

    Homooctamer.1 Publication

    Structurei

    Secondary structure

    1
    370
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 166Combined sources
    Helixi19 – 224Combined sources
    Helixi23 – 275Combined sources
    Turni28 – 303Combined sources
    Beta strandi32 – 387Combined sources
    Helixi40 – 456Combined sources
    Helixi47 – 559Combined sources
    Turni56 – 583Combined sources
    Beta strandi60 – 656Combined sources
    Helixi72 – 8413Combined sources
    Beta strandi88 – 958Combined sources
    Helixi96 – 10914Combined sources
    Beta strandi112 – 1198Combined sources
    Beta strandi128 – 1336Combined sources
    Beta strandi139 – 1446Combined sources
    Beta strandi150 – 1556Combined sources
    Helixi156 – 1605Combined sources
    Helixi164 – 18724Combined sources
    Beta strandi194 – 1963Combined sources
    Helixi199 – 22426Combined sources
    Helixi230 – 25021Combined sources
    Helixi254 – 2618Combined sources
    Helixi262 – 2643Combined sources
    Helixi268 – 2714Combined sources
    Helixi274 – 28815Combined sources
    Helixi293 – 30513Combined sources
    Turni312 – 3165Combined sources
    Helixi322 – 33211Combined sources
    Helixi338 – 3414Combined sources
    Helixi347 – 36519Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JPUX-ray1.80A1-370[»]
    1JQ5X-ray1.70A1-370[»]
    1JQAX-ray2.05A1-370[»]
    ProteinModelPortaliP32816.
    SMRiP32816. Positions 2-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP32816.

    Family & Domainsi

    Domaini

    Consists of two domains that are separated by a deep cleft, in which the Zn2+ ion is bound.1 Publication

    Sequence similaritiesi

    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.

    P32816-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAAERVFISP AKYVQGKNVI TKIANYLEGI GNKTVVIADE IVWKIAGHTI
    60 70 80 90 100
    VNELKKGNIA AEEVVFSGEA SRNEVERIAN IARKAEAAIV IGVGGGKTLD
    110 120 130 140 150
    TAKAVADELD AYIVIVPTAA STDAPTSALS VIYSDDGVFE SYRFYKKNPD
    160 170 180 190 200
    LVLVDTKIIA NAPPRLLASG IADALATWVE ARSVIKSGGK TMAGGIPTIA
    210 220 230 240 250
    AEAIAEKCEQ TLFKYGKLAY ESVKAKVVTP ALEAVVEANT LLSGLGFESG
    260 270 280 290 300
    GLAAAHAIHN GFTALEGEIH HLTHGEKVAF GTLVQLALEE HSQQEIERYI
    310 320 330 340 350
    ELYLSLDLPV TLEDIKLKDA SREDILKVAK AATAEGETIH NAFNVTADDV
    360 370
    ADAIFAADQY AKAYKEKHRK
    Length:370
    Mass (Da):39,501
    Last modified:October 1, 1993 - v1
    Checksum:iE5D93264B1670F25
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M65289 Genomic DNA. Translation: AAA22477.1.
    PIRiJQ1474.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M65289 Genomic DNA. Translation: AAA22477.1.
    PIRiJQ1474.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JPUX-ray1.80A1-370[»]
    1JQ5X-ray1.70A1-370[»]
    1JQAX-ray2.05A1-370[»]
    ProteinModelPortaliP32816.
    SMRiP32816. Positions 2-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00617; UER00668.
    SABIO-RKP32816.

    Miscellaneous databases

    EvolutionaryTraceiP32816.

    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...

    Publicationsi

    1. "Cloning and characterization of a gene from Bacillus stearothermophilus var. non-diastaticus encoding a glycerol dehydrogenase."
      Mallinder P.R., Pritchard A., Moir A.
      Gene 110:9-16(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: DSM 2334 / Var. Non-diastaticus.
    2. "The identification of a lysine residue reactive to pyridoxal-5-phosphate in the glycerol dehydrogenase from the thermophile Bacillus stearothermophilus."
      Paine L.J., Perry N., Popplewell A.G., Gore M.G., Atkinson T.
      Biochim. Biophys. Acta 1202:235-243(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 84-103, MUTAGENESIS OF LYS-97.
    3. "Isolation and characterisation of the glycerol dehydrogenase from Bacillus stearothermophilus."
      Spencer P., Bown K.J., Scawen M.D., Atkinson T., Gore M.G.
      Biochim. Biophys. Acta 994:270-279(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, COFACTOR, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
    4. "Glycerol dehydrogenase: structure, specificity, and mechanism of a family III polyol dehydrogenase."
      Ruzheinikov S.N., Burke J., Sedelnikova S., Baker P.J., Taylor R., Bullough P.A., Muir N.M., Gore M.G., Rice D.W.
      Structure 9:789-802(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANT CYS-305 IN COMPLEXES WITH ZINC; NAD AND SUBSTRATE, DOMAIN, COFACTOR, SUBUNIT, MUTAGENESIS OF SER-305.

    Entry informationi

    Entry nameiGLDA_GEOSE
    AccessioniPrimary (citable) accession number: P32816
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: October 1, 1993
    Last modified: January 20, 2016
    This is version 83 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, Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.