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Glycerol dehydrogenase (GDH) (GLDH) (EC 1.1.1.6)

 GLDA_ECOLI              Reviewed;         367 AA.
P0A9S5; P32665; P78132; Q2M8P1;
19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
19-JUL-2005, sequence version 1.
28-MAR-2018, entry version 104.
RecName: Full=Glycerol dehydrogenase;
Short=GDH;
Short=GLDH;
EC=1.1.1.6;
Name=gldA; OrderedLocusNames=b3945, JW5556;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=8265357; DOI=10.1093/nar/21.23.5408;
Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J.,
Daniels D.L.;
"Analysis of the Escherichia coli genome. IV. DNA sequence of the
region from 89.2 to 92.8 minutes.";
Nucleic Acids Res. 21:5408-5417(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[4]
PROTEIN SEQUENCE OF 1-8.
STRAIN=K12;
PubMed=17895580; DOI=10.1266/ggs.82.291;
Otsuka Y., Koga M., Iwamoto A., Yonesaki T.;
"A role of RnlA in the RNase LS activity from Escherichia coli.";
Genes Genet. Syst. 82:291-299(2007).
[5]
FUNCTION, CHARACTERIZATION, SUBSTRATE SPECIFICITY, ENZYME REGULATION,
SUBUNIT, AND PH DEPENDENCE.
PubMed=40950;
Tang C.-T., Ruch F.E. Jr., Lin E.C.C.;
"Purification and properties of a nicotinamide adenine dinucleotide-
linked dehydrogenase that serves an Escherichia coli mutant for
glycerol catabolism.";
J. Bacteriol. 140:182-187(1979).
[6]
FUNCTION, DEVELOPMENTAL STAGE, AND INDUCTION.
PubMed=8132480; DOI=10.1128/jb.176.6.1796-1800.1994;
Truniger V., Boos W.;
"Mapping and cloning of gldA, the structural gene of the Escherichia
coli glycerol dehydrogenase.";
J. Bacteriol. 176:1796-1800(1994).
[7]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC
PARAMETERS, AND ROLE IN DIHYDROXYACETONE METABOLISM.
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=18179582; DOI=10.1111/j.1574-6968.2007.01032.x;
Subedi K.P., Kim I., Kim J., Min B., Park C.;
"Role of GldA in dihydroxyacetone and methylglyoxal metabolism of
Escherichia coli K12.";
FEMS Microbiol. Lett. 279:180-187(2008).
[8]
ROLE IN ANAEROBIC FERMENTATION OF GLYCEROL.
PubMed=18632294; DOI=10.1016/j.ymben.2008.05.001;
Gonzalez R., Murarka A., Dharmadi Y., Yazdani S.S.;
"A new model for the anaerobic fermentation of glycerol in enteric
bacteria: trunk and auxiliary pathways in Escherichia coli.";
Metab. Eng. 10:234-245(2008).
-!- FUNCTION: 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.
{ECO:0000269|PubMed:18179582, ECO:0000269|PubMed:18632294,
ECO:0000269|PubMed:40950, ECO:0000269|PubMed:8132480}.
-!- CATALYTIC ACTIVITY: Glycerol + NAD(+) = glycerone + NADH.
{ECO:0000269|PubMed:18179582}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
Note=Binds 1 zinc ion per subunit. {ECO:0000250};
-!- ENZYME REGULATION: Inhibited by Cu(2+).
{ECO:0000269|PubMed:40950}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.30 mM for dihydroxyacetone (at 25 degrees Celsius and pH 7)
{ECO:0000269|PubMed:18179582};
KM=0.85 mM for glycolaldehyde (at 25 degrees Celsius and pH 7)
{ECO:0000269|PubMed:18179582};
KM=0.50 mM for methylglyoxal (at 25 degrees Celsius and pH 7)
{ECO:0000269|PubMed:18179582};
KM=56 mM for glycerol (at 25 degrees Celsius and pH 7)
{ECO:0000269|PubMed:18179582};
Note=The catalytic efficiency of the reverse reaction
(dihydroxyacetone reduction) is more than 100-fold higher than
that of the forward direction (glycerol oxidation).;
pH dependence:
Optimum pH is 5.5-6.0 for dihydroxyacetone reduction and 9.5-
10.0 for glycerol oxidation. {ECO:0000269|PubMed:40950};
-!- PATHWAY: Polyol metabolism; glycerol fermentation; glycerone
phosphate from glycerol (oxidative route): step 1/2.
-!- SUBUNIT: Homodimer and homooctamer. {ECO:0000269|PubMed:40950}.
-!- DEVELOPMENTAL STAGE: Expression is higher during stationary phase
than during logarithmic growth. {ECO:0000269|PubMed:8132480}.
-!- INDUCTION: Full expression of gldA is achieved by induction with
hydroxyacetone and stationary-phase growth conditions.
{ECO:0000269|PubMed:8132480}.
-!- SIMILARITY: Belongs to the iron-containing alcohol dehydrogenase
family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAC43051.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; U00006; AAC43051.1; ALT_INIT; Genomic_DNA.
EMBL; U00096; AAC76927.2; -; Genomic_DNA.
EMBL; AP009048; BAE77365.1; -; Genomic_DNA.
PIR; D65201; D65201.
RefSeq; NP_418380.4; NC_000913.3.
RefSeq; WP_000374004.1; NZ_LN832404.1.
ProteinModelPortal; P0A9S5; -.
SMR; P0A9S5; -.
BioGrid; 4262653; 14.
BioGrid; 852737; 1.
DIP; DIP-47916N; -.
IntAct; P0A9S5; 1.
STRING; 316385.ECDH10B_4134; -.
PaxDb; P0A9S5; -.
PRIDE; P0A9S5; -.
EnsemblBacteria; AAC76927; AAC76927; b3945.
EnsemblBacteria; BAE77365; BAE77365; BAE77365.
GeneID; 948440; -.
KEGG; ecj:JW5556; -.
KEGG; eco:b3945; -.
PATRIC; fig|1411691.4.peg.2759; -.
EchoBASE; EB1849; -.
EcoGene; EG11904; gldA.
eggNOG; ENOG4105DCT; Bacteria.
eggNOG; COG0371; LUCA.
HOGENOM; HOG000031784; -.
InParanoid; P0A9S5; -.
KO; K00005; -.
OMA; WYEASVS; -.
PhylomeDB; P0A9S5; -.
BioCyc; EcoCyc:GLYCDEH-MONOMER; -.
BioCyc; MetaCyc:GLYCDEH-MONOMER; -.
SABIO-RK; P0A9S5; -.
UniPathway; UPA00617; UER00668.
PRO; PR:P0A9S5; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0019147; F:(R)-aminopropanol dehydrogenase activity; IDA:EcoCyc.
GO; GO:0008888; F:glycerol dehydrogenase [NAD+] activity; IDA:EcoCyc.
GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0019588; P:anaerobic glycerol catabolic process; IMP:EcoCyc.
GO; GO:0051596; P:methylglyoxal catabolic process; IMP:EcoCyc.
InterPro; IPR001670; ADH_Fe/gldA.
InterPro; IPR018211; ADH_Fe_CS.
InterPro; IPR016205; Glycerol_DH.
PANTHER; PTHR43616; PTHR43616; 1.
Pfam; PF00465; Fe-ADH; 1.
PIRSF; PIRSF000112; Glycerol_dehydrogenase; 1.
PROSITE; PS00913; ADH_IRON_1; 1.
PROSITE; PS00060; ADH_IRON_2; 1.
1: Evidence at protein level;
Complete proteome; Direct protein sequencing; Glycerol metabolism;
Metal-binding; NAD; Oxidoreductase; Reference proteome; Zinc.
CHAIN 1 367 Glycerol dehydrogenase.
/FTId=PRO_0000087828.
NP_BIND 94 98 NAD. {ECO:0000250}.
NP_BIND 116 119 NAD. {ECO:0000250}.
METAL 171 171 Zinc; catalytic. {ECO:0000250}.
METAL 254 254 Zinc; catalytic. {ECO:0000250}.
METAL 271 271 Zinc; catalytic. {ECO:0000250}.
BINDING 37 37 NAD. {ECO:0000250}.
BINDING 121 121 Substrate. {ECO:0000250}.
BINDING 125 125 NAD. {ECO:0000250}.
BINDING 127 127 NAD; via carbonyl oxygen. {ECO:0000250}.
BINDING 131 131 NAD. {ECO:0000250}.
BINDING 171 171 Substrate. {ECO:0000250}.
BINDING 254 254 Substrate. {ECO:0000250}.
BINDING 271 271 Substrate. {ECO:0000250}.
SEQUENCE 367 AA; 38712 MW; F6F3F275B4091F28 CRC64;
MDRIIQSPGK YIQGADVINR LGEYLKPLAE RWLVVGDKFV LGFAQSTVEK SFKDAGLVVE
IAPFGGECSQ NEIDRLRGIA ETAQCGAILG IGGGKTLDTA KALAHFMGVP VAIAPTIAST
DAPCSALSVI YTDEGEFDRY LLLPNNPNMV IVDTKIVAGA PARLLAAGIG DALATWFEAR
ACSRSGATTM AGGKCTQAAL ALAELCYNTL LEEGEKAMLA AEQHVVTPAL ERVIEANTYL
SGVGFESGGL AAAHAVHNGL TAIPDAHHYY HGEKVAFGTL TQLVLENAPV EEIETVAALS
HAVGLPITLA QLDIKEDVPA KMRIVAEAAC AEGETIHNMP GGATPDQVYA ALLVADQYGQ
RFLQEWE


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