GLDA_ECOLI
ID GLDA_ECOLI Reviewed; 367 AA.
AC P0A9S5; P32665; P78132; Q2M8P1;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Glycerol dehydrogenase;
DE Short=GDH;
DE Short=GLDH;
DE EC=1.1.1.6;
GN Name=gldA; OrderedLocusNames=b3945, JW5556;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 1-8.
RC STRAIN=K12;
RX PubMed=17895580; DOI=10.1266/ggs.82.291;
RA Otsuka Y., Koga M., Iwamoto A., Yonesaki T.;
RT "A role of RnlA in the RNase LS activity from Escherichia coli.";
RL Genes Genet. Syst. 82:291-299(2007).
RN [5]
RP FUNCTION, CHARACTERIZATION, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION,
RP SUBUNIT, AND PH DEPENDENCE.
RX PubMed=40950; DOI=10.1128/jb.140.1.182-187.1979;
RA Tang C.-T., Ruch F.E. Jr., Lin E.C.C.;
RT "Purification and properties of a nicotinamide adenine dinucleotide-linked
RT dehydrogenase that serves an Escherichia coli mutant for glycerol
RT catabolism.";
RL J. Bacteriol. 140:182-187(1979).
RN [6]
RP FUNCTION, DEVELOPMENTAL STAGE, AND INDUCTION.
RX PubMed=8132480; DOI=10.1128/jb.176.6.1796-1800.1994;
RA Truniger V., Boos W.;
RT "Mapping and cloning of gldA, the structural gene of the Escherichia coli
RT glycerol dehydrogenase.";
RL J. Bacteriol. 176:1796-1800(1994).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS,
RP AND ROLE IN DIHYDROXYACETONE METABOLISM.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=18179582; DOI=10.1111/j.1574-6968.2007.01032.x;
RA Subedi K.P., Kim I., Kim J., Min B., Park C.;
RT "Role of GldA in dihydroxyacetone and methylglyoxal metabolism of
RT Escherichia coli K12.";
RL FEMS Microbiol. Lett. 279:180-187(2008).
RN [8]
RP ROLE IN ANAEROBIC FERMENTATION OF GLYCEROL.
RX PubMed=18632294; DOI=10.1016/j.ymben.2008.05.001;
RA Gonzalez R., Murarka A., Dharmadi Y., Yazdani S.S.;
RT "A new model for the anaerobic fermentation of glycerol in enteric
RT bacteria: trunk and auxiliary pathways in Escherichia coli.";
RL Metab. Eng. 10:234-245(2008).
CC -!- FUNCTION: Catalyzes the NAD-dependent oxidation of glycerol to
CC dihydroxyacetone (glycerone). Allows microorganisms to utilize glycerol
CC as a source of carbon under anaerobic conditions. In E.coli, an
CC important role of GldA is also likely to regulate the intracellular
CC level of dihydroxyacetone by catalyzing the reverse reaction, i.e. the
CC conversion of dihydroxyacetone into glycerol. Possesses a broad
CC substrate specificity, since it is also able to oxidize 1,2-propanediol
CC and to reduce glycolaldehyde, methylglyoxal and hydroxyacetone into
CC ethylene glycol, lactaldehyde and 1,2-propanediol, respectively.
CC {ECO:0000269|PubMed:18179582, ECO:0000269|PubMed:18632294,
CC ECO:0000269|PubMed:40950, ECO:0000269|PubMed:8132480}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycerol + NAD(+) = dihydroxyacetone + H(+) + NADH;
CC Xref=Rhea:RHEA:13769, ChEBI:CHEBI:15378, ChEBI:CHEBI:16016,
CC ChEBI:CHEBI:17754, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945; EC=1.1.1.6;
CC Evidence={ECO:0000269|PubMed:18179582};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250};
CC -!- ACTIVITY REGULATION: Inhibited by Cu(2+). {ECO:0000269|PubMed:40950}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.30 mM for dihydroxyacetone (at 25 degrees Celsius and pH 7)
CC {ECO:0000269|PubMed:18179582};
CC KM=0.85 mM for glycolaldehyde (at 25 degrees Celsius and pH 7)
CC {ECO:0000269|PubMed:18179582};
CC KM=0.50 mM for methylglyoxal (at 25 degrees Celsius and pH 7)
CC {ECO:0000269|PubMed:18179582};
CC KM=56 mM for glycerol (at 25 degrees Celsius and pH 7)
CC {ECO:0000269|PubMed:18179582};
CC Note=The catalytic efficiency of the reverse reaction
CC (dihydroxyacetone reduction) is more than 100-fold higher than that
CC of the forward direction (glycerol oxidation).;
CC pH dependence:
CC Optimum pH is 5.5-6.0 for dihydroxyacetone reduction and 9.5-10.0 for
CC glycerol oxidation. {ECO:0000269|PubMed:40950};
CC -!- PATHWAY: Polyol metabolism; glycerol fermentation; glycerone phosphate
CC from glycerol (oxidative route): step 1/2.
CC -!- SUBUNIT: Homodimer and homooctamer. {ECO:0000269|PubMed:40950}.
CC -!- DEVELOPMENTAL STAGE: Expression is higher during stationary phase than
CC during logarithmic growth. {ECO:0000269|PubMed:8132480}.
CC -!- INDUCTION: Full expression of gldA is achieved by induction with
CC hydroxyacetone and stationary-phase growth conditions.
CC {ECO:0000269|PubMed:8132480}.
CC -!- SIMILARITY: Belongs to the iron-containing alcohol dehydrogenase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC43051.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U00006; AAC43051.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76927.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE77365.1; -; Genomic_DNA.
DR PIR; D65201; D65201.
DR RefSeq; NP_418380.4; NC_000913.3.
DR RefSeq; WP_000374004.1; NZ_STEB01000037.1.
DR PDB; 5ZXL; X-ray; 2.79 A; A/B/C/D=1-367.
DR PDBsum; 5ZXL; -.
DR AlphaFoldDB; P0A9S5; -.
DR SMR; P0A9S5; -.
DR BioGRID; 4262653; 14.
DR BioGRID; 852737; 1.
DR DIP; DIP-47916N; -.
DR IntAct; P0A9S5; 1.
DR STRING; 511145.b3945; -.
DR jPOST; P0A9S5; -.
DR PaxDb; P0A9S5; -.
DR PRIDE; P0A9S5; -.
DR EnsemblBacteria; AAC76927; AAC76927; b3945.
DR EnsemblBacteria; BAE77365; BAE77365; BAE77365.
DR GeneID; 66672144; -.
DR GeneID; 948440; -.
DR KEGG; ecj:JW5556; -.
DR KEGG; eco:b3945; -.
DR PATRIC; fig|1411691.4.peg.2759; -.
DR EchoBASE; EB1849; -.
DR eggNOG; COG0371; Bacteria.
DR HOGENOM; CLU_044754_1_0_6; -.
DR InParanoid; P0A9S5; -.
DR OMA; ALHGEQC; -.
DR PhylomeDB; P0A9S5; -.
DR BioCyc; EcoCyc:GLYCDEH-MON; -.
DR BioCyc; MetaCyc:GLYCDEH-MON; -.
DR BRENDA; 1.1.1.6; 2026.
DR SABIO-RK; P0A9S5; -.
DR UniPathway; UPA00617; UER00668.
DR PRO; PR:P0A9S5; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0019147; F:(R)-aminopropanol dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0008888; F:glycerol dehydrogenase [NAD+] activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0019588; P:anaerobic glycerol catabolic process; IMP:EcoCyc.
DR GO; GO:0051596; P:methylglyoxal catabolic process; IMP:EcoCyc.
DR InterPro; IPR001670; ADH_Fe/GldA.
DR InterPro; IPR018211; ADH_Fe_CS.
DR InterPro; IPR016205; Glycerol_DH.
DR PANTHER; PTHR43616; PTHR43616; 1.
DR Pfam; PF00465; Fe-ADH; 1.
DR PIRSF; PIRSF000112; Glycerol_dehydrogenase; 1.
DR PROSITE; PS00913; ADH_IRON_1; 1.
DR PROSITE; PS00060; ADH_IRON_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Glycerol metabolism;
KW Metal-binding; NAD; Oxidoreductase; Reference proteome; Zinc.
FT CHAIN 1..367
FT /note="Glycerol dehydrogenase"
FT /id="PRO_0000087828"
FT BINDING 37
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 94..98
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 116..119
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 121
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 125
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 127
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 131
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 254
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 254
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 271
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 271
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 9..14
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 17..20
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 21..25
FT /evidence="ECO:0007829|PDB:5ZXL"
FT TURN 26..28
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 38..54
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 58..63
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 70..82
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 86..93
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 94..106
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 125..131
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 148..153
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 154..159
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 162..185
FT /evidence="ECO:0007829|PDB:5ZXL"
FT STRAND 192..195
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 197..223
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 228..248
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 252..261
FT /evidence="ECO:0007829|PDB:5ZXL"
FT TURN 265..268
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 271..285
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 290..302
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 309..312
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 318..330
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 335..338
FT /evidence="ECO:0007829|PDB:5ZXL"
FT HELIX 345..364
FT /evidence="ECO:0007829|PDB:5ZXL"
SQ 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
