GLDA_GEOSE
ID GLDA_GEOSE Reviewed; 370 AA.
AC P32816;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Glycerol dehydrogenase;
DE Short=GDH;
DE Short=GLDH;
DE Short=GlyDH;
DE EC=1.1.1.6;
GN Name=gldA; Synonyms=gld;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 2334 / Var. Non-diastaticus;
RX PubMed=1339360; DOI=10.1016/0378-1119(92)90438-u;
RA Mallinder P.R., Pritchard A., Moir A.;
RT "Cloning and characterization of a gene from Bacillus stearothermophilus
RT var. non-diastaticus encoding a glycerol dehydrogenase.";
RL Gene 110:9-16(1992).
RN [2]
RP PROTEIN SEQUENCE OF 84-103, AND MUTAGENESIS OF LYS-97.
RX PubMed=8399385; DOI=10.1016/0167-4838(93)90010-o;
RA Paine L.J., Perry N., Popplewell A.G., Gore M.G., Atkinson T.;
RT "The identification of a lysine residue reactive to pyridoxal-5-phosphate
RT in the glycerol dehydrogenase from the thermophile Bacillus
RT stearothermophilus.";
RL Biochim. Biophys. Acta 1202:235-243(1993).
RN [3]
RP FUNCTION, COFACTOR, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=2493267; DOI=10.1016/0167-4838(89)90304-x;
RA Spencer P., Bown K.J., Scawen M.D., Atkinson T., Gore M.G.;
RT "Isolation and characterisation of the glycerol dehydrogenase from Bacillus
RT stearothermophilus.";
RL Biochim. Biophys. Acta 994:270-279(1989).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANT CYS-305 IN COMPLEXES WITH
RP ZINC; NAD AND SUBSTRATE, DOMAIN, COFACTOR, SUBUNIT, AND MUTAGENESIS OF
RP SER-305.
RX PubMed=11566129; DOI=10.1016/s0969-2126(01)00645-1;
RA Ruzheinikov S.N., Burke J., Sedelnikova S., Baker P.J., Taylor R.,
RA Bullough P.A., Muir N.M., Gore M.G., Rice D.W.;
RT "Glycerol dehydrogenase: structure, specificity, and mechanism of a family
RT III polyol dehydrogenase.";
RL Structure 9:789-802(2001).
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. Is also able to use
CC various diols as substrates, such as propan-1,2-diol, butan-2,3-diol,
CC ethan-1,2-diol, and 3-mercapto-1,2-dihydroxypropane.
CC {ECO:0000269|PubMed:2493267}.
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 -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:11566129, ECO:0000269|PubMed:2493267};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:11566129,
CC ECO:0000269|PubMed:2493267};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.8 mM for glycerol {ECO:0000269|PubMed:2493267};
CC KM=121 uM for NAD(+) {ECO:0000269|PubMed:2493267};
CC pH dependence:
CC Optimum pH is 6.0-8.5. {ECO:0000269|PubMed:2493267};
CC -!- PATHWAY: Polyol metabolism; glycerol fermentation; glycerone phosphate
CC from glycerol (oxidative route): step 1/2.
CC -!- SUBUNIT: Homooctamer. {ECO:0000269|PubMed:11566129}.
CC -!- DOMAIN: Consists of two domains that are separated by a deep cleft, in
CC which the Zn(2+) ion is bound. {ECO:0000269|PubMed:11566129}.
CC -!- SIMILARITY: Belongs to the iron-containing alcohol dehydrogenase
CC family. {ECO:0000305}.
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DR EMBL; M65289; AAA22477.1; -; Genomic_DNA.
DR PIR; JQ1474; JQ1474.
DR PDB; 1JPU; X-ray; 1.80 A; A=1-370.
DR PDB; 1JQ5; X-ray; 1.70 A; A=1-370.
DR PDB; 1JQA; X-ray; 2.05 A; A=1-370.
DR PDBsum; 1JPU; -.
DR PDBsum; 1JQ5; -.
DR PDBsum; 1JQA; -.
DR AlphaFoldDB; P32816; -.
DR SMR; P32816; -.
DR BRENDA; 1.1.1.6; 623.
DR SABIO-RK; P32816; -.
DR UniPathway; UPA00617; UER00668.
DR EvolutionaryTrace; P32816; -.
DR GO; GO:0008888; F:glycerol dehydrogenase [NAD+] activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019588; P:anaerobic glycerol catabolic process; IEA:UniProtKB-UniPathway.
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; Zinc.
FT CHAIN 1..370
FT /note="Glycerol dehydrogenase"
FT /id="PRO_0000087826"
FT BINDING 39
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 96..100
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 118..121
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 123
FT /ligand="substrate"
FT BINDING 127
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 129
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 133
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 173
FT /ligand="substrate"
FT BINDING 173
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 256
FT /ligand="substrate"
FT BINDING 256
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 274
FT /ligand="substrate"
FT BINDING 274
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT MUTAGEN 97
FT /note="K->H: Loss of activity."
FT /evidence="ECO:0000269|PubMed:8399385"
FT MUTAGEN 305
FT /note="S->C: No effect on affinity for substrates."
FT /evidence="ECO:0000269|PubMed:11566129"
FT STRAND 11..16
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 19..22
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 23..27
FT /evidence="ECO:0007829|PDB:1JQ5"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 32..38
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 40..45
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 47..55
FT /evidence="ECO:0007829|PDB:1JQ5"
FT TURN 56..58
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 72..84
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 88..95
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 96..109
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 112..119
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 128..133
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 139..144
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 150..155
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 156..160
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 164..187
FT /evidence="ECO:0007829|PDB:1JQ5"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 199..224
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 230..250
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 254..261
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 268..271
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 274..288
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 293..305
FT /evidence="ECO:0007829|PDB:1JQ5"
FT TURN 312..316
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 322..332
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 338..341
FT /evidence="ECO:0007829|PDB:1JQ5"
FT HELIX 347..365
FT /evidence="ECO:0007829|PDB:1JQ5"
SQ SEQUENCE 370 AA; 39501 MW; E5D93264B1670F25 CRC64;
MAAERVFISP AKYVQGKNVI TKIANYLEGI GNKTVVIADE IVWKIAGHTI VNELKKGNIA
AEEVVFSGEA SRNEVERIAN IARKAEAAIV IGVGGGKTLD TAKAVADELD AYIVIVPTAA
STDAPTSALS VIYSDDGVFE SYRFYKKNPD LVLVDTKIIA NAPPRLLASG IADALATWVE
ARSVIKSGGK TMAGGIPTIA AEAIAEKCEQ TLFKYGKLAY ESVKAKVVTP ALEAVVEANT
LLSGLGFESG GLAAAHAIHN GFTALEGEIH HLTHGEKVAF GTLVQLALEE HSQQEIERYI
ELYLSLDLPV TLEDIKLKDA SREDILKVAK AATAEGETIH NAFNVTADDV ADAIFAADQY
AKAYKEKHRK
