P0A9S5 (GLDA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glycerol dehydrogenase
Short name=GDH
Short name=GLDH
EC=1.1.1.6

Gene names

Name:	gldA
Ordered Locus Names:	b3945, JW5556

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	367 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.5 Ref.6 Ref.7 Ref.8
Catalytic activity	Glycerol + NAD+ = glycerone + NADH. Ref.7
Cofactor	Binds 1 zinc ion per subunit By similarity.
Enzyme regulation	Inhibited by Cu2+. Ref.5
Pathway	Polyol metabolism; glycerol fermentation; glycerone phosphate from glycerol (oxidative route): step 1/2.
Subunit structure	Homodimer and homooctamer. Ref.5
Developmental stage	Expression is higher during stationary phase than during logarithmic growth. Ref.6
Induction	Full expression of gldA is achieved by induction with hydroxyacetone and stationary-phase growth conditions. Ref.5 Ref.6
Sequence similarities	Belongs to the iron-containing alcohol dehydrogenase family.
Biophysicochemical properties	Kinetic parameters: The catalytic efficiency of the reverse reaction (dihydroxyacetone reduction) is more than 100-fold higher than that of the forward direction (glycerol oxidation). KM=0.30 mM for dihydroxyacetone (at 25 degrees Celsius and pH 7) Ref.7 KM=0.85 mM for glycolaldehyde (at 25 degrees Celsius and pH 7) KM=0.50 mM for methylglyoxal (at 25 degrees Celsius and pH 7) KM=56 mM for glycerol (at 25 degrees Celsius and pH 7) pH dependence: Optimum pH is 5.5-6.0 for dihydroxyacetone reduction and 9.5-10.0 for glycerol oxidation.
Sequence caution	The sequence AAC43051.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Glycerol metabolism
Ligand	Metal-binding NAD Zinc
Molecular function	Oxidoreductase
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	anaerobic glycerol catabolic process Inferred from mutant phenotype Ref.8. Source: EcoCyc methylglyoxal catabolic process Inferred from mutant phenotype Ref.8. Source: EcoCyc
Molecular_function	(R)-aminopropanol dehydrogenase activity Inferred from direct assay PubMed 359547. Source: EcoCyc glycerol dehydrogenase [NAD+] activity Inferred from direct assay Ref.5. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 367	367	Glycerol dehydrogenase		PRO_0000087828
Regions
	Nucleotide binding	94 – 98	5	NAD By similarity
	Nucleotide binding	116 – 119	4	NAD By similarity
Sites
	Metal binding	171	1	Zinc; catalytic By similarity
	Metal binding	254	1	Zinc; catalytic By similarity
	Metal binding	271	1	Zinc; catalytic By similarity
	Binding site	37	1	NAD By similarity
	Binding site	121	1	Substrate By similarity
	Binding site	125	1	NAD By similarity
	Binding site	127	1	NAD; via carbonyl oxygen By similarity
	Binding site	131	1	NAD By similarity
	Binding site	171	1	Substrate By similarity
	Binding site	254	1	Substrate By similarity
	Binding site	271	1	Substrate By similarity

Sequences

	Sequence		Length	Mass (Da)
	P0A9S5 [UniParc]. Last modified July 19, 2005. Version 1. Checksum: F6F3F275B4091F28	FASTA	367	38,712
	10 20 30 40 50 60 MDRIIQSPGK YIQGADVINR LGEYLKPLAE RWLVVGDKFV LGFAQSTVEK SFKDAGLVVE 70 80 90 100 110 120 IAPFGGECSQ NEIDRLRGIA ETAQCGAILG IGGGKTLDTA KALAHFMGVP VAIAPTIAST 130 140 150 160 170 180 DAPCSALSVI YTDEGEFDRY LLLPNNPNMV IVDTKIVAGA PARLLAAGIG DALATWFEAR 190 200 210 220 230 240 ACSRSGATTM AGGKCTQAAL ALAELCYNTL LEEGEKAMLA AEQHVVTPAL ERVIEANTYL 250 260 270 280 290 300 SGVGFESGGL AAAHAVHNGL TAIPDAHHYY HGEKVAFGTL TQLVLENAPV EEIETVAALS 310 320 330 340 350 360 HAVGLPITLA QLDIKEDVPA KMRIVAEAAC AEGETIHNMP GGATPDQVYA ALLVADQYGQ RFLQEWE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[2]	"The complete genome sequence of Escherichia coli K-12." 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. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"A role of RnlA in the RNase LS activity from Escherichia coli." Otsuka Y., Koga M., Iwamoto A., Yonesaki T. Genes Genet. Syst. 82:291-299(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-8. Strain: K12.
[5]	"Purification and properties of a nicotinamide adenine dinucleotide-linked dehydrogenase that serves an Escherichia coli mutant for glycerol catabolism." Tang C.-T., Ruch F.E. Jr., Lin E.C.C. J. Bacteriol. 140:182-187(1979) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CHARACTERIZATION, SUBSTRATE SPECIFICITY, ENZYME REGULATION, SUBUNIT, PH DEPENDENCE.
[6]	"Mapping and cloning of gldA, the structural gene of the Escherichia coli glycerol dehydrogenase." Truniger V., Boos W. J. Bacteriol. 176:1796-1800(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DEVELOPMENTAL STAGE, INDUCTION.
[7]	"Role of GldA in dihydroxyacetone and methylglyoxal metabolism of Escherichia coli K12." Subedi K.P., Kim I., Kim J., Min B., Park C. FEMS Microbiol. Lett. 279:180-187(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS, ROLE IN DIHYDROXYACETONE METABOLISM. Strain: K12 / MG1655 / ATCC 47076.
[8]	"A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli." Gonzalez R., Murarka A., Dharmadi Y., Yazdani S.S. Metab. Eng. 10:234-245(2008) [PubMed] [Europe PMC] [Abstract] Cited for: ROLE IN ANAEROBIC FERMENTATION OF GLYCEROL.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U00006 Genomic DNA. Translation: AAC43051.1. Different initiation. U00096 Genomic DNA. Translation: AAC76927.2. AP009048 Genomic DNA. Translation: BAE77365.1.
PIR	D65201.
RefSeq	NP_418380.4. NC_000913.2. YP_491506.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0A9S5.
SMR	P0A9S5. Positions 8-360.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-47916N.
IntAct	P0A9S5. 1 interaction.
STRING	511145.b3945.
Proteomic databases
PaxDb	P0A9S5.
PRIDE	P0A9S5.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC76927; AAC76927; b3945. BAE77365; BAE77365; BAE77365.
GeneID	12933659. 948440.
KEGG	ecj:Y75_p3242. eco:b3945.
PATRIC	32123413. VBIEscCol129921_4067.
Organism-specific databases
EchoBASE	EB1849.
EcoGene	EG11904. gldA.
Phylogenomic databases
eggNOG	COG0371.
HOGENOM	HOG000031784.
KO	K00005.
OMA	YLMLPHN.
ProtClustDB	PRK09423.
Enzyme and pathway databases
BioCyc	EcoCyc:GLYCDEH-MONOMER. ECOL316407:JW5556-MONOMER. MetaCyc:GLYCDEH-MONOMER.
SABIO-RK	P0A9S5.
UniPathway	UPA00617; UER00668.
Gene expression databases
Genevestigator	P0A9S5.
Family and domain databases
InterPro	IPR001670. ADH_Fe. IPR018211. ADH_Fe_CS. IPR016205. Glycerol_DH. [Graphical view]
Pfam	PF00465. Fe-ADH. 1 hit. [Graphical view]
PIRSF	PIRSF000112. Glycerol_dehydrogenase. 1 hit.
PROSITE	PS00913. ADH_IRON_1. 1 hit. PS00060. ADH_IRON_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

GLDA_ECOLI

Accession

Primary (citable) accession number: P0A9S5
Secondary accession number(s): P32665, P78132, Q2M8P1

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2005
Last sequence update:	July 19, 2005
Last modified:	May 1, 2013
This is version 74 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program