Reviewed, UniProtKB/Swiss-Prot P32816 (GLDA_BACST)

Names and origin

Protein names

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

Gene names

Name:	gldA
Synonyms:	gld

Organism

Bacillus stearothermophilus (Geobacillus stearothermophilus)

Taxonomic identifier

1422 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	370 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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. 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. Ref.3
Catalytic activity	Glycerol + NAD+ = glycerone + NADH.
Cofactor	Binds 1 zinc ion per subunit. Ref.3 Ref.4
Pathway	Polyol metabolism; glycerol fermentation; glycerone phosphate from glycerol (oxidative route): step 1/2.
Subunit structure	Homooctamer. Ref.4
Domain	Consists of two domains that are separated by a deep cleft, in which the Zn2+ ion is bound. Ref.4
Sequence similarities	Belongs to the iron-containing alcohol dehydrogenase family.
biophysicochemical properties	Kinetic parameters: KM=3.8 mM for glycerol KM=121 µM for NAD+ pH dependence: Optimum pH is 6.0-8.5.

Ontologies

Keywords
Biological process	Glycerol metabolism
Ligand	Metal-binding NAD Zinc
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	glycerol metabolic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	glycerol dehydrogenase activity Inferred from electronic annotation. Source: EC zinc 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 – 370

370

Glycerol dehydrogenase

PRO_0000087826

Regions

Nucleotide binding

96 – 100

5

NAD

Nucleotide binding

118 – 121

4

NAD

Sites

Metal binding

173

1

Zinc; catalytic

Metal binding

256

1

Zinc; catalytic

Metal binding

274

1

Zinc; catalytic

Binding site

39

1

NAD

Binding site

123

1

Substrate

Binding site

127

1

NAD

Binding site

129

1

NAD; via carbonyl oxygen

Binding site

133

1

NAD

Binding site

173

1

Substrate

Binding site

256

1

Substrate

Binding site

274

1

Substrate

Experimental info

Mutagenesis

97

1

K → H: Loss of activity. Ref.2

Mutagenesis

305

1

S → C: No effect on affinity for substrates. Ref.4

Secondary structure

1

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370

Helix Strand Turn

Details...

Beta strand

5 – 8

4

Beta strand

11 – 16

6

Helix

19 – 22

4

Helix

23 – 27

5

Turn

28 – 30

3

Beta strand

32 – 38

7

Helix

40 – 45

6

Helix

47 – 56

10

Beta strand

60 – 65

6

Helix

72 – 85

14

Beta strand

88 – 95

8

Helix

96 – 109

14

Beta strand

112 – 119

8

Beta strand

128 – 130

3

Beta strand

150 – 155

6

Helix

156 – 160

5

Helix

164 – 187

24

Beta strand

194 – 196

3

Helix

199 – 224

26

Helix

230 – 250

21

Helix

254 – 261

8

Helix

262 – 264

3

Helix

268 – 271

4

Helix

274 – 288

15

Helix

293 – 305

13

Turn

312 – 316

5

Helix

322 – 332

11

Helix

338 – 341

4

Helix

347 – 365

19

Sequences

	Sequence		Length	Mass (Da)
	P32816-1 [UniParc]. Last modified October 1, 1993. Version 1. Checksum: E5D93264B1670F25	FASTA	370	39,501
	10 20 30 40 50 60 MAAERVFISP AKYVQGKNVI TKIANYLEGI GNKTVVIADE IVWKIAGHTI VNELKKGNIA 70 80 90 100 110 120 AEEVVFSGEA SRNEVERIAN IARKAEAAIV IGVGGGKTLD TAKAVADELD AYIVIVPTAA 130 140 150 160 170 180 STDAPTSALS VIYSDDGVFE SYRFYKKNPD LVLVDTKIIA NAPPRLLASG IADALATWVE 190 200 210 220 230 240 ARSVIKSGGK TMAGGIPTIA AEAIAEKCEQ TLFKYGKLAY ESVKAKVVTP ALEAVVEANT 250 260 270 280 290 300 LLSGLGFESG GLAAAHAIHN GFTALEGEIH HLTHGEKVAF GTLVQLALEE HSQQEIERYI 310 320 330 340 350 360 ELYLSLDLPV TLEDIKLKDA SREDILKVAK AATAEGETIH NAFNVTADDV ADAIFAADQY 370 AKAYKEKHRK

References

[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: 1339360] [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: 8399385] [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: 2493267] [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: 11566129] [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.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M65289 Genomic DNA. Translation: AAA22477.1.

PIR

JQ1474.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1JPU	X-ray	1.80	A	1-370	[»]
1JQ5	X-ray	1.70	A	1-370	[»]
1JQA	X-ray	2.05	A	1-370	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.1.1.6. 266715.

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_BACST

Accession

Primary (citable) accession number: P32816

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1993
Last modified:	June 16, 2009
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)