Glycerin dehydrogenase
| Glycerin dehydrogenase | ||
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| Ribbon model of the glycerine dehydrogenase from Geobacillus stearothermophilus , complexed with glycerine ; according to PDB 1JQA | ||
| other names |
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| Mass / length primary structure | 367 amino acids | |
| Secondary to quaternary structure | Homodimers and homooctamers | |
| Cofactor | Zn 2+ | |
| Identifier | ||
| Gene name (s) | gldA (EcoliWiki) | |
| External IDs |
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| Enzyme classification | ||
| EC, category | 1.1.1.6 , oxidoreductase | |
| Response type | Dehydration | |
| Substrate | Glycerin + NAD + | |
| Products | Dihydroxyacetone + NADH + H + | |
| Occurrence | ||
| Parent taxon | bacteria | |
Glycerine dehydrogenase is an enzyme that catalyzes the dehydrogenation of glycerine to dihydroxyacetone in bacteria . This enzyme belongs to the family of oxidoreductases , with the hydroxyl group acting as a donor and NAD + as an acceptor .
In particular, this enzyme is a metal-dependent alcohol dehydrogenase that plays a role in glycerol metabolism. In addition, this enzyme has already been isolated from numerous bacteria, for example Geobacillus stearothermophilus , Klebsiella aerogenes (formerly known as Enterobacter aerogenes or “ Aerobacter aerogenes ”), Enterococcus faecalis , Erwinia aeroidea and Bacillus megaterium . However, due to its thermostability, most studies were carried out with the bacterium Geobacillus stearothermophilus .
structure
Glycerol dehydrogenase is a homooctamer consisting of eight identical monomer subunits, which in turn consist of a single polypeptide chain of 367 amino acids. Each of these subunits contains 9 β-sheets and 14 α-helices within two different domains (the N -terminus contains 162 and the C -terminus 206 amino acids). The area between the two termini serves as the active center of the enzyme. The active center consists of a bound metal ion , a binding center for the nicotinamide ring and a binding site for the substrate.
Studies have shown that the active center contains a Zn 2+ ion as a cofactor. These zinc ions form tetrahedral dipole interactions between the amino acid residues Asp173, His256 and His274, as well as a water molecule.
The NAD + binding site, which resembles the Rossmann fold within the N -terminal domain, extends from the surface of the enzyme to the cleft containing the active site. The nicotinamide ring (active area of NAD + ) results in the formation of a hydrophobic pocket, consisting of the amino acid residues Asp100, Asp123, Ala124, Ser127, Leu129, Val131, Asp173, His174 and Phe247.
Finally, the substrate binding site consists of the residues Asp123, His256, His274 and a water molecule.
function
The enzyme catalyzes the dehydrogenation of glycerine to dihydroxyacetone. In contrast to the common metabolic pathways for metabolizing glycerine, glycerine dehydrogenase effectively oxidizes glycerine in anaerobic metabolic processes under ATP-independent conditions, which is a useful mechanism in the breakdown of glycerine in bacteria. In addition, the enzyme selectively oxidizes the hydroxyl group on the C2 atom to form a ketone rather than oxidizing a terminal hydroxyl group to form an aldehyde .
Catalyzed equilibrium
+ NAD + + NADH + H + 
Glycerine is oxidized and dehydrated by glycerine dehydrogenase. In addition to the reduction equivalent NADH, dihydroxyacetone is formed.
mechanism
After NAD + is bound to the enzyme, the glycerine binds to the active center, so that two coordinated interactions between two neighboring hydroxyl groups and the neighboring zinc ion arise. The enzyme then catalyzes the base-assisted deprotonation of the hydroxyl group on the C2 atom to form an alcoholate . The zinc atom serves to stabilize the negative charge in the alcoholate intermediate before the excess electron density around the oxygen atom shifts to form a double bond with the C2 atom. The hydride is then removed from the secondary carbon and now acts as a nucleophile in the electron transfer to the nicotinamide ring of the NAD + . As a result, the hydrogen proton removed from the base was released into the surrounding solution; This is followed by the release of the dihydroxyacetone as a product, then the NADH by the enzyme.
Industrial importance
Glycerin is a by-product in the production of biodiesel . When biodiesel production grew exponentially, the raw glycerine was produced in large quantities from the transesterification of vegetable oils. Despite the widespread use of pure glycerine in the food industry, cosmetics, pharmaceuticals and many other industries, it is comparatively expensive to purify the raw glycerine to the highest degree of purity. In biotechnology, a modified enzymatic conversion of raw glycerine can lead to a wide range of products, e.g. B. 1,3-propanediol , 1,2-propanediol , succinic acid , dihydroxyacetone, hydrogen, polyglycerin and polyester .
Classification
Another classification takes place under the glycerine dehydrogenases:
| enzyme | Enzyme classification | gene | UniProt | reaction | annotation |
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| Glycerine dehydrogenase (acceptor) | EC 1.1.99.22 | - | - | Glycerine + acceptor dihydroxyacetone + reduced acceptor | Has pyrroloquinoline quinone as a cofactor. |
| Glycerine dehydrogenase (NADP + ) | EC 1.1.1.72 | gldB (AspGD) | Q7Z8L1 | Glycerin + NADP + D -glyceraldehyde + NADPH + H + | Participates in the glycerolipid metabolism. |
| Glycerol-2-dehydrogenase (NADP + ) | EC 1.1.1.156 | GCY1 (SGD) | P14065 | Glycerin + NADP + dihydroxyacetone + NADPH + H + | Participates in glycerolipid metabolism. |
Individual evidence
- ^ Robert Main Burton, Nathan O. Kaplan: A DPN SPECIFIC GLYCEROL DEHYDROGENASE FROM AEROBACTER AEROGENES . In: Journal of the American Chemical Society . 75, No. 4, February 1953, pp. 1005-1006. doi : 10.1021 / ja01100a520 .
- ↑ Ec Lin, B. Magasanik: The activation of glycerol dehydrogenase from Aerobacter aerogenes by monovalent cations . (PDF) In: J. Biol. Chem . 235, No. 6, June 1960, pp. 1820-1823. PMID 14417009 .
- ↑ NJ Jacobs, PJ VanDemark: COMPARISON OF THE MECHANISM OF GLYCEROL OXIDATION IN AEROBICALLY AND ANAEROBICALLY GROWN STREPTOCOCCUS FAECALIS . (PDF) In: Journal of Bacteriology . 79, No. 4, April 1960, pp. 532-538. PMID 14406375 .
- ↑ Mamoru Sugiura, Tsutomu Oikawa, Kazuyuki Hirano, Hiroshi Shimizu, Fumio Hirata: Purification and Some Properties of Glycerol Dehydrogenase from Erwinia aroideae . In: Chemical & Pharmaceutical Bulletin . 26, No. 3, 1978, pp. 716-721. doi : 10.1248 / cpb.26.716 .
- ↑ Margrit Scharschmidt, Gerhard Pfleiderer, Harald Metz, Wolfgang Brümmer: Isolation and characterization of glycerine dehydrogenase from Bacillus megaterium . In: Hoppe-Seyler's Journal for Physiological Chemistry . 364, No. 2, 1983, pp. 911-922. doi : 10.1515 / bchm2.1983.364.2.911 .
- ↑ P. Spencer, KJ Bown, MD Scawen, T. Atkinson, MG Gore: Isolation and characterization of the glycerol dehydrogenase from Bacillus stearothermophilus . In: Biochemica et Biophysica Acta . 994, No. 3, February 23, 1989, pp. 270-279. doi : 10.1016 / 0167-4838 (89) 90304-X .
- ↑ SN Ruzheinikov, S. Sedelnikova, PJ Baker, R. Taylor, PA Bullough, NM Muir, MG Gore, DW Rice: Glycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase . (PDF) In: Structure . 9, No. 9, September 2001, pp. 789-802. doi : 10.1016 / s0969-2126 (01) 00645-1 . PMID 11566129 .
- ↑ Betty N. Leichus, John S. Blanchard: Isotopic Analysis of the Reaction Catalyzed by glycerol dehydrogenase . In: Biochemistry . 33, No. 48, 1994, pp. 14642-14649. doi : 10.1021 / bi00252a033 . PMID 7981227 .
- ^ Sharon Hammes-Schiffer and Stephen J. Benkovic: Relating Protein Motion to Catalysis . In: Annual Review of Biochemistry . 75, No. 1, July 2006, pp. 519-541. doi : 10.1146 / annurev.biochem.75.103004.142800 . PMID 16756501 .
- ↑ Naresh Pachauri, Brian He: Value-added Utilization of Crude Glycerol from Biodiesel Production: A Survey of Current Research Activities. (PDF) In: American Society of Agricultural and Biological Engineers. June 2006, accessed June 5, 2016 .