This enzyme belongs to the family of lyases, specifically the aldehyde-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase (D-glyceraldehyde-3-phosphate-forming). Other names in common use include phosphodeoxyriboaldolase, deoxyriboaldolase, deoxyribose-5-phosphate aldolase, 2-deoxyribose-5-phosphate aldolase, and 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase.
Enzyme Mechanism
Mechanism of DERA catalysis. First, substrate is shown, followed by stabilizing interactions at the active site. Finally, key lysine residues and the carbinolamine intermediate are shown. Based on PDB 1JCL
Amongst aldolases, DERA is one of the 2 only aldolases able to use two aldehydes as substrate (the other one being FSA).[1] Crystallography shows that the enzyme is a Class I aldolase, so the mechanism proceeds via the formation of a Schiff base with Lys167 at the active site. A nearby residue, Lys201, is critical to reaction by increasing the acidity of protonated Lys167, so Schiff base formation can occur more readily.[2]
As equilibrium of the reaction as written lies on the side of reactant, DERA can also used to catalyze the backward aldol reaction. The enzyme has been found to exhibit some promiscuity by accepting various carbonyl compounds as substrates: acetaldehyde can be replaced with other small aldehydes or acetone; and a variety of aldehydes can be used in place of D-glyceraldehyde 3-phosphate. However, due to the spatial arrangement of stabilizing interactions of the electrophilic aldehyde at the active site, the aldol reaction is stereospecific and gives the (S)-configuration at the reactive carbon. Molecular modeling of the active site showed a hydrophilic pocket formed by Thr170 and Lys172 to stabilize C2-hydroxy group of D-glyceraldehyde 3-phosphate, while the C2-hydrogen atom is stabilized in a hydrophobic pocket. When a racemic mixture of glyceraldehyde 3-phosphate is used as the substrate, only the D-isomer reacted.[3]
In solution, DERAs are found in homodimers or homotetramers. The oligomeric nature of the enzyme does not contribute to enzymatic activity, but serves to increase thermal stability through hydrophobic interactions and hydrogen bonding between interfacial residues.[5]
DERA is part of the inducible deo operon in bacteria which allows for the conversion of exogenous deoxyribonucleosides for energy generation.[6] The products of DERA, glyceraldehyde-3-phosphate and acetaldehyde (subsequently converted to acetyl CoA) can enter the glycolysis and Kreb’s cycle pathways respectively.
In humans, DERA is mainly expressed in lungs, liver and colon and is necessary for the cellular stress response. After induction of oxidative stress or mitochondrial stress, DERA colocalizes with stress granules and associates with YBX1, a known stress granule protein. Cells with high DERA expression were able to utilize exogenous deoxyinosine to produce ATP when starved of glucose and incubated with mitochondrial uncoupler FCCP.[7]
Industrial Relevance
DERA used in islatravir biocatalysis. Bonds formed by DERA are highlighted in red.
DERA is being used in chemical syntheses as a tool for green, enantioselective aldol reactions. Formation of the deoxyribose skeleton from small molecules can facilitate the synthesis of nucleoside reverse transcriptase inhibitors.[8] For example, DERA was used in a mixture of five enzymes in the biocatalytic synthesis of islatravir.[9]
DERA used in Atorvastatin biocatalysis. The portion of Atorvastatin which was derived from the DERA catalyzed reaction is indicated.
DERA has also been used to perform tandem aldol reactions with three aldehyde substrates, with reaction equilibrium driven by the formation of the six-membered cyclic hemiacetal.[10] This intermediate has been used in the synthesis of statin drugs, such as atorvastatin,[11]rosuvastatin and mevastatin.[12]
Natural DERAs show low tolerance to high concentrations of acetaldehyde[13] due to the formation of the highly reactive crotonaldehyde intermediate that irreversibly inactivates the enzyme.[14] This features hampers the industrial applications of DERA as the concentration of acetaldehyde used will be limited. To overcome this, directed evolution has been used to improve the acetaldehyde tolerance of DERA to up to 400mM.[9]
Related Research Articles
The aldol reaction is a reaction in organic chemistry that combines two carbonyl compounds to form a new β-hydroxy carbonyl compound. Its simplest form might involve the nucleophilic addition of an enolized ketone to another:
Aldolase B also known as fructose-bisphosphate aldolase B or liver-type aldolase is one of three isoenzymes of the class I fructose 1,6-bisphosphate aldolase enzyme, and plays a key role in both glycolysis and gluconeogenesis. The generic fructose 1,6-bisphosphate aldolase enzyme catalyzes the reversible cleavage of fructose 1,6-bisphosphate (FBP) into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP) as well as the reversible cleavage of fructose 1-phosphate (F1P) into glyceraldehyde and dihydroxyacetone phosphate. In mammals, aldolase B is preferentially expressed in the liver, while aldolase A is expressed in muscle and erythrocytes and aldolase C is expressed in the brain. Slight differences in isozyme structure result in different activities for the two substrate molecules: FBP and fructose 1-phosphate. Aldolase B exhibits no preference and thus catalyzes both reactions, while aldolases A and C prefer FBP.
Fructose-bisphosphate aldolase, often just aldolase, is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P). Aldolase can also produce DHAP from other (3S,4R)-ketose 1-phosphates such as fructose 1-phosphate and sedoheptulose 1,7-bisphosphate. Gluconeogenesis and the Calvin cycle, which are anabolic pathways, use the reverse reaction. Glycolysis, a catabolic pathway, uses the forward reaction. Aldolase is divided into two classes by mechanism.
In enzymology, a phosphopentomutase is an enzyme that catalyzes the chemical reaction
The enzyme 2-dehydro-3-deoxy-6-phosphogalactonate aldolase catalyzes the chemical reaction
The enzyme 2-dehydro-3-deoxy-D-pentonate aldolase catalyzes the chemical reaction
The enzyme 2-dehydro-3-deoxy-L-pentonate aldolase catalyzes the chemical reaction
The enzyme 2-dehydro-3-deoxy-phosphogluconate aldolase, commonly known as KDPG aldolase, catalyzes the chemical reaction
The enzyme 4-hydroxy-2-oxovalerate aldolase catalyzes the chemical reaction
The enzyme 5-dehydro-2-deoxyphosphogluconate aldolase catalyzes the chemical reaction
The enzyme indole-3-glycerol-phosphate lyase catalyzes the chemical reaction
The enzyme L-fuculose-phosphate aldolase (EC 4.1.2.17) catalyzes the chemical reaction
The enzyme tagatose-bisphosphate aldolase catalyzes the chemical reaction
The enzyme threonine aldolase is an enzyme that catalyzes the chemical reaction
In enzymology, a 1-deoxy-d-xylulose-5-phosphate synthase (EC 2.2.1.7) is an enzyme in the non-mevalonate pathway that catalyzes the chemical reaction
In enzymology, an acetoin-ribose-5-phosphate transaldolase is an enzyme that catalyzes the chemical reaction
In enzymology, a 3-deoxy-8-phosphooctulonate synthase (EC 2.5.1.55) is an enzyme that catalyzes the chemical reaction
3-Deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase is the first enzyme in a series of metabolic reactions known as the shikimate pathway, which is responsible for the biosynthesis of the amino acids phenylalanine, tyrosine, and tryptophan. Since it is the first enzyme in the shikimate pathway, it controls the amount of carbon entering the pathway. Enzyme inhibition is the primary method of regulating the amount of carbon entering the pathway. Forms of this enzyme differ between organisms, but can be considered DAHP synthase based upon the reaction that is catalyzed by this enzyme.
D-threonine aldolase is an enzyme with systematic name D-threonine acetaldehyde-lyase (glycine-forming). This enzyme catalyses the following chemical reaction
Multiple Michael/aldol reaction is a consecutive series of reactions composed of either Michael addition reactions or aldol reactions. More than two steps of reaction are usually involved. This reaction has been used for synthesis of large macrocyclic or polycyclic ring structures.
References
↑ Chambre, Domitille; Guérard-Hélaine, Christine; Darii, Ekaterina; Mariage, Aline; Petit, Jean-Louis; Salanoubat, Marcel; de Berardinis, Véronique; Lemaire, Marielle; Hélaine, Virgil (2019). "2-Deoxyribose-5-phosphate aldolase, a remarkably tolerant aldolase towards nucleophile substrates". Chemical Communications. 55 (52): 7498–7501. doi:10.1039/c9cc03361k. PMID31187106.
1 2 Heine, Andreas; Luz, John G.; Wong, Chi-Huey; Wilson, Ian A. (October 2004). "Analysis of the Class I Aldolase Binding Site Architecture Based on the Crystal Structure of 2-Deoxyribose-5-phosphate Aldolase at 0.99Å Resolution". Journal of Molecular Biology. 343 (4): 1019–1034. doi:10.1016/j.jmb.2004.08.066. PMID15476818.
↑ Lokanath, N. K.; Shiromizu, I.; Ohshima, N.; Nodake, Y.; Sugahara, M.; Yokoyama, S.; Kuramitsu, S.; Miyano, M.; Kunishima, N. (1 October 2004). "Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability". Acta Crystallographica Section D. 60 (10): 1816–1823. doi:10.1107/S0907444904020190. ISSN0907-4449. PMID15388928.
1 2 Huffman, Mark A.; Fryszkowska, Anna; Alvizo, Oscar; Borra-Garske, Margie; Campos, Kevin R.; Canada, Keith A.; Devine, Paul N.; Duan, Da; Forstater, Jacob H.; Grosser, Shane T.; Halsey, Holst M.; Hughes, Gregory J.; Jo, Junyong; Joyce, Leo A.; Kolev, Joshua N.; Liang, Jack; Maloney, Kevin M.; Mann, Benjamin F.; Marshall, Nicholas M.; McLaughlin, Mark; Moore, Jeffrey C.; Murphy, Grant S.; Nawrat, Christopher C.; Nazor, Jovana; Novick, Scott; Patel, Niki R.; Rodriguez-Granillo, Agustina; Robaire, Sandra A.; Sherer, Edward C.; Truppo, Matthew D.; Whittaker, Aaron M.; Verma, Deeptak; Xiao, Li; Xu, Yingju; Yang, Hao (5 December 2019). "Design of an in vitro biocatalytic cascade for the manufacture of islatravir". Science. 366 (6470): 1255–1259. Bibcode:2019Sci...366.1255H. doi:10.1126/science.aay8484. PMID31806816. S2CID208738388.
↑ GIJSEN, H. J. M.; WONG, C.-H. (18 August 2010). "ChemInform Abstract: Unprecedented Asymmetric Aldol Reactions with Three Aldehyde Substrates Catalyzed by 2-Deoxyribose-5-phosphate Aldolase". ChemInform. 26 (15): no. doi:10.1002/chin.199515259. ISSN0931-7597.
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