2-Deoxy-D-ribose-5-phosphate aldolase (DERA): applications and modifications

Abstract

2-Deoxy-D-ribose-5-phosphate aldolase (DERA) is a class I aldolase that offers access to several building blocks for organic synthesis. It catalyzes the stereoselective C-C bond formation between acetaldehyde and numerous other aldehydes. However, the practical application of DERA as a biocatalyst is limited by its poor tolerance towards industrially relevant concentrations of aldehydes, in particular acetaldehyde. Therefore, the development of proper experimental conditions, including protein engineering and/or immobilization on appropriate supports, is required. The present review is aimed to provide a brief overview of DERA, its history, and progress made in understanding the functioning of the enzyme. Furthermore, the current understanding regarding aldehyde resistance of DERA and the various optimizations carried out to modify this property are discussed.

Keywords: Aldol reaction; Aldolase; C–C bond; DERA; Immobilization; Protein engineering.

Scheme 1

a, b The aldol reaction is very versatile but at the same time, a lack of control of acceptor and donor as well as the reaction conditions can lead to a mixture of products

Scheme 2

Four groups of aldolases according to the functionality of their donor substrates, above the arrows (acetaldehyde, dihydroxyacetone (phosphate), pyruvate dependent or phosphoenolpyruvate, and glycine)

Scheme 3

The in vivo 2-deoxy-d-ribose-5-phosphate reaction catalyzed by DERA

Scheme 4

a General class I aldolase mechanism shows the role of enamine intermediate in the chemical mechanism. b Two-dimensional diagram shows the active side contacts

Scheme 5

a Synthesis of epothilone A using DERA as catalyst due to synthesis of two fragments 4 and 5. PMP = 4-methoxyphenyl. b DERA as a catalyst for the preparation of statin intermediates

Scheme 6

a DERA as a catalyst for the preparation of deoxysugars and thymidine or 2′-deoxyinosine. b Coupled DERA-RAMA-catalyzed sequential aldol reactions. c Coupled DERA-NeuAc-catalyzed sequential aldol reactions

Fig. 1

a Crystal structure of monomerized E. coli DERA shows aldol product bridging the catalytically active lysine Lys167 to a nearby cysteine Cys47 (PDB ID: 5EL1). b Proposed reaction mechanism showing the enzyme deactivation. c The crystal structure of DERA_LB Glu78Lys (PDB ID: 4XBS). The mutant Lys78 forms hydrogen bonds with Gly71 and Val96 at distances of 2.8 and 2.9 Å, and one salt bridge with Asp113 at a distance of 2.6 Å