Expression, purification and crystallization of a novel metagenome‐derived salicylaldehyde dehydrogenase from Alpine soil. Issue 4 (28th March 2022)

• Record Type: Journal Article
• Authors: Dandare, Shamsudeen Umar; Håkansson, Maria; Svensson, L. Anders; Timson, David J.; Allen, Christopher C. R.
• Is Part Of: Acta crystallographica. Volume 78:Issue 4(2022)
• Page Start: 161
• Page End: 169
• Publication Date: 2022-03-28
• Subjects: metagenome -- salicylaldehyde dehydrogenase -- alphaproteobacteria -- Alpine soil -- purification -- crystallography; Crystallography -- Periodicals; Crystals -- Periodicals; 548
• DOI: 10.1107/S2053230X22002345
• Languages: English
• ISSNs: 2053-230X

Abstract

Abstract : Gene‐targeted assembly was used to mine a novel salicylaldehyde dehydrogenase from an Alpine soil metagenome. The enzyme was cloned, expressed, purified and crystallized: it is the first metagenome‐derived aldehyde dehydrogenase to be crystallized. Analysis of the crystal structure shows that it adopts the standard conformation of the aldehyde dehydrogenase superfamily and a carboxylic acid was found to be a putative ligand of this enzyme. Abstract : Salicylaldehyde dehydrogenase (SALD) catalyses the last reaction in the upper pathway of naphthalene degradation: the oxidation of salicylaldehyde to salicylate. This enzyme has been isolated and studied from a few organisms that belong to the betaproteobacteria and gammaproteobacteria, predominantly Pseudomonas putida . Furthermore, there is only one crystal structure of this enzyme, which was obtained from P. putida G7. Here, crystallographic studies and analysis of the crystal structure of an Alpine soil metagenome‐derived SALD (SALDAP ) from an alphaproteobacterium are presented. The SALDAP gene was discovered using gene‐targeted sequence assembly and it was cloned into a pLATE51 vector. The recombinant protein was overexpressed in Escherichia coli BL21 (DE3) cells and the soluble protein was purified to homogeneity. The protein crystallized at 20°C and diffraction data from the crystals were collected at a resolution of 1.9 Å. The crystal belonged to the orthorhombic space group C 2221, with unit‐cell parameters a = 116.8, b = 121.7, c = 318.0 Å. Analysis of the crystal structure revealed its conformation to be similar to the organization of the aldehyde dehydrogenase superfamily with three domains: the catalytic, NAD + ‐binding and bridging domains. The crystal structure of NahF from P. putida G7 was found to be the best structural homologue of SALDAP, even though the enzymes share only 48% amino‐acid identity. Interestingly, a carboxylic acid (protocatechuic acid) was found to be a putative ligand of the enzyme and differential scanning fluorimetry was employed to confirm ligand binding. These findings open up the possibility of studying the mechanism(s) of product inhibition and biocatalysis of carboxylic acids using this enzyme and other related aldehyde dehydrogenases.