6BRM

The crystal structure of isothiocyanate hydrolase from Delia radicum gut bacteria

Summary for 6BRM

• Entry DOI: 10.2210/pdb6brm/pdb
• Descriptor: Putative metal-dependent isothiocyanate hydrolase SaxA, ZINC ION, FORMIC ACID, ... (4 entities in total)
• Functional Keywords: isothiocyanate hydrolase, itc, saxa, drgb3_saxa, hydrolase
• Biological source: Pectobacterium carotovorum (Erwinia carotovora)
• Total number of polymer chains: 8
• Total formula weight: 242858.64

Authors

Tan, K.,van den Bosch, T.,Joachimiak, A.,Welte, C. (deposition date: 2017-11-30, release date: 2018-01-31, Last modification date: 2023-10-04)

Primary citation

van den Bosch, T.J.M.,Tan, K.,Joachimiak, A.,Welte, C.U.
Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria.
Appl. Environ. Microbiol., 84:-, 2018

PubMed Abstract: Isothiocyanates (ITCs) are produced by cruciferous plants to protect them against herbivores and infection by microbes. These compounds are of particular interest due to their antimicrobial and anticarcinogenic properties. The breakdown of ITCs in nature is catalyzed by isothiocyanate hydrolases (ITCases), a novel family within the metallo-β-lactamase (MBL)-fold superfamily of proteins. genes that code for ITCases are particularly widespread in insect- and plant-associated bacteria. Enzymatic characterization of seven phylogenetically related but distinct ITCases revealed similar activities on six selected ITCs, suggesting that phylogenetic diversity does not determine the substrate specificity of ITCases. X-ray crystallography studies of two ITCases sharing 42% amino acid sequence identity revealed a highly conserved tertiary structure. Notable features of ITCases include a hydrophobic active site with two Zn ions coordinating water/hydroxide and a flexible cap that is implicated in substrate recognition and covers the active site. This report reveals the function and structure of the previously uncharacterized family of isothiocyanate hydrolases within the otherwise relatively well-studied superfamily of metallo-β-lactamases. This study explores a newly discovered protein in the β-lactamase superfamily, namely, SaxA, or isothiocyanate hydrolase. Isothiocyanates are defensive compounds found in many cabbage-related crop plants and are currently being investigated for their antimicrobial and anticarcinogenic properties. We show that isothiocyanate hydrolases are responsible for the breakdown of several of these plant defensive chemicals and suggest their potential for mitigating the beneficial effects of isothiocyanates in crop protection and cancer prevention.

PubMed: 29752272
DOI: 10.1128/AEM.00478-18

Experimental method

X-RAY DIFFRACTION (2.55 Å)