The crystal structure of isothiocyanate hydrolase from Delia radicum gut bacteria

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Functional Profiling and Crystal Structures of Isothiocyanate Hydrolases Found in Gut-Associated and Plant-Pathogenic Bacteria.

van den Bosch, T.J.M.Tan, K.Joachimiak, A.Welte, C.U.

(2018) Appl Environ Microbiol 84

  • DOI: https://doi.org/10.1128/AEM.00478-18
  • Primary Citation of Related Structures:  

  • 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. saxA 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 2+ 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. IMPORTANCE 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 in vitro and suggest their potential for mitigating the beneficial effects of isothiocyanates in crop protection and cancer prevention.

  • Organizational Affiliation

    Department of Environmental Microbiology, Institute of Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative metal-dependent isothiocyanate hydrolase SaxA
A, B, C, D, E
A, B, C, D, E, F, G, H
269Pectobacterium carotovorumMutation(s): 0 
Find proteins for A0A0N7FW12 (Pectobacterium carotovorum)
Explore A0A0N7FW12 
Go to UniProtKB:  A0A0N7FW12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0N7FW12
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
I [auth A]
J [auth A]
L [auth B]
AA [auth H],
BA [auth H],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
V [auth F],
W [auth F],
X [auth G],
Y [auth G]
Query on FMT

Download Ideal Coordinates CCD File 
K [auth A],
P [auth C],
U [auth E],
Z [auth G]
C H2 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.163α = 90
b = 79.526β = 89.98
c = 90.408γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094585, GM115586
Nederlandse Organisatie voor Wetenschappelijk OnderzoekNetherlandsSIAM Gravitation Grant 024.002.002

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description