Molecule of the Month: Dehalogenases
Bacteria destroy toxic environmental pollutants that include chlorine or bromine atoms.
Exploring the Structure
Three structures of a reductive dehalogenase (PDB entries 5m2g, 5m92, 5m8u) capture the enzyme as it successively removes bromine atoms from a brominated compound. The cobamide cofactor (light blue) helps position the molecule by interacting with a hydroxyl group, and six tryptophan and tyrosine amino acids (dark blue) make a cage around the active site to interact with the halogen atoms. The structure with tribromophenol (carbon in white, bromine in pink, and oxygen in red) is shown here. Click on the image to explore this and the other structures in more detail.
Topics for Further Discussion
- There are many structures of dehalogenases with different halogenated compounds—try searching for “dehalogenases” to see them. There are also many enzymes that add halogen atoms to compounds. Search for “halogenases” to explore the structures of some of them.
- You can use the Ligand page to explore the properties of the cobamide cofactor and vitamin B12.
Related PDB-101 Resources
- Browse Molecules and the Environment
- Browse Enzymes
- M Fincker & AM Spormann (2017) Biochemistry of reductive dehalogenation. Annual Review of Biochemistry 86, 357-386.
- 5m2g, 5m92, 5m8u: C Kunze, M Bommer, WR Hagen, M Uksa, H Dobbek, T Schubert & G Diekert (2017) Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer. Nature Communications 8, 15858.
- 4ur0: M Bommer, C Kunze, J Fesseler, T Schubert, G Diekert & H Dobbek (2014) Structural basis for organohalide respiration. Science 346, 455-458.
- 1jud: T Hisano, Y Hata, T Fujii, JQ Liu, T Kurihara, N Esaki & K Soda (1996) Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold. Journal of Biological Chemistry 271, 20322-20330.
- DB Janssen, F Pries & JR van der Ploeg (1994) Genetics and biochemistry of dehalogenating enzymes. Annual Review of Microbiology 48, 163-191.
- 2dhc: KH Verschueren, F Seljee, HJ Rozeboom, KH Kalk & BW Dijkstra (1993) Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase. Nature 363, 693-698.
April 2018, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2018_4