Insights into Reductive Dehalogenase Function Obtained from Crystal Structures

  • Holger Dobbek
  • David LeysEmail author


Reductive dehalogenases are a class of corrinoid and [4Fe–4S] cluster-dependent enzymes that are arguably key to organohalide respiration. Recently, the first crystal structures for these enzymes were reported, including one representative of both a respiratory as well as a nonrespiratory catabolic reductive dehalogenase. The comparison made between both structures establishes two highly conserved elements: the configuration of the redox chain within the protein and the Tyr–Lys/Arg active site dyad involved in proton transfer to the substrate. In contrast, the substrate binding elements are highly distinct. These insights serve to guide further study of RdhA structure–function relationships.


Direct Electron Transfer Halogen Bond Sulfur Cluster Substrate Binding Pocket Reductive Dehalogenases 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Adrian L, Szewzyk U, Wecke J, Gorisch H (2000) Bacterial dehalorespiration with chlorinated benzenes. Nature 408(6812):580–583. doi: 10.1038/35046063 CrossRefPubMedGoogle Scholar
  2. Banerjee R, Ragsdale SW (2003) The many faces of vitamin B-12: catalysis by cobalamin-dependent enzymes. Annu Rev Biochem 72:209–247. doi: 10.1146/annurev.biochem.72.121801.161828 CrossRefPubMedGoogle Scholar
  3. Bommer M, Kunze C, Fesseler J, Schubert T, Diekert G, Dobbek H (2014) Structural basis for organohalide respiration. Science 346(6208):455–458. doi: 10.1126/science.1258118 CrossRefPubMedGoogle Scholar
  4. Brown KL (2005) Chemistry and enzymology of vitamin B-12. Chem Rev 105(6):2075–2149CrossRefPubMedGoogle Scholar
  5. Bunge M, Adrian L, Kraus A, Opel M, Lorenz WG, Andreesen JR, Gorisch H, Lechner U (2003) Reductive dehalogenation of chlorinated dioxins by an anaerobic bacterium. Nature 421(6921):357–360. doi: 10.1038/nature01237 CrossRefPubMedGoogle Scholar
  6. Chen K, Huang LL, Xu CF, Liu XM, He J, Zinder SH, Li SP, Jiang JD (2013) Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide. Mol Microbiol 89(6):1121–1139CrossRefPubMedGoogle Scholar
  7. Futagami T, Goto M, Furukawa K (2008) Biochemical and genetic bases of dehalorespiration. Chem Rec 8(1):1–12. doi: 10.1002/tcr.20134 CrossRefPubMedGoogle Scholar
  8. Gribble GW (1998) Naturally occurring organohalogen compounds. Acc Chem Res 31(3):141–152. doi: 10.1021/ar9701777 CrossRefGoogle Scholar
  9. Holliger C, Wohlfarth G, Diekert G (1998) Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol Rev 22(5):383–398. doi: 10.1111/j.1574-6976.1998.tb00377.x CrossRefGoogle Scholar
  10. Holscher T, Krajmalnik-Brown R, Ritalahti KM, Von Wintzingerode F, Gorisch H, Loffler FE, Adrian L (2004) Multiple nonidentical reductive-dehalogenase-homologous genes are common in dehalococcoides. Appl Environ Microbiol 70(9):5290–5297. doi: 10.1128/AEM.70.9.5290-5297.2004 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Hug LA, Edwards EA (2013) Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens. Front Microbiol 4:341. doi: 10.3389/fmicb.2013.00341 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Hug LA, Maphosa F, Leys D, Loffler FE, Smidt H, Edwards EA, Adrian L (2013) Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Philos Trans R Soc B 368(1616):2012. doi: 10.1098/rstb.2012.0322 (ARTN0322)CrossRefGoogle Scholar
  13. John M, Schmitz RP, Westermann M, Richter W, Diekert G (2006) Growth substrate dependent localization of tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans. Arch Microbiol 186(2):99–106. doi: 10.1007/s00203-006-0125-5 CrossRefPubMedGoogle Scholar
  14. Koutmos M, Gherasim C, Smith JL, Banerjee R (2011) Structural basis of multifunctionality in a vitamin B-12-processing enzyme. J Biol Chem 286(34):29780–29787CrossRefPubMedPubMedCentralGoogle Scholar
  15. Krasotkina J, Walters T, Maruya KA, Ragsdale SW (2001) Characterization of the B12- and iron–sulfur-containing reductive dehalogenase from desulfitobacterium chlororespirans. J Biol Chem 276(44):40991–40997. doi: 10.1074/jbc.M106217200 CrossRefPubMedGoogle Scholar
  16. Krautler B, Fieber W, Ostermann S, Fasching M, Ongania KH, Gruber K, Kratky C, Mikl C (2003) The cofactor of tetrachloroethene reductive dehalogenase of Dehalospirillum multivorans is norpseudo-B-12, a new type of a natural corrinoid. Helv Chim Acta 86(11):3698–3716. doi: 10.1002/hlca.200390313 CrossRefGoogle Scholar
  17. Lai QL, Li GZ, Shao ZZ (2012) Genome Sequence of Nitratireductor pacificus type strain pht-3B. J Bacteriol 194(24):6958CrossRefPubMedPubMedCentralGoogle Scholar
  18. Mac Nelly A, Kai M, Svatos A, Diekert G, Schubert T (2014) Functional heterologous production of reductive dehalogenases from Desulfitobacterium hafniense strains. Appl Environ Microbiol 80(14):4313–4322. doi: 10.1128/AEM.00881-14 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Maillard J, Schumacher W, Vazquez F, Regeard C, Hagen WR, Holliger C (2003) Characterization of the corrinoid iron–sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. Appl Environ Microbiol 69(8):4628–4638CrossRefPubMedPubMedCentralGoogle Scholar
  20. Munro AW, Girvan HM, McLean KJ (2007) Variations on a (t)heme—novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily. Nat Prod Rep 24(3):585–609CrossRefPubMedGoogle Scholar
  21. Neumann A, Wohlfarth G, Diekert G (1996) Purification and characterization of tetrachloroethene reductive dehalogenase from Dehalospirillum multivorans. J Biol Chem 271(28):16515–16519CrossRefPubMedGoogle Scholar
  22. Neumann A, Siebert A, Trescher T, Reinhardt S, Wohlfarth G, Diekert G (2002) Tetrachloroethene reductive dehalogenase of Dehalospirillum multivorans: substrate specificity of the native enzyme and its corrinoid cofactor. Arch Microbiol 177(5):420–426. doi: 10.1007/s00203-002-0409-3 CrossRefPubMedGoogle Scholar
  23. Oberg G (2002) The natural chlorine cycle–fitting the scattered pieces. Appl Microbiol Biotechnol 58(5):565–581. doi: 10.1007/s00253-001-0895-2 CrossRefPubMedGoogle Scholar
  24. Parthasarathy A, Stich TA, Lohner ST, Lesnefsky A, Britt RD, Spormann AM (2015) Biochemical and EPR-spectroscopic investigation into heterologously expressed vinyl chloride reductive dehalogenase (VcrA) from Dehalococcoides mccartyi strain VS. J Am Chem Soc 137(10):3525–3532. doi: 10.1021/ja511653d CrossRefPubMedPubMedCentralGoogle Scholar
  25. Payne KA, Quezada CP, Fisher K, Dunstan MS, Collins FA, Sjuts H, Levy C, Hay S, Rigby SE, Leys D (2015) Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature 517(7535):513–516. doi: 10.1038/nature13901 CrossRefPubMedGoogle Scholar
  26. Richardson RE (2013) Genomic insights into organohalide respiration. Curr Opin Biotechnol 24(3):498–505. doi: 10.1016/j.copbio.2013.02.014 CrossRefPubMedGoogle Scholar
  27. Sjuts H, Fisher K, Dunstan MS, Rigby SE, Leys D (2012) Heterologous expression, purification and cofactor reconstitution of the reductive dehalogenase PceA from Dehalobacter restrictus. Protein Expr Purif 85(2):224–229. doi: 10.1016/j.pep.2012.08.007 CrossRefPubMedGoogle Scholar
  28. Smidt H, de Vos WM (2004) Anaerobic microbial dehalogenation. Annu Rev Microbiol 58:43–73CrossRefPubMedGoogle Scholar
  29. Studer A, Vuilleumier S, Leisinger T (1999) Properties of the methylcobalamin:H4folate methyltransferase involved in chloromethane utilization by Methylobacterium sp. strain CM4. Eur J Biochem 264(1):242–249CrossRefPubMedGoogle Scholar
  30. Studer A, Stupperich E, Vuilleumier S, Leisinger T (2001) Chloromethane: tetrahydrofolate methyl transfer by two proteins from Methylobacterium chloromethanicum strain CM4. Eur J Biochem 268(10):2931–2938. doi: 10.1046/j.1432-1327.2001.02182.x CrossRefPubMedGoogle Scholar
  31. van de Pas BA, Smidt H, Hagen WR, van der Oost J, Schraa G, Stams AJ, de Vos WM (1999) Purification and molecular characterization of ortho-chlorophenol reductive dehalogenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans. J Biol Chem 274(29):20287–20292CrossRefPubMedGoogle Scholar
  32. Wohlfarth G, Diekert G (1997) Anaerobic dehalogenases. Curr Opin Biotechnol 8(3):290–295CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu BerlinBerlinGermany
  2. 2.MIB, University of ManchesterManchesterUK

Personalised recommendations