Molecular basis of halorespiration control by CprK, a CRP‐FNR type transcriptional regulator

Abstract

SummaryCertain bacteria are able to conserve energy via the reductive dehalogenation of halo-organic compounds in a respiration-type metabolism. The transcriptional regulator CprK from Desulfitobacterium spp. induces expression of halorespiratory genes upon binding of o-chlorophenol ligands and is reversibly inactivated by oxygen through disulphide bond formation. We report crystal structures of D. hafniense CprK in the ligand-free (both oxidation states), ligand-bound (reduced) and DNA-bound states, making it the first member of the widespread CRP-FNR superfamily for which a complete structural description of both redox-dependent and allosteric molecular rearrangements is available. In conjunction with kinetic and thermodynamic ligand binding studies, we provide a model for the allosteric mechanisms underpinning transcriptional control. Amino acids that play a key role in this mechanism are not conserved in functionally distinct CRP-FNR members. This suggests that, despite significant structural homology, distinct allosteric mechanisms are used, enabling this protein family to control a very wide range of processes.

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

“…Like CAP, CooA and CprK suffer from irregularities in coiled-coil heptad-repeat sequences. However, in contrast to the situation with CAP, in CooA and CprK, a multitude of interactions between the C-helices and the remainder of the effector domain seem to provide the crucial contacts needed for the coiled-coil stability (24)(25)(26). Apparently, the structural mechanisms that allow effectormediated activation of CooA and CprK are distinct and do not involve the coil-to-helix transition seen in CAP.…”

“…The present results provide a framework for understanding and discussing allosteric control of the more than 400 members of the CAP/regulator of fumarate and nitrate reduction (FNR) protein superfamily of transcriptional regulatory factors (23), which share the same overall structural organization as CAP but respond to a broad, chemically diverse, range of allosteric effectors. In carbon monoxide oxidation activator (CooA; effector ϭ CO) and o-chlorophenol reductive dehalogenase transcription regulator (CprK) (effector ϭ ortho-chlorophenolacetic acid), 2 members of the CAP/FNR superfamily for which structural data are available (24)(25)(26), the C-helix and the intersubunit C-helix/CЈ-helix coiled coil seem to be fully structured in the absence of effector. Like CAP, CooA and CprK suffer from irregularities in coiled-coil heptad-repeat sequences.…”

Posttranslational control of transcription factor FixK 2 , a key regulator for the Bradyrhizobium japonicum –soybean symbiosis

“…23). More complex is the mechanism of Desulfitobacterium hafniense CprK, whose activation requires not only a structural change induced by ochlorophenol binding but also a redox switch (24). Only the reduced variant binds to DNA.…”

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

“…Most of rdh gene clusters are also associated with one rdhK subunit in various orientations. The rdhK-encoded proteins clearly belong to the large family of CRP/Fnr regulatory proteins from which CprK members of Desulfitobacterium dehalogenans and Desulfitobacterium hafniense DCB-2 were extensively studied and represent the paradigmatic DNA-binding regulatory protein for the respective chlorophenol reductive dehalogenase (cpr) operons [48][49][50][51][52][53][54][55][56] figure 3). First, a strong correlation could be established between the level of sequence identity (see also electronic supplementary material, table S7) and the genetic organization of the predicted rdh operons.…”