Hammett analysis of a C-C hydrolase-catalysed reaction using synthetic 6-aryl-2-hydroxy-6-ketohexa-2,4-dienoic acid substrates

The molecular basis for inhibition of BphD, a C-C bond hydrolase involved in polychlorinated biphenyls degradation: large 3-substituents prevent tautomerization

The microbial degradation of polychlorinated biphenyls (PCBs) by the biphenyl catabolic (Bph) pathway is limited in part by the pathway's fourth enzyme, BphD. BphD catalyzes an unusual carbon-carbon bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA), in which the substrate is subject to histidine-mediated enol-keto tautomerization prior to hydrolysis. Chlorinated HOPDAs such as 3-Cl HOPDA inhibit BphD. Here we report that BphD preferentially hydrolyzed a series of 3-substituted HOPDAs in the order H>F>Cl>Me, suggesting that catalysis is affected by steric, not electronic, determinants. Transient state kinetic studies performed using wild-type BphD and the hydrolysis-defective S112A variant indicated that large 3-substituents inhibited His-265-catalyzed tautomerization by 5 orders of magnitude. Structural analyses of S112A.3-Cl HOPDA and S112A.3,10-diF HOPDA complexes revealed a non-productive binding mode in which the plane defined by the carbon atoms of the dienoate moiety of HOPDA is nearly orthogonal to that of the proposed keto tautomer observed in the S112A.HOPDA complex. Moreover, in the 3-Cl HOPDA complex, the 2-hydroxo group is moved by 3.6 A from its position near the catalytic His-265 to hydrogen bond with Arg-190 and access of His-265 is blocked by the 3-Cl substituent. Nonproductive binding may be stabilized by interactions involving the 3-substituent with non-polar side chains. Solvent molecules have poor access to C6 in the S112A.3-Cl HOPDA structure, more consistent with hydrolysis occurring via an acyl-enzyme than a gem-diol intermediate. These results provide insight into engineering BphD for PCB degradation.

The Tautomeric Half-reaction of BphD, a C-C Bond Hydrolase

BphD of Burkholderia xenovorans LB400 catalyzes an unusual C-C bond hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to afford benzoic acid and 2-hydroxy-2,4-pentadienoic acid (HPD). An enol-keto tautomerization has been proposed to precede hydrolysis via a gem-diol intermediate. The role of the canonical catalytic triad (Ser-112, His-265, Asp-237) in mediating these two half-reactions remains unclear. We previously reported that the BphD-catalyzed hydrolysis of HOPDA (lambda(max) is 434 nm for the free enolate) proceeds via an unidentified intermediate with a red-shifted absorption spectrum (lambda(max) is 492 nm) (Horsman, G. P., Ke, J., Dai, S., Seah, S. Y. K., Bolin, J. T., and Eltis, L. D. (2006) Biochemistry 45, 11071-11086). Here we demonstrate that the S112A variant generates and traps a similar intermediate (lambda(max) is 506 nm) with a similar rate, 1/tau approximately 500 s(-1). The crystal structure of the S112A:HOPDA complex at 1.8-A resolution identified this intermediate as the keto tautomer, (E)-2,6-dioxo-6-phenyl-hex-3-enoate. This keto tautomer did not accumulate in either the H265A or the S112A/H265A double variants, indicating that His-265 catalyzes tautomerization. Consistent with this role, the wild type and S112A enzymes catalyzed tautomerization of the product HPD, whereas H265A variants did not. This study thus identifies a keto intermediate, and demonstrates that the catalytic triad histidine catalyzes the tautomerization half-reaction, expanding the role of this residue from its purely hydrolytic function in other serine hydrolases. Finally, the S112A:HOPDA crystal structure is more consistent with hydrolysis occurring via an acyl-enzyme intermediate than a gem-diol intermediate as solvent molecules have poor access to C6, and the closest ordered water is 7 A away.

Kinetic and structural insight into the mechanism of BphD, a C-C bond hydrolase from the biphenyl degradation pathway

Kinetic and structural analyses of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) hydrolase from Burkholderia xenovorans LB400 (BphD(LB400)) provide insight into the catalytic mechanism of this unusual serine hydrolase. Single turnover stopped-flow analysis at 25 degrees C showed that the enzyme rapidly (1/tau(1) approximately 500 s(-1)) transforms HOPDA (lambda(max) = 434 nm) into a species with electronic absorption maxima at 473 and 492 nm. The absorbance of this enzyme-bound species (E:S) decayed in a biphasic manner (1/tau(2) = 54 s(-1), 1/tau(3) = 6 s(-1) approximately k(cat)) with simultaneous biphasic appearance (48 and 8 s(-1)) of an absorbance band at 270 nm characteristic of one of the products, 2-hydroxypenta-2,4-dienoic acid (HPD). Increasing solution viscosity with glycerol slowed 1/tau(1) and 1/tau(2) but affected neither 1/tau(3) nor k(cat), suggesting that 1/tau(2) may reflect diffusive HPD dissociation, and 1/tau(3) represents an intramolecular event. Product inhibition studies suggested that the other product, benzoate, is released after HPD. Contrary to studies in a related hydrolase, we found no evidence that ketonized HOPDA is partially released prior to hydrolysis, and, therefore, postulate that the biphasic kinetics reflect one of two mechanisms, pending assignment of E:S (lambda(max) = 492 nm). The crystal structures of the wild type, the S112C variant, and S112C incubated with HOPDA were each determined to 1.6 A resolution. The latter reveals interactions between conserved active site residues and the dienoate moiety of the substrate. Most notably, the catalytic residue His265 is hydrogen-bonded to the 2-hydroxy/oxo substituent of HOPDA, consistent with a role in catalyzing ketonization. The data are more consistent with an acyl-enzyme mechanism than with the formation of a gem-diol intermediate.

Biphenyl degradation kinetics by Burkholderia xenovorans LB400 in two-phase partitioning bioreactors

Biphenyl could be successfully degraded by Burkholderia xenovorans LB400, initially described as Pseudomonas sp. LB400, in two-phase partitioning bioreactors (TPPBs). TPPBs are comprised of an aqueous, cell containing phase, and an immiscible, biocompatible organic phase that partitions toxic and/or poorly soluble substrates (in this case biphenyl) based on maintaining a thermodynamic equilibrium. The critical LogKO/W of the organism was found to be approximately 5.5, indicating that solvents with a LogKO/W larger than 5.5 are suitable as delivery phases for B. xenovorans LB400. Two solvents selected for the TPPB system were octadecene and bis(2-ethylhexyl)sebacate (BES). In one experiment a total of 6.6 g biphenyl per l aqueous-phase-equivalent (biphenyl delivered in solvent, at an aqueous phase to solvent ratio of 10) could be degraded in 25 h during batch operation with octadecene. The specific growth rate and the half saturation constant of the Monod model were estimated to be mumax=0.25 h-1 and KS=0.0001 g l-1, and the yield coefficient was YX/S=0.48 g biomass per g biphenyl. These parameter estimates were used to predict the time course of biphenyl degradation at different initial substrate concentrations and with biphenyl delivered from the two solvents with different partitioning behaviour for biphenyl. The predictions were validated by experimental data, confirming the microbial kinetics as well as the expected partitioning effects.

Synthetic 6-aryl-2-hydroxy-6-ketohexa-2,4-dienoic acid substrates for C–C hydrolase BphD: investigation of a general base catalytic mechanism

A chemical synthesis of the 2-hydroxy-6-ketohexa-2,4-dienoic acid intermediates on bacterial meta-cleavage pathways has been established, using a Heck coupling strategy. Coupling of ethyl 3-bromo-2-acetoxyacrylate with 1-aryl vinyl ketals or 1-aryl allylic alcohols proceeded in 70-90% yield. Heck coupling with an alkyl vinyl ketal was also successful, allowing the synthesis of an alkyl-substituted ring fission intermediate. The synthetic ring fission intermediates were used to investigate the enzymatic reaction catalysed by C-C hydrolase BphD from Pseudomonas LB400. A reduced substrate analogue 2,6-dihydroxy-6-phenylhexa-2,4-dienoic acid was processed enzymatically to benzaldehyde by C-C hydrolase BphD, consistent with a catalytic mechanism involving general base-catalysed attack of water to give a gem-diol intermediate, and not consistent with a nucleophilic mechanism. A series of para-substituted 2-hydroxy-6-keto-6-phenylhexa-2,4-dienoic acid substrates were assayed against BphD, and the derived Hammett plot (rho=-0.71) is consistent with a departing carbanion in the transition state for C-C cleavage.