Graduation Year


Date of Thesis Acceptance

Spring 5-13-2015

Major Department or Program



Tim Machonkin


PcpA is a bacterial non-heme Fe(II) enzyme that oxidatively cleaves 2,6-dichlorohydroquinone as a part of the pentachlorophenol (PCP) degradation pathway of Sphingobium chlorophenolicum. It has been shown to be specific for ortho-dihalohydroquinones. Possible sources of this specificity include the substrate pKa, and halogen bonding and/or metal-halogen secondary bonding, both of which depend upon halogen polarizability. Substrate binding titrations showed a similar small shift in pKa values between the free substrate and the substrate bound to the enzyme for all substrates. This suggests that PcpA may lack an active site base needed to deprotonate the substrate, in contrast to the closely related catechol extradiol dioxygenase enzymes. Steady-state kinetic studies showed that 2,6-difluorohydroquinone is a poor substrate, similar to 2,6-methylhydroquinone, unlike 2,6-dichloro- and 2,6- dibromohydroquinone. The pH dependence of the kinetics of these substrates provides additional insights into the role of substrate pKa. Together, these studies suggest that both a polarizable halogen substituent and the pKa of the substrate play important roles in defining the substrate specificity of PcpA.

Page Count


Subject Headings

Hydrogen-ion concentration (pH) -- Measurement, Polarization -- Halogens, Ferric oxide (Fe(II)), Halogen compounds, Enzymes -- Analysis, Chemical kinetics -- Data processing, Whitman College -- Dissertation collection 2015 -- Chemistry Department

Permanent URL

Document Type

Whitman Community Accessible Thesis

Terms of Use

If you have questions about permitted uses of this content, please contact the ARMINDA administrator

Available for download on Sunday, May 13, 2018



Rights Statement

Rights Statement

In Copyright. URI:
This Item is protected by copyright and/or related rights. You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).