Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product and water mediated inhibition

OAKLEY, Aaron, Zbyněk PROKOP, Michal BOHÁČ, Jan KMUNÍČEK, Tomáš JEDLIČKA, Marta MONINCOVÁ, Ivana KUTÁ-SMATANOVÁ, Yuji NAGATA, Jiří DAMBORSKÝ and Matthew WILCE. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product and water mediated inhibition. Biochemistry. 2002, vol. 41, No 15, p. 4847-4855. ISSN 0006-2960.

Basic information

• Original name: Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product and water mediated inhibition
• Authors: OAKLEY, Aaron (36 Australia), Zbyněk PROKOP (203 Czech Republic), Michal BOHÁČ (203 Czech Republic), Jan KMUNÍČEK (203 Czech Republic), Tomáš JEDLIČKA (203 Czech Republic), Marta MONINCOVÁ (203 Czech Republic), Ivana KUTÁ-SMATANOVÁ (203 Czech Republic), Yuji NAGATA (392 Japan), Jiří DAMBORSKÝ (203 Czech Republic, guarantor) and Matthew WILCE (36 Australia).
• Edition: Biochemistry, 2002, 0006-2960.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 4.064
• RIV identification code: RIV/00216224:14310/02:00006262
• Organization unit: Faculty of Science
• UT WoS: 000175012900011
• Keywords in English: X-RAY; DEHALOGENATION; ENZYME; PROTEIN ENGINEERING; INHIBITION
• Tags: dehalogenation, Enzyme, inhibition, Protein engineering, x-ray

Abstract

The hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalysed by a/b-hydrolases called haloalkane dehalogenases. The study of haloalkane dehalogenases is vital for the development of these enzymes if they are to be utilized for bioremediation of organohalide-contaminated industrial waste. We report the kinetic and structural analysis of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) in complex with each of 1,2-dichloroethane and 1,2-dichloropropane and the reaction product of 1-chlorobutane turnover. Activity studies showed very weak, but detectable activity of LinB with 1,2-dichloroethane (0.012 nmol.s-1.mg-1 of enzyme) and 1,2-dichloropropane (0.027 nmol.s-1.mg-1 of enzyme). These activities are much weaker compared, for example, to activity of LinB with 1-chlorobutane (68.169 nmol.s-1.mg-1 of enzyme). Inhibition analysis reveals that both 1,2-dichloroethane and 1,2-dichloropropane act as simple competitive inhibitors of the substrate 1-chlorobutane and that 1,2-dichloroethane binds to LinB with lower affinity than 1,2-dichloropropane. Docking calculations on the enzyme in the absence of active site water molecules and halide ions confirms that these compounds could bind productively. However, when these moieties were included in the calculations, they bound in the manner similar to that observed in the crystal structure. These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking.

Links

• ME 276, research and development project: Name: Racionální re-design mikrobiálních enzymů podílejících se na degradaci toxických organických polutantů

Investor: Ministry of Education, Youth and Sports of the CR, Rational re-design of microbial enzymes involved in degradation of toxic organic pollutants.

• MSM 143100005, plan (intention): Name: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Structure-function Relationships and their role in the Metabolism