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Function assignment within the haloacid dehalogenase superfamily


Please use this identifier to cite or link to this item: http://hdl.handle.net/1928/17480

Function assignment within the haloacid dehalogenase superfamily

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Title: Function assignment within the haloacid dehalogenase superfamily
Author: huang, hua
Advisor(s): Dunaway-Mariano, Debra
Committee Member(s): Kirk, Martin
Mariano, Patrick
Allen, Karen
Department: University of New Mexico. Dept. of Chemistry
Subject: HAD Superfamily
LC Subject(s): Haloacid dehalogenase--Structure-activity relationships.
Degree Level: Doctoral
Abstract: The HaloacidDehalogenase Enzyme Superfamily (HADSF) is a ubiquitous family of enzymes. Presently, more than 45,000 deposited gene sequences encode proteins of the HADSF, and only a fraction of these have defined structure and/or function. The work described in this thesis focuses on function determination in several members of the HADSF. An integrated bioinformatic-protein structure-enzyme mechanism approach was used to differentiate and track D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GHMB) and histidinol phosphatephosphatase (HisB)orthologues; 2-keto-3-deoxynononic acid 9-phosphatephosphatase (KDN9PP) and 2-keto-3-deoxy-D-manno-octulosonic acid 8-phosphatephosphatase (KDO8PP)orthologues; inorganic pyrophosphatase and -phosphoglucomutase(-PGM) orthologues. In addition, a structure-function/bioinformatic analysis was carried-out on the bifunctional 1,3-diposphoglycerate acyltransferase/Cys-S-glyceryl-3-phosphate phosphatase (FKBH). Each study began with the examination of the genome context of the encoding gene of the target HADSF member. Based on this analysis possible catalytic functions were posited. In vitro activity assays were then applied to test possible substrates. Having identified a potential physiological substrate the X-ray structure of the enzyme-substrate (or substrate analog) complex was determined. From this structure the substrate recognition residues were identified. These residues were replaced by site directed mutagenesis and the impact on substrate binding and catalysis was determined by measuring the steady-state kinetic constants kcatand kcat/Km for each of the mutant enzymes. Residues shown to be important were used as sequence markers to identify among the sequence homologues identified in BLAST searches the most confidently defined orthologues. The final step used in the function annotation procedure was to examine the genome context of the encoding gene of each putative orthologue. These data were then used to formulate the proposal for in vivo function.
Graduation Date: December 2011
URI: http://hdl.handle.net/1928/17480

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