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University of Illinois – Urbana-Champaign

1. Groninger-Poe, Fiona. Functional assignments in the enolase superfamily: investigations of two divergent groups of D-galacturonate dehydratases and galactarate dehydratase-III.

Degree: PhD, 0318, 2014, University of Illinois – Urbana-Champaign

More than a decade after the genomic age, full genome sequencing is cost-effective and fast, allowing for the deposit of an ever increasing number of DNA sequences. New fields have arisen from this availability of genomic information, and the way we think about biochemistry and enzymology has been transformed. Unfortunately, there is no robust method for accurately determining the functions of enzymes encoded by these sequences that matches the speed in which genomes are deposited into public databases. Functional assignment of enzymes remains of utmost importance in understanding microbial metabolism and has applications in agriculture by examining bacterial plant pathogen metabolism and additionally in human health by providing metabolic context to the human gut microbiome. To aid in the functional identification of proteins, enzymes can be grouped into superfamilies which share common structural motifs as well as mechanistic features. To this end, the enolase superfamily is an excellent model system for functional assignment because more than half of the members still lack functional identification. Structurally, these enzymes contain substrate specificity residues in the N-terminal capping domain and catalytic residues in the C-terminal barrel domain. Mechanistically, each enzyme catalyzes the abstraction of a proton alpha to a carboxylate on the substrate before proceeding to dehydration, epimerization, deamination, racemization or cycloisomerization. There have been enough studies of this superfamily to provide valuable insight into the types of reactions performed based on catalytic residues and substrate specificity residues, laying the groundwork for functional characterization of unknown members. In this thesis, I address the problem of functional assignment by utilizing computational, structural, biochemical, and microbiological techniques to assign previously undiscovered functions to three groups of enzymes in the enolase superfamily that were previously unknown: the Microscilla group of D-galacturonate dehydratases, the Geobacillus group of D-galacturonate dehydratases, and galactarate dehydratase-III from Agrobacterium tumefaciens strain C58. Although the two groups of D-galacturonate dehydratases produce an identical product, they act through different mechanisms and have different structural elements. The functional assignments of these enzymes contribute to our understanding of the potential mechanisms and functions possible in this superfamily. The Microscilla group of D-galacturonate dehydratases (GalurDs) from Microscilla species PRE-1, Streptomyces coelicolor A3(2), Saccarophagus degradans 2-40, Pseudoalteromonas atlantica T6c and others utilize D-galacturonate to produce 5-keto-4-deoxygalacturonate in dehydration reaction consistent with known acid-sugar dehydratases in the enolase superfamily. These enzymes house a KxK motif on the second beta strand and a H/D dyad at the seventh and sixth beta strand in the barrel domain. These enzymes are found in organisms that degrade agar. In… Advisors/Committee Members: Gerlt, John A. (advisor), Gerlt, John A. (Committee Chair), Cronan, John E. (committee member), Fratti, Rutilio A. (committee member), Huang, Raven H. (committee member).

Subjects/Keywords: enolase superfamily; D-galacturonate; D-galacturonate dehydratase; m-galactararate; m-galactarate dehydratase

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Groninger-Poe, F. (2014). Functional assignments in the enolase superfamily: investigations of two divergent groups of D-galacturonate dehydratases and galactarate dehydratase-III. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/50351

Chicago Manual of Style (16th Edition):

Groninger-Poe, Fiona. “Functional assignments in the enolase superfamily: investigations of two divergent groups of D-galacturonate dehydratases and galactarate dehydratase-III.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed April 01, 2020. http://hdl.handle.net/2142/50351.

MLA Handbook (7th Edition):

Groninger-Poe, Fiona. “Functional assignments in the enolase superfamily: investigations of two divergent groups of D-galacturonate dehydratases and galactarate dehydratase-III.” 2014. Web. 01 Apr 2020.

Vancouver:

Groninger-Poe F. Functional assignments in the enolase superfamily: investigations of two divergent groups of D-galacturonate dehydratases and galactarate dehydratase-III. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2020 Apr 01]. Available from: http://hdl.handle.net/2142/50351.

Council of Science Editors:

Groninger-Poe F. Functional assignments in the enolase superfamily: investigations of two divergent groups of D-galacturonate dehydratases and galactarate dehydratase-III. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/50351

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