Discovery of Function in the Enolase Superfamily

In the genomic era, advanced sequencing techniques have enabled an exponential growth of the protein sequence databases. Although the abundance of genomic sequences is valuable, the correctness of the gene annotations poses a problem--approximately one-half of the deposited sequences are incorrectly annotated. We are using the enolase superfamily as a model system to try to solve that problem. To date, >4000 members have been identified in the enolase superfamily, of which ∼50% have unknown functions. The muconate lactonizing enzyme (MLE) subgroup contains a family of enzymes that catalyze the epimerization of dipeptide substrates. Identification of function of unknown members of the MLE subgroup, based on sequence information and homology modeling, has been successful. A novel D-Ala-D/L-Ala and a unique L-Ala-D/L-Glu epimerase (AEE) were identified and kinetically characterized from Cytophaga hutchinsonii (k cat/KM of 5.5 x 104 M -1s-1) and Bacteroides thetaiotaomicron (kcat/KM of 5.8 x 104 M-1s-1), respectively. Computational predictions, provided by Prof. Matthew Jacobson's laboratory at UCSF, were proven correct for both enzymes. In collaboration with Prof. Steven Almo's laboratory at Albert Einstein College of Medicine, an X-ray crystal structure was solved at 1.6 A resolution for the B. thetaiotaomicron AEE, establishing the correctness of the predicted homology model.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biochemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2014

Author dc:creator

• Lukk, Tiit

Contributors dc:contributor

• Gerlt, John A.

• Chemistry, Biochemistry

Identifier

(UMI)AAI3406780

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/72347