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Structure to function : case studies of hotdog-fold superfamily thioesterases from Escherichia coli.


Please use this identifier to cite or link to this item: http://hdl.handle.net/1928/21052

Structure to function : case studies of hotdog-fold superfamily thioesterases from Escherichia coli.

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dc.contributor.author Latham, John A.
dc.date.accessioned 2012-08-28T16:33:51Z
dc.date.available 2012-08-28T16:33:51Z
dc.date.issued 2012-08-28
dc.date.submitted July 2012
dc.identifier.uri http://hdl.handle.net/1928/21052
dc.description.abstract My doctoral research primarily focuses on the Escherichia coli hotdog-fold thioesterases ydiI and ybgC. The ydiI gene is colocalized in the operon ydiHIJ. A substrate screen provided evidence that YdiI prefers aryl-CoA substrates and discriminated against the analogous aryl-ACP, unlike the paralog YbdB which works on 2,4-DHB-EntB in the enterobactin synthesis pathway. A bioinformatic approach showed that in some bacteria, ydiI is colocalized with genes from the menaquinone pathway. YdiI was shown to catalyze the hydrolysis of DHNA-CoA with physiological relevance (kcat/KM ~ 105). Furthermore, the E. coli YdiI- strain was shown to have perturbed growth, in good agreement with other menaquinone enzyme knockout experiments. Taking into account the evidence provided, YdiI is likely the DHNA-CoA thioesterase in the menaquinone pathway. Within the substrate binding pocket, changes to the YdiI Val68 to the YbdB equivalent of Met resulted in perturbed catalytic efficiency towards lauroyl-CoA, however not towards its physiological substrate DHNA-CoA. The YbdB M68V mutant resulted in increased efficiency towards lauroyl-CoA and DHNA-CoA, seemingly making it a gatekeeper. Secondly, YdiI catalyzes the hydrolysis of acyl-CoA's using a Glu63, His54, and Gln48 triad determined by mutagenesis experiments. The utilization of 18-O incorporation and rapid-quench techniques provided insight into YdiI's catalytic mechanism. A single phase multiple turnover reaction and the incorporation of 18-O in single turnover reactions suggests that ydiI uses a general base catalytic mechanism where Glu63 is the activating residue. The second E. coli hotdog-fold thioesterase protein discussed within is YbgC. YbgC is encoded by the first ORF of the tol-pal gene cluster. Previous work on the H. influenzae homologue demonstrated affinity for short chain acyl-CoA's and tandem affintity purificiation experiments showed E. coli YbgC co-purifies with ACP. No previous attempts to screen for acyl-ACP have been made. To screen YbgC for ACP activity, a method was developed to stoichiometrically construct acyl-ACP's, using apoACP, BF1558 acyl-transferase and acyl-CoA. The E. coli YbgC demonstrated preference for long chain acyl-CoA's and their analogous acyl-ACPs. To understand the nature of ACP binding to YbgC, SAXS analysis was carried out on the complex demonstrating that 2 ACP molecules bind to 1 dimer of YbgC. en_US
dc.language.iso en_US en_US
dc.subject hotdog-fold en_US
dc.subject thioesterase en_US
dc.subject YdiI en_US
dc.subject YbgC en_US
dc.subject acyl-ACP en_US
dc.subject menaquinone en_US
dc.subject coenzyme a en_US
dc.subject.lcsh Esterases--Structure-activity relationships.
dc.subject.lcsh Escherichia coli--Physiology.
dc.title Structure to function : case studies of hotdog-fold superfamily thioesterases from Escherichia coli. en_US
dc.type Dissertation en_US
dc.description.degree Chemistry en_US
dc.description.level Doctoral en_US
dc.description.department University of New Mexico. Dept. of Chemistry en_US
dc.description.advisor Dunaway-Mariano, Debra
dc.description.committee-member Mariano, Patrick
dc.description.committee-member Bear, David
dc.description.committee-member Melancon, Charles

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