Document Type


Date of Degree

Summer 2013

Degree Name

PhD (Doctor of Philosophy)

Degree In

Chemical and Biochemical Engineering

First Advisor

Subramanian, Mani

First Committee Member

Peeples, Tonya

Second Committee Member

Murhammer, David

Third Committee Member

Nuxoll, Eric

Fourth Committee Member

Weiss, David


Pseudomonassp. CBB1 degraded caffeine via C-8 oxidation. Previously, a novel quinone-dependent caffeine dehydrogenase (Cdh) was shown to catalyze the oxidation of caffeine to 1,3,7-trimethyluric acid (TMU). Initial metabolite analysis using resting cells and partially purified extract of CBB1 identified transient accumulation 1,3,7-trimethyl-5-hydroxyisourate (TM-HIU), and 3,6,8-trimethylallantoin (TMA). TMA structure was confirmed; chiral analysis revealed that it was racemic. In contrast, a time-course reaction showed that one of the enantiomers of TMA accumulated nine times, and racemized in three hours. Based on this, it was proposed that TMU was converted to TM-HIU and enantiomeric TMA.

A 43-kDa NADH-dependent TMU mononxygenase (TmuM) was purified and shown to convert TMU to unstable TM-HIU. The enzyme belonged to a new family of FAD-dependent monooxygenases. The enzyme was specific for methyluric acid with no activity on uric acid. Homology model of TmuM revealed a larger, more hydrophobic active site compared to analogous uricase in the uric acid pathway.

Genes encoding heterotrimeric Cdh (cdhA,B,C) and TmuM (tmuM), were located on a 25.2-kb fragment in CBB1 genome. Gene cluster analysis relative to similar cluster in uric acid degrading organisms identified five more putative genes of the C-8 oxidation pathway, namely tmuH, tmuD, orf1, orf2, and orf3. First three genes were assigned encoding TM-HIU hydrolase (TM-HIU to TM-OHCU), TM-OHCU decarboxylase (TM-OHCU to stereospecific TMA (proposed S-(+)-TMA)), and trimethylallantoinase (stereospecific TMA to TMAA), respectively. Further, orf2 and orf3 are proposed to encode for YlbA and ArgE like hydrolase and deacetylase, which convert TMAA to glyoxylate, di- and monomethylurea. This is the first report of (a) TMA structure (b) TMU monooxygenase and TM-HIU (hydroxylation product of TMU), and (c) complete delineation of C-8 oxidation pathway by a combination of enzymology and cluster analysis.

Excessive consumption of caffeine in various forms has created a need for a rapid diagnostic test, esp. for nursing mothers and infants. Cdh was hypothesized to be suitable for this test. Sensitivity of the test was shown to be 1 ppm. A colorimetric test with partially purified Cdh and INT-dye was optimized to detect within a minute, caffeine in drugs, nursing mother's milk, and differentiate decaffeinated beverages.


C-8 Oxidation, Caffeine, Diagnostic test, TMU monooxygenase, trimethyl-5-hydroxyisourate, Trimethylallantoin


xix, 201 pages


Includes bibliographical references (pages 191-201).


Copyright 2013 Sujit Kumar Mohanty