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Eighth Southeast Enzyme Conference Eighth Southeast Enzyme Conference Saturday, April 8, 2017 Georgia State University Atlanta, GA Urban Life Building 140 Decatur Street Room 220 Eighth Southeast Enzyme Conference Saturday, April 8, 2017 Supported by generous contributions from: Southeast Enzyme Conference (SEC) Meeting Year Program Site Chair Site Chair I 2010 Giovanni Gadda Will Lovett GSU II 2011 Nigel Richards Giovanni Gadda / GSU Will Lovett III 2012 Robert Phillips Giovanni Gadda / GSU Will Lovett IV 2013 Holly Ellis Giovanni Gadda / GSU Neil Renfroe / Will Lovett V 2014 Liz Howell Giovanni Gadda / GSU Will Lovett / Neil Renfroe / Robert Daniel VI 2015 Anne-Frances Giovanni Gadda / GSU Miller Will Lovett / Gwen Kenny / Robert Daniel VII 2016 Pablo Sobrado Giovanni Gadda / GSU Will Lovett / Crystal Smitherman Rosenberg / Robert Daniel / Will Thacker VIII 2017 Ellen Moomaw Giovanni Gadda / GSU Will Lovett / Crystal Smitherman Rosenberg / Will Thacker / Anthony Banks IX 2018 Table of Contents: Supporters Page 3 Schedule Page 7 Abstracts of Oral Presentations Page 8 Abstracts of Posters Page 21 List of Registered Participants Page 127 Schedule: Location: Urban Life Building, Room 220: All Talks 15 min plus Q&A up to 20 min total! 8:00-8:30 Coffee 8:30-8:40 Opening Remarks: Ellen Moomaw, Kennesaw State University, Kennesaw Session 1 - Discussion Leader: Zac Wood, University of Georgia, Athens 8:40-9:00 Naga Sandhya Guntaka, University of Florida, Gainesville Crystal structure and functional analysis of ClbQ, an unusual intermediate-releasing thioesterase from the colibactin biosynthetic pathway 9:00-9:20 Daniel Ouedraogo, Georgia State University, Atlanta Role of loop L1 dynamics in Pseudomonas aeruginosa D-Arginine dehydrogenase 9:20-9:40 Shanzhi Wang, University of Arkansas, Little Rock Dissecting the roles of the enzymatic and scaffolding functions of EXO1 in vivo 9:40-10:50 Poster Session 1 (Numbers 1-52 presenting.) Session 2 - Discussion Leader: Anne-Frances Miller, University of Kentucky, Lexington 11:00-11:20 H. Diessal Duan, University of Kentucky, Lexington FixAB at the heart of flavin-based electron bifurcation in diazotrophic bacteria 11:20-11:40 Mingjie Li, Mississippi State University, Mississippi State The thermodynamics of metal and substrate binding to taurine/α-ketoglutaratedependent oxygenase (TauD) from E. coli 11:40-12:00 Charlie Carter, University of North Carolina, Chapel Hill Do transitions between conformational substates help stabilize chemical transition states? Combinatorial thermodynamic cycle analysis 12:00-1:00 Group Photo followed by Lunch Break Session 3 - Discussion Leader: Kevin Francis, Texas A&M University, Kingsville 1:00-1:20 Kaiyuan Zheng, Auburn University, Auburn Elucidation of the biosynthesis pathway for the key coenzyme of methanogenesis and anaerobic methane oxidation 1:20-1:40 Prashasti Kumar, University of Tennessee, Knoxville Insights into a low promiscuous aminoglycoside modifying enzyme, aminoglycoside N3 acetyltransferase-VIA 1:40-2:50 Poster Session 2 (Numbers 53-105 presenting.) Keynote Presentation - Discussion Leader: Ellen Moomaw, Kennesaw State University 3:00-4:00 Pablo Sobrado, Virginia Polytechnic Institute and State University, Blacksburg Targeting siderophore biosynthesis: structure, mechanism, and inhibition of flavindependent N-monoooxygenases 4:00 Concluding Remarks: Ellen Moomaw, Kennesaw State University, Kennesaw 4:30-6:30 Post Conference Networking Social @ Ellis Hotel Session 1: Zac Wood Discussion Leader Crystal Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway Naga Sandhya Guntaka1, Steven D. Bruner1 1Departments of Chemistry, University of Florida, Gainesville, Florida 32611 Small molecule microbial secondary metabolites by regulating host-microbe interactions play an important role in all aspects of disease etiology and treatment. Colibactin is a secondary metabolite linked to the progression and pathogenesis of colorectal cancer (CRC) and inflammatory bowel disease (IBD) by inducing DNA damage in host cells. The chemical details of the colibactin and the biosynthetic pathway are emerging but clearly are unusual and noncanonical. Our research addresses a key aspect of colibactin biosynthesis, the occurrence of multiple metabolites and the biosynthetic rationale for this. Recent studies suggest an atypical role of ClbQ, a type II editing thioesterase in releasing pathway intermediates from the assembly line (1) and genetic deletion of ClbQ has been shown to abolish colibactin cytotoxic activity (2). Presented is an interdisciplinary approach to address the role of ClbQ, using enzyme structure, organic synthesis of substrates/intermediates and mechanistic analysis. The 2.0 Å crystal structure and biochemical characterization of ClbQ reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate between carrier proteins in the pathway. As reported in earlier studies (1), late- stage cyclized intermediates are not the preferred substrates for ClbQ. However, late-stage linear precolibactin intermediates are hydrolyzed. Our data, combined with previous reports, support a novel role of ClbQ in facilitating the promiscuous offloading of premature precolibactin metabolites and suggest novel insights into colibactin biosynthesis. 1. Li, Z.-R., Li, J., Gu, J.-P., Lai, J. Y. H., Duggan, B. M., Zhang, W.-P., Li, Z.-L., Li, Y.-X., Tong, R.-B., Xu, Y., Lin, D.-H., Moore, B. S., and Qian, P.-Y. (2016) Divergent biosynthesis yields a cytotoxic aminomalonate-containing precolibactin. Nat. Chem. Biol. 12, 773–775. 2. Cougnoux, A., Dalmasso, G., Martinez, R., Buc, E., Delmas, J., Gibold, L., Sauvanet, P., Darcha, C., Déchelotte, P., Bonnet, M., Pezet, D., Wodrich, H., Darfeuille-Michaud, A., and Bonnet, R. (2014) Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype. Gut. 63(12), 1932-42. 9 Role of Loop L1 Dynamics in Pseudomonas aeruginosa D-Arginine Dehydrogenase Daniel Ouedraogo1, Michael Souffrant1, Sheena Vasquez1,5, Donald Hamelberg1, 3, 4, and Giovanni Gadda1, 2, 3, 4, * 1Department of Chemistry, 2Department of Biology, 3Center for Diagnostics and Therapeutics, 4Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States, 5University of Georgia, Athens, Georgia 30602 The conformational changes of mobile loops positioned at the entrance of active sites of enzymes often participate in catalysis to control the access to the active site, to orient catalytic residues and to shield the active site from the bulk solvent.1, 2 Previous crystallographic data on D- arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) showed the presence of an active site loop L1 with two different peptidyl regions including residues 45-47 located at the FAD-binding site and residues 50-56 positioned at the entrance of the active site.3 In the two peptidyl regions of loop L1, only the S45, A46 and Y53 residues adopt major conformational changes corresponding to the open (ligand-free) and closed (product-bound) conformations.3 In the closed conformation the side chain of Y53 prevent the exit of the product from the active site whereas the side chain of A46 swings closer to the FAD and the side chain of S45 points away from the FAD.3 In the open conformation Y53 points away from the active, while the side chain of A46 swings away from the FAD and the side chain of S45 points closer to the FAD. The alternate conformations of the S46 and A46 residues, which are not in direct contact with the substrate, have been dubbed the Ser/Ala switch.3 In this study, S45 was mutated to alanine and A46 to glycine. The role of the conformational change of the Ser/Ala switch in PaDADH was studied through molecular dynamics, steady-state and rapid reaction kinetics techniques. Molecular dynamics of loop L1 showed higher probabilities in the S45A and A46G variant enzymes to be in the open conformation compared to the wild-type PaDADH, consistent with an exposed active site to the solvent. The flavin fluorescence intensity was ~2-fold higher in the S45A and A46G variant enzymes with respect to the wild-type PaDADH, with a 9 nm bathochromic shift of the emission band. The kcat/Km values with D-arginine in both variants, were ~13-fold lower in comparison with the wild- type PaDADH. Moreover, a hollowed pH-profile was observed on the kcat value with D-arginine consistent with restricted proton movements in catalysis. Rapid reaction kinetic data showed no saturation with the slow substrate D-leucine in the reductive half-reaction for the variant enzymes. All taken together the data indicate that the dynamics of loop L1 is important for substrate binding and catalysis in PaDADH. Support: NSF CHE-1506518 (G.G.) (1) Hanoian, P., Liu, C. T., Hammes-Schiffer, S., and Benkovic, S. (2015) Perspectives on electrostatics and conformational motions in enzyme catalysis. Acc. Chem. Res. 48, 482-489. (2) Gora, A., Brezovsky, J., and Damborsky, J. (2013) Gates of enzymes. Chem. Rev. 113, 5871- 5923. (3) Fu, G., Yuan, H., Li, C., Lu, C. D., Gadda, G., and Weber, I. T. (2010) Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase. Biochemistry 49, 8535-8545. 10 Dissecting the roles of the enzymatic and scaffolding functions of EXO1 in vivo Shanzhi Wang1, Kyeryoung Lee2, Richard Chahwan3, Yongwei Zhang2, Catherine Tang2, Sergio Roa2,
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