Areas of Interest
Our group studies protein structure using X-ray crystallography in order to understand protein function. We use the three-dimensional structures of proteins to understand molecular mechanisms of biological processes and to develop hypotheses about function, which we test through experiments in our lab or by collaboration. Two current projects illustrate our approach.
Glutamine amidotransferases are complex enzymes that produce ammonia from the amide group of glutamine, and channel the ammonia through an intra-molecular tunnel to a second active site where it is added to a second substrate. Amidotransferases occur in a variety of pathways for biosynthesis of nitrogenous molecules, including purine and pyrimidine bases, cofactors, aminosugars and amino acids. Our crystal structures of glutamine PRPP amidotransferase (purine pathway), GMP synthetase (guanine pathway), imidazole glycerol phosphate synthase (histidine pathway) and other enzymes show that the chemical steps of glutamine hydrolysis and amination occur independently, but that they are coordinated by the protein through a variety of conformational switches. Our analysis of the structures has shown how each enzyme keeps its glutaminase active site in an inactive state until the second substrate is bound and ready to accept the labile ammonia. Currently challenges are to understand the conformational switches used for cross-talk by the distant active sites and to study new amidotransferases that have been detected in genome sequences.
The replication machinery of alphaviruses and flaviviruses also represents a complex catalytic system. These positive-sense RNA viruses encode enzymes for genome replication, RNA capping, RNA unwinding and polyprotein processing. Specific protein-protein complexes, as yet poorly characterized, coordinate the catalytic activities and specify particular RNA or protein substrates at appropriate times in the viral life cycle. Our structural studies of individual enzymes and enzyme complexes aim to elucidate mechanisms of catalysis and of time-dependent activation and specificity.
Honors & Awards
Elected Fellow, National Academy of Sciences, 2020
Elected Fellow, American Crystallographic Association, 2018
Distinguished Faculty Lectureship Award in Biomedical Research, University of Michigan Medical School, 2016
Elected Fellow, American Association for the Advancement of Science, 2007
Herbert Newby McCoy Award, Purdue University, 2001
National Institutes of Health MERIT Award, 1998–2008
Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway.
Fraley AE, Caddell Haatveit K, Ye Y, Kelly SP, Newmister SA, Yu F, Williams RM, Smith JL, Houk KN, Sherman DH.
J Am Chem Soc. 2020; 142: 2244–52.
Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis.
Skiba MA, Tran CL, Dan Q, Sikkema AP, Klaver Z, Gerwick WH, Sherman DH, Smith JL.
Structure. 2020; 28: 63–74.
Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences.
Meagher JL, Takata M, Gonçalves-Carneiro D, Keane SC, Rebendenne A, Ong H, Orr VK, MacDonald MR, Stuckey JA, Bieniasz PD, Smith JL.
Proc Natl Acad Sci U S A. 2019; 116: 24303–9.
Flexibility in nucleic acid binding is central to APOBEC3H antiviral activity.
Bohn JA, DaSilva J, Kharytonchyk S, Mercedes M, Vosters J, Telesnitsky A, Hatziioannou T, Smith JL.
J Virol. 2019; 93: e01275–19.
Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase.
Dan Q, Newmister SA, Klas KR, Fraley AE, McAfoos TJ, Somoza AD, Sunderhaus JD, Ye Y, Shende VV, Yu F, Sanders JN, Brown WC, Zhao L, Paton RS, Houk KN, Smith JL, Sherman DH, Williams RM.
Nat Chem. 2019; 11: 972–80.
Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization.
Benítez AR, Tweedy S, Baker Dockrey SA, Lukowski AL, Wymore T, Khare D, Brooks CL 3rd, Palfey BA, Smith JL, Narayan ARH.
ACS Catal. 2019; 9: 3633–40.
For a list of publications from MyNCBI, click HERE