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
Mildred Cohn Award in Biological Chemistry, ASBMB, 2022
Dorothy Crowfoot Hodgkin Award, The Protein Society, 2021
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
Structure of a modular polyketide synthase reducing region.
McCullough TM, Dhar A, Akey DL, Konwerski JR, Sherman DH, Smith JL.
Structure. 2023; 31: 1109–20.
Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction.
Chiang CH, Wymore T, Rodríguez Benítez A, Hussain A, Smith JL, Brooks CL 3rd, Narayan ARH.
Proc Natl Acad Sci U S A. 2023; 120: e2218248120.
Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A.
Kelly SP, Shende VV, Flynn AR, Dan Q, Ye Y, Smith JL, Tsukamoto S, Sigman MS, Sherman DH.
J Am Chem Soc. 2022; 144: 19326–36.
A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA.
Pham VV, Gao M, Meagher JL, Smith JL, D'Souza VM.
Commun Biol. 2022; 5: 819.
Structural Basis for Control of Methylation Extent in Polyketide Synthase Metal-Dependent C-Methyltransferases.
Lao Y, Skiba MA, Chun SW, Narayan ARH, Smith JL.
ACS Chem Biol. 2022; 17: 2088–98.
Triple-Negative Breast Cancer Cells Recruit Neutrophils by Secreting TGF-β and CXCR2 Ligands.
SenGupta S, Hein LE, Xu Y, Zhang J, Konwerski JR, Li Y, Johnson C, Cai D, Smith JL, Parent CA.
Front Immunol. 2021; 12: 659996.
Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction.
Biering SB, Akey DL, Wong MP, Brown WC, Lo NTN, Puerta-Guardo H, Tramontini Gomes de Sousa F, Wang C, Konwerski JR, Espinosa DA, Bockhaus NJ, Glasner DR, Li J, Blanc SF, Juan EY, Elledge SJ, Mina MJ, Beatty PR, Smith JL, Harris E.
Science. 2021; 371: 194–200.
For a list of publications from MyNCBI, click HERE