A5013013509- Metalloenzymes and iron-sulfur proteins
- RNA modifications and cancer
- Porphyrin Metabolism and Disorders
- Folate and B Vitamins Research
- Biochemical and Molecular Research
- RNA and protein synthesis mechanisms
- Metal-Catalyzed Oxygenation Mechanisms
- CO2 Reduction Techniques and Catalysts
- Enzyme Structure and Function
- Metabolism and Genetic Disorders
- Peptidase Inhibition and Analysis
- Heme Oxygenase-1 and Carbon Monoxide
- Amino Acid Enzymes and Metabolism
- Redox biology and oxidative stress
- Metal-Organic Frameworks: Synthesis and Applications
- Polyamine Metabolism and Applications
- Electrocatalysts for Energy Conversion
- Photosynthetic Processes and Mechanisms
- Advanced Proteomics Techniques and Applications
- Venomous Animal Envenomation and Studies
- HIV/AIDS drug development and treatment
- Microbial Natural Products and Biosynthesis
- Metal complexes synthesis and properties
- Ammonia Synthesis and Nitrogen Reduction
- Bacterial Genetics and Biotechnology
University of Utah
2016-2025
Salt Lake Regional Medical Center
2020
University of Arizona
2006-2016
Milbank Memorial Fund
2014
University of Michigan
1996-2013
United States University
2013
University of Wisconsin–Madison
1996-2006
University of Minnesota
1996-2000
Arizona State University
2000
Albert Einstein College of Medicine
2000
Riboswitches are RNA regulatory elements that govern gene expression by recognition of small molecule ligands via a high affinity aptamer domain. Molecular can lead to active or attenuated states controlling accessibility mRNA signals necessary for transcription translation. Key areas inquiry focus on how an attains specificity its effector, the extent which folds prior encountering ligand, and ligand binding alters signal accessibility. Here we present crystal structures preQ(1) riboswitch...
The bacterium Escherichia coli possesses 16S and 23S rRNA strands that have 36 chemical modification sites with 17 different structures. Nanopore direct RNA sequencing using a protein nanopore sensor helicase brake, which is also sensor, was applied to the rRNAs. current levels, base calling profile, dwell times for modifications relative unmodified synthetic controls found signatures nearly all modifications. Signatures clustered were determined by selective of writer knockout E. RNAs...
Deazapurine-containing secondary metabolites comprise a broad range of structurally diverse nucleoside analogues found throughout biology, including various antibiotics produced by species Streptomyces bacteria and the hypermodified tRNA bases queuosine archaeosine. Despite early interest in deazapurines as antibiotic, antiviral, antineoplastic agents, biosynthetic route toward deazapurine production has remained largely elusive for more than 40 years. Here we present first vitro preparation...
Transfer RNA is one of the most richly modified biological molecules. Biosynthetic pathways that introduce these modifications are underexplored, largely because their absence does not lead to obvious phenotypes under normal growth conditions. Queuosine (Q) a hypermodified base found in wobble positions tRNA Asp, Asn, His, and Tyr from bacteria mankind. Using liquid chromatography MS methods, we have screened 1,755 single gene knockouts Escherichia coli identified key final step biosynthesis...
Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ(1) riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present crystal structure a aptamer in complex precursor preQ(0). highly compact core features stem capped by well organized decaloop. recognized within deep pocket via Watson-Crick...
Toyocamycin nitrile hydratase (TNH) is a protein hexamer that catalyzes the hydration of toyocamycin to produce sangivamycin. The structure hexameric TNH and arrangement subunits within complex, however, have not been solved by NMR or X-ray crystallography. Native mass spectrometry (MS) clearly shows composed two copies each α, β, γ subunits. Previous surface induced dissociation (SID) tandem on quadrupole time-of-flight (QTOF) platform suggests dimer αβγ trimers; furthermore, results...
7-Carboxy-7-deazaguanine (CDG) synthase (QueE) catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH(4)) to CDG in third step biosynthetic pathway all 7-deazapurines. Here we present a detailed characterization QueE from Bacillus subtilis delineate mechanism CPH(4) CDG. is member radical S-adenosyl-l-methionine (SAM) superfamily, which use bound [4Fe-4S](+) cluster catalyze reductive cleavage SAM cofactor generate methionine and...
Ribosomally synthesized post-translationally modified peptides (RiPPs) are encoded in the genomes of a wide variety microorganisms, proximity open reading frames that encode enzymes conduct extensive modifications, many which novel. Recently, members radical S-adenosyl-l-methionine (SAM) superfamily have been identified these biosynthetic clusters. Herein, we demonstrate putative SAM enzyme, MftC, oxidatively decarboxylates C-terminus MftA peptide presence accessory protein MftB. The...
Peptide-derived natural products are a class of metabolites that afford the producing organism selective advantage over other organisms in their biological niche. While polypeptide antibiotics produced by nonribosomal synthetases (NRPS) most widely recognized, ribosomally synthesized and post-translationally modified peptides (RiPPs) an emerging group with diverse structures functions. Both NRPS derived RiPPs undergo extensive post-translational modifications to produce structural diversity....
Peptidylglycine monooxygenase is a copper-dependent enzyme that catalyzes C-alpha hydroxylation of glycine extended pro-peptides, critical post-translational step in peptide hormone processing. The canonical mechanism posits dioxygen binds at the mononuclear M-center to generate Cu(II)-superoxo species capable H atom abstraction from peptidyl substrate, followed by long-range electron tunneling CuH center. Recent crystallographic and biochemical data have challenged this mechanism,...
Venoms of brown spiders in the genus Loxosceles contain phospholipase D enzyme toxins that can cause severe dermonecrosis and even death humans. These cleave substrates sphingomyelin lysophosphatidylcholine mammalian tissues, releasing choline head group. The other products substrate cleavage have previously been reported to be monoester phospholipids, which would result from hydrolysis. Using 31P NMR mass spectrometry we demonstrate recombinant toxins, as well whole venoms diverse species,...
Queuosine (Q) was discovered in the wobble position of a transfer RNA (tRNA) 47 years ago, yet final biosynthetic enzyme responsible for Q-maturation, epoxyqueuosine (oQ) reductase (QueG), only recently identified. QueG is cobalamin (Cbl)-dependent, [4Fe-4S] cluster-containing protein that produces hypermodified nucleoside Q situ on four tRNAs. To understand how able to perform epoxide reduction, an unprecedented reaction Cbl-dependent enzyme, we have determined series high resolution...
Abstract Post-transcriptional modifications can impact the stability and functionality of many different classes RNA molecules are an especially important aspect tRNA regulation. It is hypothesized that cells orchestrate rapid responses to changing environmental conditions by adjusting specific types levels modifications. We uncovered strong evidence in support this global regulation hypothesis examining effects well-conserved modifying enzyme MiaA extraintestinal pathogenic Escherichia coli...
Radical S-adenosyl-l-methionine (RS) enzymes operate on a variety of substrates and catalyze wide range complex radical-mediated transformations. non-α-carbon thioether peptides (ranthipeptides) are class ribosomally synthesized post-translationally modified (RiPPs). The RS enzyme PapB catalyzes the formation cross-links between Cys/Asp (or Cys/Glu) residues located in six Cys-X3-Asp/Glu motifs. In this report, using minimal substrate that contains single cross-link motif, we explore scope...
Bioactive peptides generally require post-translational processing to convert them their fully active forms. Peptidylglycine monooxygenase (PHM) is a copper-dependent enzyme that catalyzes C-alpha hydroxylation of glycine-extended pro-peptide, critical step in peptide amidation. A canonical mechanism based on experimental and theoretical considerations proposes molecular oxygen reacts at the mononuclear CuM-center form reactive Cu(II)-superoxo intermediate capable H-atom abstraction from...
In the course of catalysis or signaling, large multimodular proteins often undergo conformational changes that reposition modules with respect to one another. The mechanisms direct reorganization in these are considerable importance, but distinguishing alternate conformations is a challenge. Cobalamin-dependent methionine synthase (MetH) 136-kDa enzyme cobalamin chromophore; color reflects conformation protein. contains four and catalyzes three different methyl transfer reactions require...