Structure determination of reaction intermediates in macromolecular complexes

Project: Research project


DESCRIPTION (provided by applicant): The objective of the proposed research is to determine structures of reaction intermediates in two separate metalloenzyme systems that operate within macromolecular complexes. The first specific aim will determine structures of intermediates in oxygen-mediated activation of class Ib ribonucleotide reductase, found only in prokaryotes and recently discovered to employ a novel dimanganese(III)-tyrosyl radical cofactor for catalysis. This project will be completed during the K99 funding period and will crystallographically characterize early reaction intermediates via freeze trapping and mutagenesis techniques. Later intermediates will be stabilized by exploiting the pH and temperature dependence of the reaction and its susceptibility to isotope effects. Spectroscopic characterization of reaction intermediates in the crystal will provide independent verification of structures. The essential nature of the enzyme and its function as the primary mode of deoxynucleotide production in a number of human pathogens makes its activation reaction a possible new avenue for novel antibiotic development. The second aim will explore substrate-bound structures of an RNA methylase that uses a [4Fe-4S] cluster, S-adenosyl-L-methionine (SAM) cofactor to catalyze a mechanistically novel methyl transfer reaction at an unactivated carbon center. The enzyme to be studied (Escherichia coli RlmN) specifically methylates a position that imparts the capacity to modulate translation within the peptidyl transferase center of the large subunit (23S) of the ribosome. RlmN is related to a methylase (Staphylococcus aureus Cfr) with a slightly different site selectivity. Cfr-mediated methylation of the 23S ribosom is implicated in resistance to antibiotics that target the PTC. RlmN and Cfr target a specific adenine site within the 23S subunit and are most active in the context of large fragments of the ribosome. The goal of the proposed work is to gain structural information about RlmN bound to minimal and increasingly large fragments of its substrate and to investigate the structures of trapped reaction intermediates. This work will begin during the K99 funding period and will continue during the independent phase. Understanding the structure of the enzyme bound to its substrate and at various states in the reaction pathway will provide critical information about the structural basis for mechanism and specificity and will lay the foundation to elucidate evolution of antibiotic resistance in Cfr. PUBLIC HEALTH RELEVANCE: The proposed work, determining X-ray crystal structures of reaction intermediates in two distinct prokaryotic enzymes that operate within macromolecular complexes, is motivated by the information it will provide about the mechanistic details of the reactions catalyzed, both of which are completely novel. The important roles these enzymes play in nucleotide metabolism and regulation in prokaryotes, with connections to analogous enzymes in human pathogens, may allow the information gained in this study to be exploited in the development of new antibiotic therapies.
Effective start/end date3/1/126/30/16


  • National Institutes of Health: $27,518.00
  • National Institutes of Health: $237,105.00
  • National Institutes of Health: $249,000.00
  • National Institutes of Health: $82,554.00
  • National Institutes of Health: $243,053.00


Macromolecular Substances
Reaction intermediates
Anti-Bacterial Agents
tRNA Methyltransferases
Chemical activation
Peptidyl Transferases
Ribonucleotide Reductases
Factor IX
Escherichia coli