Insights into the Substrate Uptake Mechanism of Mycobacterium Tuberculosis Ribose 5-Phosphate Isomerase and Perspectives on Drug Development
Leonardo Bartkevihi,
Ícaro P. Caruso,
Bruna Martins,
José R. M. Pires,
Danielle M. P. Oliveira,
Cristiane Dinis Anobom,
Fabio C. L. Almeida
Affiliations
Leonardo Bartkevihi
Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
Ícaro P. Caruso
National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
Bruna Martins
Laboratório de Bioquímica Estrutural de Proteínas (LaBEP), Institute of Chemistry, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
José R. M. Pires
Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
Danielle M. P. Oliveira
Laboratório de Bioquímica Estrutural de Proteínas (LaBEP), Institute of Chemistry, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
Cristiane Dinis Anobom
Laboratório de Bioquímica Estrutural de Proteínas (LaBEP), Institute of Chemistry, Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
Fabio C. L. Almeida
Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
The active site of the dimeric ribose 5-phosphate isomerase B (RpiB) contains a solvent-exposed barrier formed by residues H12, R113, R137, and R141, which is closed upon the complexation of phosphate. The substrate ribose 5-phosphate (R5P) has to overcome the surface barrier to reach an internal cavity and then bind in the linear configuration of ribose to the interface between the two subunits. NMR and molecular dynamics simulation are suitable methods to describe the transient nature of the RpiB active site and help our understanding of the mechanism of substrate entrance. In this study, we show that the entrance of the nucleotides AMP/ADP into the internal cavity of mycobacterium tuberculosis RpiB (MtRpiB) does not involve a canonical open/close-lid conformational transition usually observed in many enzymes. Instead, a flipping mechanism in which the nucleotide phosphate interacts with the surface barrier followed by the flip of the nitrogenous base and ribose is responsible for changing the substrate/ligand orientation from a solvent-exposed to a buried state. Based on these results, we propose a substrate/inhibitor uptake mechanism that could provide a basis for rational drug design using MtRpiB, which is an essential enzyme and a good target for drug development.
