Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery
Abstract
Nicotinate mononucleotide adenylyltransferase NadD is an essential enzyme in the biosynthesis of the NAD cofactor, which has been implicated as a target for developing new antimycobacterial therapies. Here we report the crystal structure of Mycobacterium tuberculosis NadD (MtNadD) at a resolution of 2.4 Å. A remarkable new feature of the MtNadD structure, compared with other members of this enzyme family, is a 310 helix that locks the active site in an over-closed conformation. As a result, MtNadD is rendered inactive as it is topologically incompatible with substrate binding and catalysis. Directed mutagenesis was also used to further dissect the structural elements that contribute to the interactions of the two MtNadD substrates, i.e. ATP and nicotinic acid mononucleotide (NaMN). For inhibitory profiling of partially active mutants and wild type MtNadD, we used a small molecule inhibitor of MtNadD with moderate affinity (Ki ~ 25 μM) and antimycobacterial activity (MIC80) ~ 40-80 μM). This analysis revealed interferences with some of the residues in the NaMN binding subsite consistent with the competitive inhibition observed for the NaMN substrate (but not ATP). A detailed steady-state kinetic analysis of MtNadD suggests that ATP must first bind to allow efficient NaMN binding and catalysis. This sequentialmore »
- Authors:
-
- Sanford-Burnham Medical Research Institute, La Jolla, CA (United States)
- Vertex Pharmaceuticals Inc., Boston, MA (United States)
- Polytechnic Univ. of Marche, Ancona (Italy)
- Russian Academy of Sciences, Moscow (Russia)
- Harvard School of Public Health, Boston, MA (United States)
- Publication Date:
- Research Org.:
- Univ. of California, Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1347693
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Biological Chemistry
- Additional Journal Information:
- Journal Volume: 290; Journal Issue: 12; Journal ID: ISSN 0021-9258
- Publisher:
- American Society for Biochemistry and Molecular Biology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; enzyme inhibitor; enzyme structure; NAD biosynthesis; protein engineering; protein targeting
Citation Formats
Rodionova, Irina A., Zuccola, Harmon J., Sorci, Leonardo, Aleshin, Alexander E., Kazanov, Marat D., Ma, Chen -Ting, Sergienko, Eduard, Rubin, Eric J., Locher, Christopher P., and Osterman, Andrei L. Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery. United States: N. p., 2015.
Web. doi:10.1074/jbc.m114.628016.
Rodionova, Irina A., Zuccola, Harmon J., Sorci, Leonardo, Aleshin, Alexander E., Kazanov, Marat D., Ma, Chen -Ting, Sergienko, Eduard, Rubin, Eric J., Locher, Christopher P., & Osterman, Andrei L. Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery. United States. https://doi.org/10.1074/jbc.m114.628016
Rodionova, Irina A., Zuccola, Harmon J., Sorci, Leonardo, Aleshin, Alexander E., Kazanov, Marat D., Ma, Chen -Ting, Sergienko, Eduard, Rubin, Eric J., Locher, Christopher P., and Osterman, Andrei L. Wed .
"Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery". United States. https://doi.org/10.1074/jbc.m114.628016. https://www.osti.gov/servlets/purl/1347693.
@article{osti_1347693,
title = {Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery},
author = {Rodionova, Irina A. and Zuccola, Harmon J. and Sorci, Leonardo and Aleshin, Alexander E. and Kazanov, Marat D. and Ma, Chen -Ting and Sergienko, Eduard and Rubin, Eric J. and Locher, Christopher P. and Osterman, Andrei L.},
abstractNote = {Nicotinate mononucleotide adenylyltransferase NadD is an essential enzyme in the biosynthesis of the NAD cofactor, which has been implicated as a target for developing new antimycobacterial therapies. Here we report the crystal structure of Mycobacterium tuberculosis NadD (MtNadD) at a resolution of 2.4 Å. A remarkable new feature of the MtNadD structure, compared with other members of this enzyme family, is a 310 helix that locks the active site in an over-closed conformation. As a result, MtNadD is rendered inactive as it is topologically incompatible with substrate binding and catalysis. Directed mutagenesis was also used to further dissect the structural elements that contribute to the interactions of the two MtNadD substrates, i.e. ATP and nicotinic acid mononucleotide (NaMN). For inhibitory profiling of partially active mutants and wild type MtNadD, we used a small molecule inhibitor of MtNadD with moderate affinity (Ki ~ 25 μM) and antimycobacterial activity (MIC80) ~ 40-80 μM). This analysis revealed interferences with some of the residues in the NaMN binding subsite consistent with the competitive inhibition observed for the NaMN substrate (but not ATP). A detailed steady-state kinetic analysis of MtNadD suggests that ATP must first bind to allow efficient NaMN binding and catalysis. This sequential mechanism is consistent with the requirement of transition to catalytically competent (open) conformation hypothesized from structural modeling. A possible physiological significance of this mechanism is to enable the down-regulation of NAD synthesis under ATP-limiting dormancy conditions. Lastly, these findings point to a possible new strategy for designing inhibitors that lock the enzyme in the inactive over-closed conformation.},
doi = {10.1074/jbc.m114.628016},
journal = {Journal of Biological Chemistry},
number = 12,
volume = 290,
place = {United States},
year = {Wed Jan 28 00:00:00 EST 2015},
month = {Wed Jan 28 00:00:00 EST 2015}
}
Web of Science
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