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Title: 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 (MIC 80) ~ 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 andmore » 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.« less

Authors:
 [1];  [2];  [3];  [1];  [4];  [1];  [1];  [5];  [2];  [1]
  1. Sanford-Burnham Medical Research Institute, La Jolla, CA (United States)
  2. Vertex Pharmaceuticals Inc., Boston, MA (United States)
  3. Polytechnic Univ. of Marche, Ancona (Italy)
  4. Russian Academy of Sciences, Moscow (Russia)
  5. 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:
Journal Article: 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. 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., and Osterman, Andrei L. Wed . "Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery". United States. doi: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}
}

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