Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824

Susan E. Cellitti; Jennifer Shaffer; David H. Jones; Tathagata Mukherjee; Meera Gurumurthy; Badry Bursulaya; Helena I. Boshoff; Inhee Choi; Amit Nayyar; Yong Sok Lee; Joseph Cherian; Pornwaratt Niyomrattanakit; Thomas Dick; Ujjini H. Manjunatha; Clifton E. Barry; Glen Spraggon; Bernhard H. Geierstanger

doi:10.1016/j.str.2011.11.001

Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824

Susan E. Cellitti
, Jennifer Shaffer
, David H. Jones
, Tathagata Mukherjee
, Meera Gurumurthy
, Badry Bursulaya
, Helena I. Boshoff
, Inhee Choi
, Amit Nayyar
, Yong Sok Lee
, Joseph Cherian
, Pornwaratt Niyomrattanakit
, Thomas Dick
, Ujjini H. Manjunatha
, Clifton E. Barry
, Glen Spraggon
, Bernhard H. Geierstanger

Center for Discovery and Innovation

Hackensack Meridian School of Medicine

Research output: Contribution to journal › Article › peer-review

Abstract

Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F ₄₂₀ deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F ₄₂₀ and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.

Original language	English
Pages (from-to)	101-112
Number of pages	12
Journal	Structure
Volume	20
Issue number	1
DOIs	https://doi.org/10.1016/j.str.2011.11.001
State	Published - Jan 11 2012

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1016/j.str.2011.11.001

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Cellitti, S. E., Shaffer, J., Jones, D. H., Mukherjee, T., Gurumurthy, M., Bursulaya, B., Boshoff, H. I., Choi, I., Nayyar, A., Lee, Y. S., Cherian, J., Niyomrattanakit, P., Dick, T., Manjunatha, U. H., Barry, C. E., Spraggon, G., & Geierstanger, B. H. (2012). Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824. Structure, 20(1), 101-112. https://doi.org/10.1016/j.str.2011.11.001

@article{bea97f4d8bd94368b6fdbdd5b67719a0,

title = "Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824",

abstract = "Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F 420 deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F 420 and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.",

author = "Cellitti, \{Susan E.\} and Jennifer Shaffer and Jones, \{David H.\} and Tathagata Mukherjee and Meera Gurumurthy and Badry Bursulaya and Boshoff, \{Helena I.\} and Inhee Choi and Amit Nayyar and Lee, \{Yong Sok\} and Joseph Cherian and Pornwaratt Niyomrattanakit and Thomas Dick and Manjunatha, \{Ujjini H.\} and Barry, \{Clifton E.\} and Glen Spraggon and Geierstanger, \{Bernhard H.\}",

note = "Funding Information: The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. This work was funded, in part, by a grant from The Bill and Melinda Gates Foundation and the Wellcome Trust through the Grand Challenges in Global Health Initiative to the Novartis Institute for Tropical Diseases (NITD) and NIAID; by the NIH intramural research program of NIAID to C.E.B. and of the Center for Information Technology to Y.S.L.; and by NITD. We would like to thank Dr. P. McPhie, Laboratory of Biochemistry and Genetics, NIDDK, NIH for allowing us to run the CD experiments and helping us with the analysis; P. Abdubek, C. Chen, J. Feuerhelm, J. Grant, H. Klock, A. Kreusch, A. Nopakun, L. Okach, C. Puckett, and T. Wooten at the Genomics Institute of the Novartis Research Foundation (GNF) for technical assistance; and S. Lesley (GNF) and C. Noble (NITD) for their valuable comments. S.E.C., U.H.M., C.E.B., G.S., and B.H.G. designed experiments and prepared the manuscript. C.E.B., U.H.M., and T.D. initiated the study and wrote the grants that provided funding. The following data were generated and analyzed by the indicated contributors: molecular biology and protein production and purification by S.E.C., J.S., T.M., and H.I.M.B.; crystallization and structure calculations by S.E.C. and G.S.; NMR by D.H.J.; activity assays by T.M. and P.N.; CD by T.M.; Trp fluorescence by M.G.; computational modeling by B.B., I.C., and Y.S.L.; and chemical synthesis by A.N. and J.C. U.H.M., C.E.B., G.S., and B.H.G. were the subteam leaders at the respective sites and supervised the respective experiments.",

year = "2012",

month = jan,

day = "11",

doi = "10.1016/j.str.2011.11.001",

language = "English",

volume = "20",

pages = "101--112",

journal = "Structure",

issn = "0969-2126",

publisher = "Cell Press",

number = "1",

}

Cellitti, SE, Shaffer, J, Jones, DH, Mukherjee, T, Gurumurthy, M, Bursulaya, B, Boshoff, HI, Choi, I, Nayyar, A, Lee, YS, Cherian, J, Niyomrattanakit, P, Dick, T, Manjunatha, UH, Barry, CE, Spraggon, G & Geierstanger, BH 2012, 'Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824', Structure, vol. 20, no. 1, pp. 101-112. https://doi.org/10.1016/j.str.2011.11.001

TY - JOUR

T1 - Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824

AU - Cellitti, Susan E.

AU - Shaffer, Jennifer

AU - Jones, David H.

AU - Mukherjee, Tathagata

AU - Gurumurthy, Meera

AU - Bursulaya, Badry

AU - Boshoff, Helena I.

AU - Choi, Inhee

AU - Nayyar, Amit

AU - Lee, Yong Sok

AU - Cherian, Joseph

AU - Niyomrattanakit, Pornwaratt

AU - Dick, Thomas

AU - Manjunatha, Ujjini H.

AU - Barry, Clifton E.

AU - Spraggon, Glen

AU - Geierstanger, Bernhard H.

N1 - Funding Information: The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. This work was funded, in part, by a grant from The Bill and Melinda Gates Foundation and the Wellcome Trust through the Grand Challenges in Global Health Initiative to the Novartis Institute for Tropical Diseases (NITD) and NIAID; by the NIH intramural research program of NIAID to C.E.B. and of the Center for Information Technology to Y.S.L.; and by NITD. We would like to thank Dr. P. McPhie, Laboratory of Biochemistry and Genetics, NIDDK, NIH for allowing us to run the CD experiments and helping us with the analysis; P. Abdubek, C. Chen, J. Feuerhelm, J. Grant, H. Klock, A. Kreusch, A. Nopakun, L. Okach, C. Puckett, and T. Wooten at the Genomics Institute of the Novartis Research Foundation (GNF) for technical assistance; and S. Lesley (GNF) and C. Noble (NITD) for their valuable comments. S.E.C., U.H.M., C.E.B., G.S., and B.H.G. designed experiments and prepared the manuscript. C.E.B., U.H.M., and T.D. initiated the study and wrote the grants that provided funding. The following data were generated and analyzed by the indicated contributors: molecular biology and protein production and purification by S.E.C., J.S., T.M., and H.I.M.B.; crystallization and structure calculations by S.E.C. and G.S.; NMR by D.H.J.; activity assays by T.M. and P.N.; CD by T.M.; Trp fluorescence by M.G.; computational modeling by B.B., I.C., and Y.S.L.; and chemical synthesis by A.N. and J.C. U.H.M., C.E.B., G.S., and B.H.G. were the subteam leaders at the respective sites and supervised the respective experiments.

PY - 2012/1/11

Y1 - 2012/1/11

N2 - Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F 420 deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F 420 and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.

AB - Tuberculosis continues to be a global health threat, making bicyclic nitroimidazoles an important new class of therapeutics. A deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis catalyzes the reduction of nitroimidazoles such as PA-824, resulting in intracellular release of lethal reactive nitrogen species. The N-terminal 30 residues of Ddn are functionally important but are flexible or access multiple conformations, preventing structural characterization of the full-length, enzymatically active enzyme. Several structures were determined of a truncated, inactive Ddn protein core with and without bound F 420 deazaflavin coenzyme as well as of a catalytically competent homolog from Nocardia farcinica. Mutagenesis studies based on these structures identified residues important for binding of F 420 and PA-824. The proposed orientation of the tail of PA-824 toward the N terminus of Ddn is consistent with current structure-activity relationship data.

UR - https://www.scopus.com/pages/publications/84862925406

U2 - 10.1016/j.str.2011.11.001

DO - 10.1016/j.str.2011.11.001

M3 - Article

C2 - 22244759

SN - 0969-2126

VL - 20

SP - 101

EP - 112

JO - Structure

JF - Structure

IS - 1

ER -

Structure of Ddn, the deazaflavin-dependent nitroreductase from Mycobacterium tuberculosis involved in bioreductive activation of PA-824

Abstract

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