Solution structure of Mycobacterium tuberculosis NmtR in the apo state: Insights into Ni(II)-mediated allostery

Chul Won Lee, Dhruva K. Chakravorty, Feng Ming James Chang, Hermes Reyes-Caballero, Yuzhen Ye, Kenneth M. Merz, David P. Giedroc

Research output: Contribution to journalArticle

Abstract

Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. How individual ArsR repressors have evolved to respond to selective stimuli is of intrinsic interest. The Ni(II)/Co(II)-specific repressor NmtR and related actinomycete nickel sensors harbor a conserved N-terminal α-NH 2-Gly2-His3-Gly4 sequence. Here, we present the solution structure of homodimeric apo-NmtR and show that the core of the molecule adopts a typical winged-helix ArsR repressor (α1-α2-α3-αR- β1-β2-α5) "open conformation" that is similar to that of the related zinc sensor Staphylococcus aureus CzrA, but harboring long, flexible N-terminal (residues 2-16) and C-terminal (residues 109-120) extensions. Binding of Ni(II) to the regulatory sites induces strong paramagnetic broadening of the α5 helical region and the extreme N-terminal tail to residue 10. Ratiometric pulse chase amidination mass spectrometry reveals that the rate of amidination of the α-amino group of Gly2 is strongly attenuated in the Ni(II) complex relative to the apo state and noncognate Zn(II) complex. Ni(II) binding also induces dynamic disorder on the microsecond to millisecond time scale of key DNA interacting regions that likely contributes to the negative regulation of DNA binding by Ni(II). Molecular dynamics simulations and quantum chemical calculations reveal that NmtR readily accommodates a distal Ni(II) hexacoordination model involving the α-amine and His3 of the N-terminal region and α5 residues Asp91′, His93′, His104, and His107, which collectively define a new metal sensing site configuration in ArsR family regulators.

Original languageEnglish (US)
Pages (from-to)2619-2629
Number of pages11
JournalBiochemistry
Volume51
Issue number12
DOIs
StatePublished - Mar 27 2012
Externally publishedYes

Fingerprint

Arsenic
Mycobacterium tuberculosis
Actinobacteria
DNA
Sensors
Pathogens
Molecular Dynamics Simulation
Ports and harbors
Nickel
Amines
Mass spectrometry
Conformations
Staphylococcus aureus
Molecular dynamics
Tail
Zinc
Mass Spectrometry
Metals
Molecules
Computer simulation

ASJC Scopus subject areas

  • Biochemistry

Cite this

Lee, C. W., Chakravorty, D. K., Chang, F. M. J., Reyes-Caballero, H., Ye, Y., Merz, K. M., & Giedroc, D. P. (2012). Solution structure of Mycobacterium tuberculosis NmtR in the apo state: Insights into Ni(II)-mediated allostery. Biochemistry, 51(12), 2619-2629. https://doi.org/10.1021/bi3001402

Solution structure of Mycobacterium tuberculosis NmtR in the apo state : Insights into Ni(II)-mediated allostery. / Lee, Chul Won; Chakravorty, Dhruva K.; Chang, Feng Ming James; Reyes-Caballero, Hermes; Ye, Yuzhen; Merz, Kenneth M.; Giedroc, David P.

In: Biochemistry, Vol. 51, No. 12, 27.03.2012, p. 2619-2629.

Research output: Contribution to journalArticle

Lee, Chul Won ; Chakravorty, Dhruva K. ; Chang, Feng Ming James ; Reyes-Caballero, Hermes ; Ye, Yuzhen ; Merz, Kenneth M. ; Giedroc, David P. / Solution structure of Mycobacterium tuberculosis NmtR in the apo state : Insights into Ni(II)-mediated allostery. In: Biochemistry. 2012 ; Vol. 51, No. 12. pp. 2619-2629.
@article{3d6de1e08c5443c4bf86b5b6cd95dd1a,
title = "Solution structure of Mycobacterium tuberculosis NmtR in the apo state: Insights into Ni(II)-mediated allostery",
abstract = "Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. How individual ArsR repressors have evolved to respond to selective stimuli is of intrinsic interest. The Ni(II)/Co(II)-specific repressor NmtR and related actinomycete nickel sensors harbor a conserved N-terminal α-NH 2-Gly2-His3-Gly4 sequence. Here, we present the solution structure of homodimeric apo-NmtR and show that the core of the molecule adopts a typical winged-helix ArsR repressor (α1-α2-α3-αR- β1-β2-α5) {"}open conformation{"} that is similar to that of the related zinc sensor Staphylococcus aureus CzrA, but harboring long, flexible N-terminal (residues 2-16) and C-terminal (residues 109-120) extensions. Binding of Ni(II) to the regulatory sites induces strong paramagnetic broadening of the α5 helical region and the extreme N-terminal tail to residue 10. Ratiometric pulse chase amidination mass spectrometry reveals that the rate of amidination of the α-amino group of Gly2 is strongly attenuated in the Ni(II) complex relative to the apo state and noncognate Zn(II) complex. Ni(II) binding also induces dynamic disorder on the microsecond to millisecond time scale of key DNA interacting regions that likely contributes to the negative regulation of DNA binding by Ni(II). Molecular dynamics simulations and quantum chemical calculations reveal that NmtR readily accommodates a distal Ni(II) hexacoordination model involving the α-amine and His3 of the N-terminal region and α5 residues Asp91′, His93′, His104, and His107, which collectively define a new metal sensing site configuration in ArsR family regulators.",
author = "Lee, {Chul Won} and Chakravorty, {Dhruva K.} and Chang, {Feng Ming James} and Hermes Reyes-Caballero and Yuzhen Ye and Merz, {Kenneth M.} and Giedroc, {David P.}",
year = "2012",
month = "3",
day = "27",
doi = "10.1021/bi3001402",
language = "English (US)",
volume = "51",
pages = "2619--2629",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "12",

}

TY - JOUR

T1 - Solution structure of Mycobacterium tuberculosis NmtR in the apo state

T2 - Insights into Ni(II)-mediated allostery

AU - Lee, Chul Won

AU - Chakravorty, Dhruva K.

AU - Chang, Feng Ming James

AU - Reyes-Caballero, Hermes

AU - Ye, Yuzhen

AU - Merz, Kenneth M.

AU - Giedroc, David P.

PY - 2012/3/27

Y1 - 2012/3/27

N2 - Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. How individual ArsR repressors have evolved to respond to selective stimuli is of intrinsic interest. The Ni(II)/Co(II)-specific repressor NmtR and related actinomycete nickel sensors harbor a conserved N-terminal α-NH 2-Gly2-His3-Gly4 sequence. Here, we present the solution structure of homodimeric apo-NmtR and show that the core of the molecule adopts a typical winged-helix ArsR repressor (α1-α2-α3-αR- β1-β2-α5) "open conformation" that is similar to that of the related zinc sensor Staphylococcus aureus CzrA, but harboring long, flexible N-terminal (residues 2-16) and C-terminal (residues 109-120) extensions. Binding of Ni(II) to the regulatory sites induces strong paramagnetic broadening of the α5 helical region and the extreme N-terminal tail to residue 10. Ratiometric pulse chase amidination mass spectrometry reveals that the rate of amidination of the α-amino group of Gly2 is strongly attenuated in the Ni(II) complex relative to the apo state and noncognate Zn(II) complex. Ni(II) binding also induces dynamic disorder on the microsecond to millisecond time scale of key DNA interacting regions that likely contributes to the negative regulation of DNA binding by Ni(II). Molecular dynamics simulations and quantum chemical calculations reveal that NmtR readily accommodates a distal Ni(II) hexacoordination model involving the α-amine and His3 of the N-terminal region and α5 residues Asp91′, His93′, His104, and His107, which collectively define a new metal sensing site configuration in ArsR family regulators.

AB - Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. How individual ArsR repressors have evolved to respond to selective stimuli is of intrinsic interest. The Ni(II)/Co(II)-specific repressor NmtR and related actinomycete nickel sensors harbor a conserved N-terminal α-NH 2-Gly2-His3-Gly4 sequence. Here, we present the solution structure of homodimeric apo-NmtR and show that the core of the molecule adopts a typical winged-helix ArsR repressor (α1-α2-α3-αR- β1-β2-α5) "open conformation" that is similar to that of the related zinc sensor Staphylococcus aureus CzrA, but harboring long, flexible N-terminal (residues 2-16) and C-terminal (residues 109-120) extensions. Binding of Ni(II) to the regulatory sites induces strong paramagnetic broadening of the α5 helical region and the extreme N-terminal tail to residue 10. Ratiometric pulse chase amidination mass spectrometry reveals that the rate of amidination of the α-amino group of Gly2 is strongly attenuated in the Ni(II) complex relative to the apo state and noncognate Zn(II) complex. Ni(II) binding also induces dynamic disorder on the microsecond to millisecond time scale of key DNA interacting regions that likely contributes to the negative regulation of DNA binding by Ni(II). Molecular dynamics simulations and quantum chemical calculations reveal that NmtR readily accommodates a distal Ni(II) hexacoordination model involving the α-amine and His3 of the N-terminal region and α5 residues Asp91′, His93′, His104, and His107, which collectively define a new metal sensing site configuration in ArsR family regulators.

UR - http://www.scopus.com/inward/record.url?scp=84859192888&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84859192888&partnerID=8YFLogxK

U2 - 10.1021/bi3001402

DO - 10.1021/bi3001402

M3 - Article

C2 - 22394357

AN - SCOPUS:84859192888

VL - 51

SP - 2619

EP - 2629

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 12

ER -