Salt-regulated reversible fibrillation of Mycobacterium tuberculosis isocitrate lyase: Concurrent restoration of structure and activity (original) (raw)
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Insight into the structural flexibility and function of Mycobacterium tuberculosis isocitrate lyase
Biochimie, 2015
Isocitrate lyase (ICL), is a key enzyme of the glyoxylate shunt crucial for the survival of Mycobacterium tuberculosis (Mtb) in macrophages during persistent infection. MtbICL catalyses the first step of this carbon anaplerosis cycle and is considered as a potential anti-tubercular drug target. The MtbICL is a tetramer with 222 symmetry, and each subunit of the enzymeis composed of 14 a-helices and 14 bstrands. We studied the conformational flexibility of the enzyme to get a deeper insight into its stability and function. Our studies show that the mutation of His180, close to the MtbICL signature sequence (K 193 KCGH 197 ) completely abolishes the oligomeric conformation and function of the enzyme. Molecular dynamics studies suggest that the loss of interaction between His180 and Tyr89 most likely alters the orientation of Tyr89 side chain, thereby causing the movement of helices a6, a12, a13 and a14 in the vicinity and affecting the tetrameric assembly. We further show that the oligomerization of MtbICL is primarily mediated by the inter subunit interactions, and strengthened by the helix swapping of a12 ea13 between adjacent subunits. Furthermore, the enzyme activity is influenced by the interactions between the residues of lid region (P 411 NSSTTALTGSTEEGQFH 428 ) and the loop region (T 391 KHQREV 397 ). Mutation of glutamates of the lid region to non homologous residues (E423A or E424A) or basic residues (E423K or E424K) inactivates the enzyme, whereas the activity is not much compromised in case of homologous mutations (E423D or E424D).
Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a crucial enzyme of the glyoxylate cycle and is a validated anti-tuberculosis drug target. Structurally distant, non-active site mutation (H46A) in MtbICL has been found to cause loss of enzyme activity. The aim of the present work was to explore the structural alterations induced by H46A mutation that caused the loss of enzyme activity. The structural and dynamic consequences of H46A mutation were studied using multiple computational methods such as docking, molecular dynamics simulation and residue interaction network analysis (RIN). Principal component analysis and cross correlation analysis revealed the difference in conformational flexibility and collective modes of motions between the wild-type and mutant enzyme, particularly in the active site region. RIN analysis revealed that the active site geometry was disturbed in the mutant enzyme. Thus, the dynamic perturbation of the active site led to enzyme transition from its active form to inactive form upon mutation. The computational analyses elucidated the mutant-specific conformational alterations, differential dominant motions, and anomalous residue level interactions that contributed to the abrogated function of mutant MtbICL. An understanding of interactions of mutant enzymes may help in modifying the existing drugs and designing improved drugs for successful control of tuberculosis.
Proteins-structure Function and Bioinformatics, 2008
Isocitrate lyase (Icl), an enzyme that plays an important role in the regulation of isocitrate flux and anaplerotic replenishment of pool of substrate required for biosynthetic process in Mycobacterium tuberculosis is a potential drug target for the antituberculosis drugs. Divalent cations induce differential effect of activation and inhibition of MtbIcl functional activity. The study for the first time demonstrates that interaction of cations with MtbIcl results in differential modulation of the enzyme structure which is probably the underlying mechanism for differential modulation of functional activity of enzyme by divalent cations. The Mg2+ and Mn2+ ions act as activators of the enzyme and in their absence no enzymatic activity was observed. These cations do not induce any significant structural alteration in the enzyme as observed by far-UV CD and solvent denaturation studies using chaotropic salts. However, the thermal denaturation studies demonstrate that they do interact with the noncatalytic α/β barrel core domain of the enzyme and destabilize it. The inhibitors Zn2+ and Cd2+ interact directly with the catalytic domain of the enzyme and unfold it as a result of which complete loss of the enzymatic activity is observed in their presence. The results obtained from the studies provide intriguing insight into the possible mechanism of divalent cation-induced changes in structure, function, and stability of MtbIcl. Proteins 2008. © 2008 Wiley-Liss, Inc.
Scientific Reports, 2017
Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence (189KKCGH193), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis. The results showed that the mutated residue increased the structural flexibility and induced conformational changes near the active site (residues 170–210) and in the C-terminal lid region (residues 411–428). Both these regions are involved in the catalytic activity of MtbICL. Upon mutation, the residual mobility of the enzyme increased, resu...
Biochemical and biophysical research communications, 2017
Mycobacterium tuberculosis isocitrate lyase (MtbICL) is a key enzyme of the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate and is a potential antituberculosis drug target. The aim of this research was to explore the structural alterations induced by L418A point mutation that caused the loss of enzyme activity. In-depth structural analyses were carried out for understanding the influence of L418A mutation using techniques, viz. molecular dynamics, principal component analysis, time-dependent secondary structure, residue interaction network and molecular docking. Since L418A mutation site is structurally far from the active site, it cannot influence the binding of the substrate directly. Our results showed that collective motions, residual mobility, and flexibility of the enzyme increased upon mutation. The mutated residue changed the global conformational dynamics of the system along with the residue-residue interaction network, leading to a lo...
Journal of Biological Chemistry, 2006
Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to form bicarbonate, a reaction required for many functions, including carbon assimilation and pH homeostasis. Carbonic anhydrases are divided into at least three classes and are believed to share a zinc-hydroxide mechanism for carbon dioxide hydration. -carbonic anhydrases are broadly spread among the domains of life, and existing structures from different organisms show two distinct active site setups, one with three protein coordinations to the zinc (accessible) and the other with four (blocked). The latter is believed to be inconsistent with the zinc-hydroxide mechanism. The Mycobacterium tuberculosis Rv3588c gene, shown to be required for in vivo growth of the pathogen, encodes a -carbonic anhydrase with a steep pH dependence of its activity, being active at pH 8.4 but not at pH 7.5. We have recently solved the structure of this protein, which was a dimeric protein with a blocked active site. Here we present the structure of the thiocyanate complexed protein in a different crystal form. The protein now forms distinct tetramers and shows large structural changes, including a carboxylate shift yielding the accessible active site. This structure demonstrated for the first time that a -carbonic anhydrase can switch between the two states. A pH-dependent dimer to tetramer equilibrium was also demonstrated by dynamic light scattering measurements. The data presented here, therefore, suggest a carboxylate shift on/off switch for the enzyme, which may, in turn, be controlled by a dimer-totetramer equilibrium.
Mechanism-based inactivator of isocitrate lyases 1 and 2 from Mycobacterium tuberculosis
Proceedings of the National Academy of Sciences of the United States of America, 2017
Isocitrate lyase (ICL, types 1 and 2) is the first enzyme of the glyoxylate shunt, an essential pathway for Mycobacterium tuberculosis (Mtb) during the persistent phase of human TB infection. Here, we report 2-vinyl-d-isocitrate (2-VIC) as a mechanism-based inactivator of Mtb ICL1 and ICL2. The enzyme-catalyzed retro-aldol cleavage of 2-VIC unmasks a Michael substrate, 2-vinylglyoxylate, which then forms a slowly reversible, covalent adduct with the thiolate form of active-site Cys191 2-VIC displayed kinetic properties consistent with covalent, mechanism-based inactivation of ICL1 and ICL2 with high efficiency (partition ratio, <1). Analysis of a complex of ICL1:2-VIC by electrospray ionization mass spectrometry and X-ray crystallography confirmed the formation of the predicted covalent S-homopyruvoyl adduct of the active-site Cys191.
Protein fibrillation is associated with a number of neurodegenerative diseases. Nevertheless, several proteins not related to disease can also form fibrils in vitro under specific conditions. In the present study, we demonstrate the reversible fibrillation of a globular protein that is modulated by salt under physiological pH. Mycobacterium tuberculosis Isocitrate lyase (MtbICL) is a crucial enzyme involved in the glyoxylate shunt and a potential drug target against M. tuberculosis infection. Under physiological pH, the enzyme self-assembles into a fibrillar structure in the absence of salt in vitro. The mature fibrillar structure of MtbICL is dynamic and restores its tetrameric structure as well as activity with the addition of salt. The kinetics of fibril formation was investigated spectroscopically using 8-Anilinonaphthalene-1sulfonic acid (ANS). Further, Transmission electron microscopy (TEM) and Atomic force microscopy (AFM) imaging also confirmed the formation of elongated fibrils in the absence of salt. The results indicate the balance between stabilizing forces and the localized electrostatic repulsions destabilizing the tetrameric MtbICL is adjusted via ion shielding. Our result is in congruence of the hypothesis that amyloid formation is an intrinsic property of most, if not all natural proteins under an appropriate set of conditions.
Scientific Reports, 2018
Microbial survival in dynamic environments requires the ability to successfully respond to abrupt changes in osmolarity. The mechanosensitive channel of large conductance (MscL) is a ubiquitous channel that facilitates the survival of bacteria and archaea under severe osmotic downshock conditions by relieving excess turgor pressure in response to increased membrane tension. A prominent structural feature of MscL, the cytoplasmic C-terminal domain, has been suggested to influence channel assembly and function. In this report, we describe the X-ray crystal structure and electrophysiological properties of a C-terminal domain truncation of the Mycobacterium tuberculosis MscL (MtMscLΔC). A crystal structure of MtMscLΔC solubilized in the detergent n-dodecyl-β-D-maltopyranoside reveals the pentameric, closed state-like architecture for the membrane spanning region observed in the previously solved full-length MtMscL. Electrophysiological characterization demonstrates that MtMscLΔC retains mechanosensitivity, but with conductance and tension sensitivity more closely resembling full length EcMscL than MtMscL. This study establishes that the C-terminal domain of MtMscL is not required for oligomerization of the full-length channel, but rather influences the tension sensitivity and conductance properties of the channel. The collective picture that emerges from these data is that each MscL channel structure has characteristic features, highlighting the importance of studying multiple homologs. Mechanosensitive (MS) channels transduce mechanical stimuli into a variety of cellular responses. MS channels are widely distributed through all kingdoms of life, including bacteria and archaea, where they play a prominent role in maintaining proper osmoregulation 1-5. Sudden changes in osmolarity, such as osmotic downshock during exposure to hypotonic conditions, increases turgor pressure across the cell membrane. This in turn increases the tension within the lipid bilayer and activates a network of MS channels which respond by opening typically nonselective pores in the membrane to release cell contents and alleviate the pressure 1,5-7. Bacterial MS channels are characterized by their relatively high and non-selective conductances, ranging from ~0.1 nS to ~3 nS under defined experimental conditions 6-8 , which is up to several orders of magnitude greater than typical for ion-selective channels 3,6,9. Of these channels, the mechanosensitive channel of large conductance (MscL) exhibits the largest conductance, with an estimated open state pore diameter of ~25-35 Å-large enough for the passage of molecules up to 9 kDa 4,7,10,11. In view of the high conductance yet small subunit size of MscL (Escherichia coli MscL (EcMscL) has 136 residues; Fig. 1), the oligomeric nature of this channel was appreciated from its initial discovery 11. Considerable efforts have been made to establish the molecular mechanism of MscL gating 3,12 , employing a variety of techniques including electrophysiology, biochemical and genetic studies, molecular dynamics
Differential spontaneous folding of mycolic acids from Mycobacterium tuberculosis
Chemistry and Physics of Lipids Volume 180, May 2014, Pages 15–22
Mycolic acids are structural components of the mycobacterial cell wall that have been implicated in the pathogenicity and drug resistance of certain mycobacterial species. They also offer potential in areas such as rapid serodiagnosis of human and animal tuberculosis. It is increasingly recognized that conformational behavior of mycolic acids is very important in understanding all aspects of their function. Atomistic molecular dynamics simulations, in vacuo, of stereochemically defined Mycobacterium tuberculosis mycolic acids show that they fold spontaneously into reproducible conformational groupings. One of the three characteristic mycolate types, the keto-mycolic acids, behaves very differently from either α-mycolic acids or methoxy-mycolic acids, suggesting a distinct biological role. However, subtle conformational behavioral differences between all the three mycolic acid types indicate that cooperative interplay of individual mycolic acids may be important in the biophysical properties of the mycobacterial cell envelope and therefore in pathogenicity.