Crystallization and preliminary X-ray crystallographic analysis of a Mycobacterium tuberculosis ferritin homolog, BfrB.

Mycobacterium tuberculosis (Mtb) is the causative agent of the deadly disease tuberculosis. Iron acquisition, regulation and storage are critical for the survival of this pathogen within a host. Thus, understanding the mechanisms of iron metabolism in Mtb will shed light on its pathogenic nature, as iron is important for infection. Ferritins are a superfamily of protein nanocages that function in both iron detoxification and storage, and Mtb contains both a predicted ferritin and a bacterioferritin. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the ferritin homolog (Mtb BfrB, Rv3841) is reported. An Mtb BfrB crystal grown at pH 6.5 using the hanging-drop vapor-diffusion technique diffracted to 2.50 Šresolution and belonged to space group C2, with unit-cell parameters a=226.2, b=226.8, c=113.7 Å, ß=94.7° and with 24 subunits per asymmetric unit. Furthermore, modeling the crystal structure of a homologous ferritin into a low-resolution small-angle X-ray scattering (SAXS) electron-density envelope is consistent with the presence of 24 subunits in the BfrB protein cage quaternary structure.

Advances in Mycobacterium tuberculosis structural genomics: investigating potential chinks in the armor of a deadly pathogen.

The waning effectiveness of established tuberculosis treatments due to the rise of multi and extensively drug-resistant strains of Mycobacterium tuberculosis, coupled with the synergism of HIV infection, demands basic research efforts to inform focused drug development programs. Structural genomics projects provide rich sources of information for the rational design of anti-tubercular drugs, aiming to exploit unique and novel protein features and interactions based on atomic resolution structures. This review compiles structures of M. tuberculosis proteins elucidated since January 2007 that are promising avenues for drug design, encompassing proteins involved with known and experimental antituberculosis drugs, metabolism, dealing with the hostile environment of the host organism, and information processing.

High throughput crystallography of TB drug targets.

Tuberculosis (TB) infects one-third of the world population. Despite 50 years of available drug treatments, TB continues to increase at a significant rate. The failure to control TB stems in part from the expense of delivering treatment to infected individuals and from complex treatment regimens. Incomplete treatment has fueled the emergence of multi-drug resistant (MDR) strains of Mycobacterium tuberculosis (Mtb). Reducing non-compliance by reducing the duration of chemotherapy will have a great impact on TB control. The development of new drugs that either kill persisting organisms, inhibit bacilli from entering the persistent phase, or convert the persistent bacilli into actively growing cells susceptible to our current drugs will have a positive effect. We are taking a multidisciplinary approach that will identify and characterize new drug targets that are essential for persistent Mtb. Targets are exposed to a battery of analyses including microarray experiments, bioinformatics, and genetic techniques to prioritize potential drug targets from Mtb for structural analysis. Our core structural genomics pipeline works with the individual laboratories to produce diffraction quality crystals of targeted proteins, and structural analysis will be completed by the individual laboratories. We also have capabilities for functional analysis and the virtual ligand screening to identify novel inhibitors for target validation. Our overarching goals are to increase the knowledge of Mtb pathogenesis using the TB research community to drive structural genomics, particularly related to persistence, develop a central repository for TB research reagents, and discover chemical inhibitors of drug targets for future development of lead compounds.

The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology.

The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.

SDZ PSC 833 the drug resistance modulator activates cellular ceramide formation by a pathway independent of P-glycoprotein.

SDZ PSC 833 (PSC 833) is a new multidrug resistance modulator. Recent studies have shown that the principal mechanism of action of PSC 833 is to bind P-glycoprotein (P-gp) and prevent cellular efflux of chemotherapeutic drugs. We previously reported that PSC 833 increases cellular ceramide levels. The present study was conducted to determine whether the impact of PSC 833 on ceramide generation is dependent on P-gp. Work was carried out using the drug-sensitive P-gp-deficient human breast adenocarcinoma cell line, MCF-7, and drug resistant MCF-7/MDR1 clone 10.3 cells (MCF-7/MDR1), which show a stable MDR1 P-gp phenotype. Overexpression of P-gp in MCF-7/MDR1 cells did not increase the levels of glucosylceramide, a characteristic which has been associated with multidrug resistant cells. Treatment of MCF-7 and MCF-7/MDR1 cells with PSC 833 caused similar ceramide elevation, in a dose-responsive manner. At 5.0 microM, PSC 833 increased ceramide levels 4- to 5-fold. The increase in ceramide levels correlated with a decrease in survival in both cell lines. The EC50 (concentration of drug that kills 50% of cells) for PSC 833 in MCF-7 and MCF-7/MDR1 cells was 7.2 +/- 0.6 and 11.0 +/- 1.0 microM, respectively. C6-Ceramide exposure diminished survival of MCF-7 cells; whereas, MCF-7/MDR1 cells were resistant to this short chain ceramide analog. Preincubation of cells with cyclosporine A, which has high affinity for P-gp, did not diminish the levels of ceramide generated upon exposure to PSC 833. These results demonstrate that PSC 833-induced cellular ceramide formation occurs independently of P-gp. As such, these data indicate that reversal of drug resistance by classical P-gp blockers may be modulated by factors unrelated to drug efflux parameters.

Cobalamin-dependent methionine synthase is a modular protein with distinct regions for binding homocysteine, methyltetrahydrofolate, cobalamin, and adenosylmethionine.

Methionine synthase (MetH) catalyzes the transfer of a methyl group from bound methylcobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. The cofactor is then remethylated by methyltetrahydrofolate. We now demonstrate that MetH is able to catalyze methylation of free cob(I)alamin with methyltetrahydrofolate. MetH had previously been shown to catalyze methylation of homocysteine with free methylcobalamin as the methyl donor, in a reaction that is first-order in added methylcobalamin, and we have confirmed this observation using homogenous enzyme. A truncated polypeptide lacking the cobalamin-binding region of the holoenzyme, MetH(2-649), was overexpressed and purified to homogeneity. MetH(2-649) catalyzes the methylation of free cob(I)alamin by methyltetrahydrofolate and the methylation of homocysteine by free methylcobalamin. Furthermore, a protein comprising residues 2-353 of the holoenzyme has now been overexpressed and purified to homogeneity, and this protein catalyzes methyl transfer from free methylcobalamin to homocysteine but not from methyltetrahydrofolate to free cob(I)alamin. The mutations Cys310Ala and Cys311Ala in MetH(2-649) completely abolish methyl transfer from exogenous methylcobalamin to homocysteine but do not affect methyl transfer from methyltetrahydrofolate to exogenous cob(I)alamin, consistent with a modular construction for MetH. We infer that MetH is a modular protein comprising four separate regions: a homocysteine binding region (residues 2-353), a methyltetrahydrofolate binding region (residues 354-649), a region responsible for binding the cobalamin prosthetic group (residues 650-896), and an AdoMet-binding domain (residues 897-1227).

Cobalamin-dependent methionine synthase from Escherichia coli: involvement of zinc in homocysteine activation.

Methionine synthase (MetH) is a modular protein with at least four distinct regions; amino acids 2-353 comprise a region responsible for binding and activation of homocysteine, amino acids 345-649 are thought to be involved in the binding and activation of methyltetrahydrofolate, amino acids 650-896 are responsible for binding of the prosthetic group methylcobalamin, and amino acids 897-1227 are involved in binding adensylmethionine and are required for reductive activation of enzyme in the cob(II)alamin form. Previous studies have shown that mutations of Cys310 or Cys311 to either alanine or serine result in loss of all detectable catalytic activity. These mutant proteins retain the ability to catalyze methyl transfer from methyltetrahydrofolate to exogenous cob(I)alamin, but have lost the ability to transfer methyl groups from exogenous methylcobalamin to homocysteine [Goulding, C. W., Postigo, D., and Matthews, R. G. (1997) Biochemistry 36, 8082-8091]. We now demonstrate that both MetH holoenzyme and a truncated MetH(2-649) protein, which lacks a cobalamin prosthetic group, contain 0.9 equiv of zinc, while the Cys310Ser and Cys311Ser mutant proteins contain less than 0.05 equiv of zinc. Addition of l-homocysteine to MetH(2-649) is accompanied by release of 1 equiv of protons/mol of protein, while addition of l-homocysteine to the Cys310Ser and Cys311Ser mutant truncated proteins does not result in proton release. The Cys310Ala and Cys311Ala mutant methylcobalamin holoenzymes have completely lost the ability to transfer the methyl group from methylcobalamin to homocysteine, suggesting that zinc is required for this reaction. Further evidence that zinc is required for catalytic activity comes from experiments in which the zinc is removed from MetH(2-1227). Removal of zinc from methylated wild-type holoenzyme by treatment with methyl methanethiolsulfonate and then with dithiothreitol and EDTA results in loss of the ability of the protein to catalyze methyl transfer from methyltetrahydrofolate to homocysteine. Reconstitution of the zinc-depleted holoenzyme results in incorporation of 0.4 equiv of zinc/mol of protein and partial restoration of the ability of the protein to catalyze homocysteine methylation.

Enzyme-catalyzed methyl transfers to thiols: the role of zinc.

Zinc has been identified as a cofactor in a growing number of proteins that utilize thiols as nucleophiles, including proteins that catalyze the transfer of methyl groups to thiols. The latter category includes the Ada protein involved in the response of E. coli to DNA alkylation, cobalamin-independent and cobalamin-dependent methionine synthase, and enzymes involved in the formation of methylcoenzyme M in methanogenesis. Farnesyl-protein transferase and geranylgeranyl-protein transferase also contain zinc and an X-ray structure of farnesyl-protein transferase has recently been determined. Within the past year, studies on the role of zinc in these proteins and in model compounds have shown that the thiol substrates are coordinated to the zinc as thiolates, suggesting a role for zinc in maintenance of thiol reactivity at neutral pH.