Mutagenesis of threonine to serine in the active site of Mycobacterium tuberculosis fructose-1,6-bisphosphatase (Class II) retains partial enzyme activity

Paracoccus binzhouensis sp. nov., isolated from activated sludge

A gram-stain-negative, non-motile and rod-shaped strain, designated wg1^T, was isolated from activated sludge obtained from wastewater treatment plant in Binzhou (Shandong province, PR China). Growth of strain wg1^T occurred at 25-45 °C (optimum, 37 °C), at pH 7.0-9.0 (optimum growth at pH 8.0) and at a salinity range of 0-4% (optimum, 1%). The chemotaxonomic, phenotypic and genomic traits were investigated. The 16S rRNA gene sequence analysis showed that strain wg1^T belonged to the genus Paracoccus. The species with highest similarity to strain wg1^T was Paracoccus communis VKM B-2787^T (98.27%), followed by Paracoccus kondratievae VKM B-2222^T (98.25%). The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C_16:0 and C_18:0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), aminoglycolipid (AGL), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), one unidentified lipid (L) and one unidentified phospholipid (PL). The genome size was 4,834,448 bp with a G+C content of 67.67 mol%. The prediction result of secondary metabolites based on genome has shown that the strain wg1^T contained 12 clusters, and the gene involved in primary metabolism showed differences in the comparison between wg1^T and reference strains. The dDDH values of strain wg1^T with P. communis VKM B-2787^T, P. kondratievae VKM B-2222^T and P. denitrificans DSM 413^T were 45.30, 30.60 and 39.50%, respectively. Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain wg1^T is considered to represent a novel species for which the name Paracoccus binzhouensis sp. nov., is proposed. The type strain is wg1^T (= KCTC 72861^T = CCTCC AB 2019400^T).

Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis

The crystal structure of the class II fructose-1,6-bisphosphatase (FBPaseII) from the important pathogen Francisella tularensis is presented at 2.4 Å resolution. Its structural and functional relationships to the closely related phosphatases from Mycobacterium tuberculosis (MtFBPaseII) and Escherichia coli (EcFBPaseII) and to the dual phosphatase from Synechocystis strain 6803 are discussed. FBPaseII from F. tularensis (FtFBPaseII) was crystallized in a monoclinic crystal form (space group P21, unit-cell parameters a = 76.30, b = 100.17, c = 92.02 Å, β = 90.003°) with four chains in the asymmetric unit. Chain A had two coordinated Mg2+ ions in its active center, which is distinct from previous findings, and is presumably deactivated by their presence. The structure revealed an approximate 222 (D2) symmetry homotetramer analogous to that previously described for MtFBPaseII, which is formed by a crystallographic dyad and which differs from the exact tetramer found in EcFBPaseII at a 222 symmetry site in the crystal. Instead, the approximate homotetramer is very similar to that found in the dual phosphatase from Synechocystis, even though no allosteric effector was found in FtFBPase. The amino-acid sequence and folding of the active site of FtFBPaseII result in structural characteristics that are more similar to those of the previously published EcFBPaseII than to those of MtFBPaseII. The kinetic parameters of native FtFBPaseII were found to be in agreement with published studies. Kinetic analyses of the Thr89Ser and Thr89Ala mutations in the active site of the enzyme are consistent with the previously proposed mechanism for other class II bisphosphatases. The Thr89Ala variant enzyme was inactive but the Thr89Ser variant was partially active, with an approximately fourfold lower Km and Vmax than the native enzyme. The structural and functional insights derived from the structure of FtFBPaseII will provide valuable information for the design of specific inhibitors.

Inositol Monophosphatase: A Bifunctional Enzyme in Mycobacterium smegmatis

Inositol monophosphatase (IMPase) is a crucial enzyme for the biosynthesis of phosphatidylinositol, an essential component in mycobacterial cell walls. IMPase A (ImpA) from Mycobacterium smegmatis is a bifunctional enzyme that also functions as a fructose-1,6-bisphosphatase (FBPase). To better understand the bifunctional nature of this enzyme, point mutagenesis was conducted on several key residues and their enzyme activity was tested. Our results along with active site models support the fact that ImpA is a bifunctional enzyme with residues Gly94, Thr95 hypothesized to be contributing to the FBPase activity and residues Trp220, Asp221 hypothesized to be contributing to the IMPase activity. Double mutants, W220A + D221A reduced both FBPase and IMPase activity drastically while the double mutant G94A + T95A surprisingly partially restored the IMPase activity compared to the single mutants. This study establishes the foundation toward obtaining a better understanding of the bifunctional nature of this enzyme.

Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition

The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus. This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and is probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis (MtFBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of MtFBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of MtFBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.