Metal-replacement studies in Bacillus stearothermophilus aldolase and a comparison of the mechanisms of class I and class II aldolases.
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ABSTRACT:
SUBMITTER: Hill HA
PROVIDER: S-EPMC1172621 | biostudies-other | 1976 Mar
REPOSITORIES: biostudies-other
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Project description:Transition path sampling is a well-known technique that generates reactive paths ensembles. Due to the atomic detail of these reactive paths, information about chemical mechanisms can be obtained. We present here a comparative study of Bacillus stearothermophilus and human heart homologues of lactate dehydrogenase (LDH). A comparison of the transition path ensemble of both enzymes revealed that small differences in the active site reverses the order of the particle transfer of the chemical step. Whereas the hydride transfer preceded the proton transfer in the human heart LDH, the order is reversed in the Bacillus stearothermophilis homologue (in the direction of pyruvate to lactate). In addition, transition state analysis revealed that the dividing region that separates reactants and products, the separatrix, is likely wider for B. stearothermophilis LDH as compared to human heart LDH. This would indicate a more variable transition process in the Bacillus enzyme.
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Project description:Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is a sulfosugar that is the anionic head group of plant, algal, and cyanobacterial sulfolipids: sulfoquinovosyl diacylglycerols. SQ is produced within photosynthetic tissues, forms a major terrestrial reservoir of biosulfur, and is an important species within the biogeochemical sulfur cycle. A major pathway for SQ breakdown is the sulfoglycolytic Embden-Meyerhof-Parnas pathway, which involves cleavage of the 6-carbon chain of the intermediate sulfofructose-1-phosphate (SFP) into dihydroxyacetone and sulfolactaldehyde, catalyzed by class I or II SFP aldolases. While the molecular basis of catalysis is understood for class I SFP aldolases, comparatively little is known about class II SFP aldolases. Here, we report the molecular architecture and biochemical basis of catalysis of two metal-dependent class II SFP aldolases from Hafnia paralvei and Yersinia aldovae. 3D X-ray structures of complexes with substrate SFP and product dihydroxyacetone phosphate reveal a dimer-of-dimers (tetrameric) assembly, the sulfonate-binding pocket, two metal-binding sites, and flexible loops that are implicated in catalysis. Both enzymes were metal-dependent and exhibited high KM values for SFP, consistent with their role in a unidirectional nutrient acquisition pathway. Bioinformatic analysis identified a range of sulfoglycolytic Embden-Meyerhof-Parnas gene clusters containing class I/II SFP aldolases. The class I and II SFP aldolases have mututally exclusive occurrence within Actinobacteria and Firmicutes phyla, respectively, while both classes of enzyme occur within Proteobacteria. This work emphasizes the importance of SQ as a nutrient for diverse bacterial phyla and the different chemical strategies they use to harvest carbon from this sulfosugar.
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Project description:The initial rates of phosphorylation of glucose catalysed by glucokinase from Bacillus stearothermophilus were measured over a wide range of glucose, MgATP2-, MgADP- and glucose 6-phosphate concentrations. The results of the effects of the inhibitors on the initial rates suggest that the reaction mechanism is essentially the ordered Bi Bi, in which glucose adds to the enzyme before MgATP2- and glucose 6-phosphate is released from the enzyme after the dissociation of MgADP-, and also suggest that the final step in which glucose 6-phosphate is released is irreversible. For many reaction schemes, the rate equations were derived on the basis of the pseudo-steady-state assumption and were used to correlate the experimental rate data. From this result, we concluded that the reaction obeys the ordered mechanism accompanied by the formation of a non-productive ternary complex, glucose-MgADP--enzyme. By using the experimental Dalziel coefficients phi i, some kinetic parameters were evaluated. The enzyme was characterized by the thermal stability and the low Michaelis constant, the values of which were 54 microM for glucose and 32 microM for MgATP2-.
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Project description:Fructose-1,6-bisphosphate (FBP) aldolase, a glycolytic enzyme, catalyzes the reversible and stereospecific aldol addition of dihydroxyacetone phosphate (DHAP) and d-glyceraldehyde 3-phosphate (d-G3P) by an unresolved mechanism. To afford insight into the molecular determinants of FBP aldolase stereospecificity during aldol addition, a key ternary complex formed by DHAP and d-G3P, comprising 2% of the equilibrium population at physiological pH, was cryotrapped in the active site of Toxoplasma gondii aldolase crystals to high resolution. The growth of T. gondii aldolase crystals in acidic conditions enabled trapping of the ternary complex as a dominant population. The obligate 3(S)-4(R) stereochemistry at the nascent C3-C4 bond of FBP requires a si-face attack by the covalent DHAP nucleophile on the d-G3P aldehyde si-face in the active site. The cis-isomer of the d-G3P aldehyde, representing the dominant population trapped in the ternary complex, would lead to re-face attack on the aldehyde and yield tagatose 1,6-bisphosphate, a competitive inhibitor of the enzyme. We propose that unhindered rotational isomerization by the d-G3P aldehyde moiety in the ternary complex generates the active trans-isomer competent for carbonyl bond activation by active-site residues, thereby enabling si-face attack by the DHAP enamine. C-C bond formation by the cis-isomer is suppressed by hydrogen bonding of the cis-aldehyde carbonyl with the DHAP enamine phosphate dianion through a tetrahedrally coordinated water molecule. The active site geometry further suppresses C-C bond formation with the l-G3P enantiomer of d-G3P. Understanding C-C formation is of fundamental importance in biological reactions and has considerable relevance to biosynthetic reactions in organic chemistry.
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