The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad

Dihydrodipicolinate synthase (DHDPS, EC 4.2.1.52) catalyses the branchpoint reaction of lysine biosynthesis in plants and microbes: the condensation of (S)-aspartate-beta-semialdehyde and pyruvate. The crystal structure of wild-type DHDPS has been published to 2.5A, revealing a tetrameric molecule comprised of four identical (beta/alpha)(8)-barrels, each containing one active site. Previous workers have hypothesised that the catalytic mechanism of the enzyme involves a catalytic triad of amino acid residues, Tyr133, Thr44 and Tyr107, which provide a proton shuttle to transport protons from the active site to solvent. We have tested this hypothesis using site-directed mutagenesis to produce three mutant enzymes: DHDPS-Y133F, DHDPS-T44V and DHDPS-Y107F. Each of these mutants has substantially reduced activity, consistent with the catalytic triad hypothesis. We have determined each mutant crystal structure to at least 2.35A resolution and compared the structures to the wild-type enzyme. All mutant enzymes crystallised in the same space group as the wild-type form and only minor differences in structure are observed. These results suggest that the catalytic triad is indeed in operation in wild-type DHDPS.     

Regulation of lysine synthesis in transgenic potato plants expressing a bacterial dihydrodipicolinate synthase in their chloroplasts

The essential amino acid lysine is synthesized in higher plants by a complex pathway that is predominantly regulated by feedback inhibition of two enzymes, namely aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS). Although DHPS is thought to play a major role in this regulation, the relative importance of AK is not known. In order to study this regulation, we have expressed in the chloroplasts of transgenic potato plants a DHPS derived from Escherichia coli at a level 50-fold above the endogenous DHPS. The bacterial enzyme is much less sensitive to lysine inhibition than its potato counterpart. DHPS activity in leaves, roots and tubers of the transgenic plants was considerably higher and more resistant to lysine inhibition than in control untransformed plants. Furthermore, this activity was accompanied by a significant increase in level of free lysine in all three tissues. Yet, the extent of lysine overproduction in potato leaves was significantly lower than that previously reported in leaves of transgenic plants expressing the same bacterial enzyme, suggesting that in potato, AK may also play a major regulatory role in lysine biosynthesis. Indeed, the elevated level of free lysine in the transgenic potato plants was shown to inhibit the lysine-sensitive AK activity in vivo. Our results support previous reports showing that DHPS is the major rate-limiting enzyme for lysine synthesis in higher plants, but they suggest that additional plant-specific regulatory factors are also involved.     

Soybean DapA mutations encoding lysine-insensitive dihydrodipicolinate synthase

In plants, the rate-limiting step in the pathway for lysine synthesis is catalyzed by the enzyme dihydrodipicolinate synthase (DS), which is encoded by the DapA gene. We previously cloned the soybean (Glycine max cv. Century) DapA gene in Escherichia coli to express functional soybean DS protein. Like the wild-type soybean DS enzyme, the DS activity encoded by the cloned gene was extremely sensitive to feedback inhibition by micromolar concentrations of lysine. Three mutants of the soybean DapA gene were constructed using PCR: one with a single amino acid substitution at codon 104, another with a single amino acid substitution at codon 112, and a mutant containing both modifications. When expressed in E. coli, the mutant DS activities were insensitive to lysine at concentrations up to 1 mM.     

Spinach leaf dihydrodipicolinate synthase: Partial purification and characterization

The first enzyme unique to lysine biosynthesis in higher plants, dihydrodipicolinate synthase, has been partially purified from spinach leaves, using ion exchange chromatography, hydrophobic interaction chromatography and gel filtration. The spinach enzyme is moderately stable to short-term exposure to heat, in contrast to the pea leaf enzyme, but is unstable on storage even at ?20°. Thiol reagents interfere with the calorimetric assay used, and so cannot be routinely used to stabilize the enzyme, which has an active sulphydryl group. The MW of the enzyme is 115000 (gel filtration). Lysine is a potent inhibitor with an I_(0.5) of 2OμM, whilst the lysine analogue S-β-aminoethylcysteinc has an I_(0.5) of 400 μM. The Kt´_m for aspartic-β-semialdehyde was determined to be 1.4mM, but this compound demonstrated marked substrate inhibition at concentrations above 7 mM, increasing the apparent S_(0.5)for the second substrate, pyruvate.     

Evolution of quaternary structure in a homotetrameric enzyme

Dihydrodipicolinate synthase (DHDPS) is an essential enzyme in (S)-lysine biosynthesis and an important antibiotic target. All X-ray crystal structures solved to date reveal a homotetrameric enzyme. In order to explore the role of this quaternary structure, dimeric variants of Escherichia coli DHDPS were engineered and their properties were compared to those of the wild-type tetrameric form. X-ray crystallography reveals that the active site is not disturbed when the quaternary structure is disrupted. However, the activity of the dimeric enzymes in solution is substantially reduced, and a tetrahedral adduct of a substrate analogue is observed to be trapped at the active site in the crystal form. Remarkably, heating the dimeric enzymes increases activity. We propose that the homotetrameric structure of DHDPS reduces dynamic fluctuations present in the dimeric forms and increases specificity for the first substrate, pyruvate. By restricting motion in a key catalytic motif, a competing, non-productive reaction with a substrate analogue is avoided. Small-angle X-ray scattering and mutagenesis data, together with a B-factor analysis of the crystal structures, support this hypothesis and lead to the suggestion that in at least some cases, the evolution of quaternary enzyme structures might serve to optimise the dynamic properties of the protein subunits.     

分析超速离心技术研究膜蛋白TmrAB

去垢剂在膜蛋白的提取纯化过程中起到必要的作用,对膜蛋白的聚合状态、结晶条件以及理化性质等方面都有较大影响.分析超速离心技术(analytical ultracentrifuge,AUC)通过测定溶液中膜蛋白-去垢剂复合物在离心场中的沉降运动轨迹,可以分析获得其沉降系数、摩尔质量、流体力学半径、结合常数等水力学和热力学性质,进而判断膜蛋白-去垢剂复合物的均一性及聚合状态.本文以嗜热菌来源的ATP结合转运蛋白(ABC transporter)TmrAB作为研究对象,利用分析超速离心技术结合分子排阻层析和冷冻电镜负染技术,研究其均一性、聚合状态以及去垢剂与膜蛋白的摩尔比.结果显示,在8倍临界胶束浓度(critical micelle concentration,CMC)的DDM条件下,TmrAB性质均一,并以异二聚体的单体形式存在,DDM与Tmr AB的摩尔比为116∶1.本研究表明,分析超速离心技术是一种测定膜蛋白分子质量、研究膜蛋白聚合状态的可靠手段.