Mutations in the active site of Escherichia coli phosphofructokinase

The enzyme-catalysed transfer of a phosphoryl group from ATP is an important reaction in a wide variety of biological processes. We demonstrate here the essential function of an aspartate group in the catalysis of phosphoryl transfer by Escherichia coli phosphofructokinase, and the minor role of an arginine residue. We have used oligonucleotide-directed mutagenesis to replace two amino-acid residues which X-ray analysis has shown to be close to the transferred phosphoryl group and we have analysed the forward and back reactions of the mutant enzymes by steady-state kinetics. Changing Asp 127 to Ser reduced the turnover number by a factor of 18,000 in the forward direction and 3,100 in the back reaction, and the Michaelis constant for fructose 1,6-bisphosphate in the reverse reaction by a factor of 45. This shows that this aspartate is a key residue in the rate enhancement by the enzyme, probably acting as a base in the reaction mechanism, and that it also destabilizes the product complex. Changing Arg 171 to Ser reduced the turnover numbers by about 3.4, showing that this arginine has only a minor effect on the catalysis.     

Y-152和K-156在果蝇ADH催化中的作用

果蝇醇脱氢酶酪氨酸－１５２（Ｙ－１５２）和赖氨酸－１５６（Ｋ－１５６）处于同类脱氢酶的保守位点。经人工定点突变和酶动力学分析,前者的苯丙氨酸（Ｙ１５２Ｆ）、组氨酸（Ｙ１５２Ｈ）和谷氨酸突变体（Ｙ１５２Ｅ）及后者的异亮氨酸突变体（Ｋ１５６Ｉ）均丧失催化活性。而半胱氨酸－１５２（Ｙ１５２Ｃ）及精氨酸－１５６（Ｋ１５６Ｒ）突变体活性分别是对应野生型的０．２５％和２．２％。此外,Ｙ１５２Ｃ和Ｋ１５６Ｒ的Ｋ     

Active-site mutants altering the cooperativity of E. coli phosphofructokinase

Crystal structures of the high- and low-activity states of the allosteric enzyme phosphofructokinase implicate three arginines in substrate binding, catalysis and cooperativity. Arginines 162 and 243 reach into the active site from an adjacent subunit and interact with the cooperative substrate fructose 6-phosphate. Mutation of these arginines to serine results in mutant enzymes with reduced substrate binding and lowered cooperativity, but with little change in their catalytic ability (kcat). Arg 72 bridges the two substrates fructose 6-phosphate and ATP, and interacts with the 1-phosphate of the product fructose 1,6-biphosphate. Mutation of this residue to serine reduces the catalytic activity, cooperativity and binding of fructose 6-phosphate and fructose 1,6-bisphosphate. In the reverse reaction, the kinetics of wild-type and the Ser 72 mutant with respect to fructose 1,6-bisphosphate are hyperbolic, whereas those of the Ser 162 and Ser 243 mutants are sigmoidal. These results show that each of the three arginines contributes to cooperativity and to the transmission of allosteric signals between the four subunit of the enzyme.     

脂肪酶基因结构和氨基酸序列的比较

采用PCGENE6 8软件系统对真菌脂肪酶基因和氨基酸序列进行了分析。真核生物中多数结构基因中含有内含子 ,但真菌脂肪酶基因几乎有一大半的是连续的 ;对于有内含子的基因 ,不同脂肪酶基因所含内含子数目各异。所有脂肪酶一级结构中都包含Gly X1 Ser X2 Gly保守序列 ,在真菌脂肪酶中该序列更保守 ;Ser、Asp/Glu和His3个氨基酸残基组成了真菌脂肪酶的活性中心 ;大多数真菌脂肪酶是糖蛋白 ,但也有一些不含糖基的脂肪酶 ,主要取决于脂肪酶一级结构中是否存在糖基化识别序列。     

Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent.

Lipases belong to a class of esterases whose activity on triglycerides is greatly enhanced at lipid-water interfaces. This phenomenon, called interfacial activation, has a structural explanation: a hydrophobic lid, which at rest covers the catalytic site, is displaced on substrate or inhibitor binding and probably interacts with the lipid matrix. Fusarium solani pisi cutinase belongs to a group of homologous enzymes of relative molecular mass 22-25K (ref. 7) capable of degrading cutin, the insoluble lipid-polyester matrix covering the surface of plants, and hydrolysing triglycerides. Cutinases differ from classical lipases in that they do not exhibit interfacial activation; they are active on soluble as well as on emulsified triglycerides. Cutinases therefore establish a bridge between esterases and lipases. We report here the three-dimensional structure of a recombinant cutinase from F. solani pisi, expressed in Escherichia coli. Cutinase is an alpha-beta protein; the active site is composed of the triad Ser 120, His 188 and Asp 175. Unlike other lipases, the catalytic serine is not buried under surface loops, but is accessible to solvent. This could explain why cutinase does not display interfacial activation.     

Is sequence conservation in interferons due to selection for functional proteins?

The human alpha-interferon (IFN-alpha) gene family consists of at least 14 potentially functional non-allelic members; the amino acid sequences they encode differ from each other by up to approximately 20% of their residues. Human IFN-beta, which is encoded by a single gene, is distantly related to the IFN-alpha family; it differs in 67% of its residues from IFN-alpha 2. There is considerable evidence that IFN-alpha and -beta compete for the same receptors on their target cells. Comparison of 14 non-allelic human IFN-alpha sequences and the IFN-beta sequence has revealed that 37 of 166 residues are completely conserved and that several of these are arranged in clusters, for example at positions 29-33, 47-50 and 136-150. It is commonly held that evolutionary conservation of amino acids indicates that the residues in question are essential for function. To test this hypothesis in the case of IFNs, we have introduced single site-directed point mutations into the strictly conserved codons 48 and 49 of the IFN-alpha 2 gene which form part of the longest uninterrupted cluster (position 47-50). We report here that the mutant proteins, containing Tyr, Ser and Cys instead of Phe48, or His instead of Gln49, have biological activities indistinguishable from those of wild-type IFN-alpha. In addition, when Glu62, a residue conserved in all known alpha and beta IFNs of man, mouse and cattle, was replaced by Lys, antiviral activity remained unchanged.     

Ser-His-Glu triad forms the catalytic site of the lipase from Geotrichum candidum

The Ser-His-Asp triad is a well known structural feature of the serine proteases. It has also been directly observed in the catalytic sites of two lipases, whose high-resolution three-dimensional structures have been determined 1,2. Lipases show a wide variety of sizes, substrate and positional specificities, and catalytic rates 3. They achieve maximal catalytic rates at oil-water interfaces. The fungus Geotrichum candidum produces several different forms of lipases, two of which have been purified to homogeneity 4,5. Two lipase genes have been identified, cloned and sequenced 6,7. Both code for proteins of 544 amino acids with a total relative molecular mass of about 60,000 (Mr 60K). The two forms are 86% identical. Their isoelectric points differ slightly, being between 4.3 and 4.6. About 7% of the total Mr is carbohydrate. Until now, only a low resolution structure of GCL has been reported 8, but no high resolution structure has followed. We now report the three-dimensional structure of a lipase from G. candidum (GCL) at 2.2 A resolution. Unlike the other lipases and serine proteases, the catalytic triad of GCL is Ser-His-Glu, with glutamic acid replacing the usual aspartate. Although the sequence similarity with the other two lipases is limited to the region near the active-site serine, there is some similarity in their three-dimensional structures. The GCL is also an alpha/beta protein with a central mixed beta sheet whose topology is similar to that of the N-terminal domain of human pancreatic lipase. As in the other lipases 1,2, the catalytic site is buried under surface loops. Sequence comparisons with proteins from the cholinesterase family suggest that they also contain the Ser-His-Glu triad.     

煤炭残渣催化氧化制备腐植酸

为了充分利用碳资源,减少废物排放,开发了一种催化氧化风化煤残渣制备腐植酸的方法.该催化氧化方法使用稀过氧化氢溶液作氧化剂,氧化铜粉末作催化剂,氧化过程在室温下进行.实验结果表明,初级残渣能够被有效地氧化成腐植酸,其转化率可达35%,且氧化生成的腐植酸在结构特征和元素组成方面与天然腐植酸相似.在氧化生成的腐植酸被分离后,氧化铜催化剂仍然存在于次级残渣中,因此还可以对次级残渣进行重复氧化以增加腐植酸的产量.     

Crystal structure of a dUTPase.

The enzyme dUTPase catalyses the hydrolysis of dUTP and maintains a low intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. dUTPase from Escherichia coli is strictly specific for its dUTP substrate, the active site discriminating between nucleotides with respect to the sugar moiety as well as the pyrimidine base. Here we report the three-dimensional structure of E. coli dUTPase determined by X-ray crystallography at a resolution of 1.9 A. The enzyme is a symmetrical trimer, and of the 152 amino acid residues in the subunit, the first 136 are visible in the crystal structure. The tertiary structure resembles a jelly-roll fold and does not show the 'classical' nucleotide-binding domain. In the quaternary structure there is a complex interaction between the subunits that may be important in catalysis. This possibility is supported by the location of conserved elements in the sequence.     

基于支持向量机的脂肪酶耐热序列与嗜热序列分类研究

从GenBank数据库中获取了微生物来源的嗜热脂肪酶序列77条,耐热脂肪酶序列65条,分别统计分析序列中20种氨基酸出现的频次,二肽片段、三肽片段出现的差异以及非相邻二元组合的偏爱性。在此基础上,利用支持向量机(SVM)进行序列分类研究。研究结果表明:在统计学意义上,20种天然氨基酸残基中,亮氨酸、脯氨酸、蛋氨酸、苯丙氨酸、色氨酸和酪氨酸在嗜热蛋白序列中出现的频率高于其在耐热蛋白中出现的频率;二肽片段KC,EE,KE,RE,VE,YI,EK,VK,EV,YV,EY,KY,VY和YY的出现频率在嗜热蛋白中显著高于其在耐热蛋白中出现的频率。三肽片段的出现频率和非相邻二元组合的序列偏爱性也显示与蛋白耐热性显著相关。训练集的分类准确率达99.65%,真实数据集的分类准确率达到98.41%。     

麦冬凝集素的氨基酸修饰和荧光光谱研究

通过对麦冬凝集素（OJL）进行特殊氨基酸的化学修饰，揭示了OJL所含的6个Trp残基只有1个位于蛋白表面，Trp、Tyr和Ser/Thr不是OJL凝集活性所必需的氨基酸，而Arg是维持其活性的必需基团.OJL在天然状态下荧光发射峰在328 nm处，Trp周围的极性较弱，处于疏水的微环境或Trp的吲哚环有特殊的构象.丙烯酰胺可以淬灭93.46%的色氨酸荧光，而CsCl和KI淬灭的程度较小，分别为41.25%和55.56%，证明Trp主要位于疏水环境.     

季膦盐和钨酸钠催化下双氧水溶液清洁氧化醇和烯烃的研究

首先合成1-羟甲基苯并三唑、1-氯甲基苯并三唑、1,4-二溴丁烷单季膦盐等几种中间体,通过熔点、红外谱图等手段对其进行了结构表征;进而合成1-三苯基膦甲基苯并三唑、双季膦盐和ω-苯并三唑基丁基季膦盐等3种催化剂.其次,对自制的3种催化剂辅助过氧化氢氧化环己醇、苯甲醇、环己烯的性能进行了评价.即利用各季膦盐与钨酸钠构成三种催化体系,在无有机溶剂条件下,实现了30%过氧化氢水溶液清洁催化环己醇、苯甲醇、环己烯为环己酮、苯甲醛(或苯甲酸)、己二酸;考察了3种催化剂分别在3种体系下的催化性能.结果表明:对于环己醇的氧化1-三苯基膦甲基苯并三唑催化剂的效果最好;对于环己烯的氧化仍是1-三苯基膦甲基苯并三唑催化剂的效果最好;对于苯甲醇的氧化ω-苯并三唑基丁基季膦盐的催化效果最好.研究发现:在苯甲醇氧化时,随催化剂种类、体系和过氧化氢加入量的不同,可以选择性地氧化成苯甲醛或苯甲酸.在环己烯氧化时,随催化剂加量、过氧化氢加入量的不同和实验室的条件等的限制选择性很大.     

A model for interfacial activation in lipases from the structure of a fungal lipase-inhibitor complex

Lipases are hydrolytic enzymes which break down triacylglycerides into free fatty acids and glycerols. They have been classified as serine hydrolases owing to their inhibition by diethyl p-nitrophenyl phosphate. Lipase activity is greatly increased at the lipid-water interface, a phenomenon known as interfacial activation. X-ray analysis has revealed the atomic structures of two triacylglycerol lipases, unrelated in sequence: the human pancreatic lipase (hPL)4, and an enzyme isolated from the fungus Rhizomucor (formerly Mucor) miehei (RmL). In both enzymes the active centres contain structurally analogous Asp-His-Ser triads (characteristic of serine proteinases), which are buried completely beneath a short helical segment, or 'lid'. Here we present the crystal structure (at 3 A resolution) of a complex of R. miehei lipase with n-hexylphosphonate ethyl ester in which the enzyme's active site is exposed by the movement of the helical lid. This movement also increases the nonpolarity of the surface surrounding the catalytic site. We propose that the structure of the enzyme in this complex is equivalent to the activated state generated by the oil-water interface.     

A serine protease triad forms the catalytic centre of a triacylglycerol lipase

True lipases attach triacylglycerols and act at an oil-water interface; they constitute a ubiquitous group of enzymes catalysing a wide variety of reactions, many with industrial potential. But so far the three-dimensional structure has not been reported for any lipase. Here we report the X-ray structure of the Mucor miehei triglyceride lipase and describe the atomic model obtained at 3.1 A resolution and refined to 1.9 A resolution. It reveals a Ser..His..Asp trypsin-like catalytic triad with an active serine buried under a short helical fragment of a long surface loop.     

捕食线虫真菌丝氨酸蛋白酶PII结构的同源模建

通过同源模建方法构建捕食线虫真菌丝氨酸蛋白酶PII的三维结构模型,并结合以往研究对其结构进行分析。结果表明,蛋白酶PII的结构具有枯草杆菌丝氨酸蛋白酶特有的a／B脚手架折叠模式,具有保守的催化三聚体和氧负离子孔结构组织,整体表现为坚固的球状折叠构型,不具备二硫键。研究结果将为进一步深入研究PII的结构和功能之间的关系奠定结构基础。     

Amino acids from ultraviolet irradiation of interstellar ice analogues

Amino acids are the essential molecular components of living organisms on Earth, but the proposed mechanisms for their spontaneous generation have been unable to account for their presence in Earth's early history. The delivery of extraterrestrial organic compounds has been proposed as an alternative to generation on Earth, and some amino acids have been found in several meteorites. Here we report the detection of amino acids in the room-temperature residue of an interstellar ice analogue that was ultraviolet-irradiated in a high vacuum at 12 K. We identified 16 amino acids; the chiral ones showed enantiomeric separation. Some of the identified amino acids are also found in meteorites. Our results demonstrate that the spontaneous generation of amino acids in the interstellar medium is possible, supporting the suggestion that prebiotic molecules could have been delivered to the early Earth by cometary dust, meteorites or interplanetary dust particles.     

Site-directed mutagenesis reveals role of mobile arginine residue in lactate dehydrogenase catalysis

The binding of substrates to lactate dehydrogenases induces a marked rearrangement of the protein structure in which a 'loop' of polypeptide (residues 98-110) closes over the active site of the enzyme. In this rearrangement, arginine 109 (a basic residue conserved in all known lactate dehydrogenase sequences and in the homologous malate dehydrogenases) moves 0.8 nm from a position in the solvent to one in the active site where its guanidinium group resides within hydrogen bonding distance of both the reactive carbonyl of pyruvate and imidazole ring of the catalytic histidine 195 (see Fig. 1). Whilst this feature of the enzyme has been commented upon previously, the function of this mobile arginine residue during catalysis has not been tested experimentally. The advent of protein engineering has now enabled us to define the role of this basic residue by substituting it with the neutral glutamine. Transient kinetic and equilibrium studies of the mutant enzyme indicate that arginine 109 enhances the polarization of the pyruvate carbonyl group in the ground state and stabilizes the transition state. The gross active-site structure of the enzyme is not altered by the mutation since an alternative catalytic function of the enzyme (rate of addition of sulphite to NAD+), which does not require hydride transfer, is insensitive to the arginine----glutamine substitution.     

A链链内二硫键移位突变胰岛素原的构建与表达

采用定点突变技术,将人胰岛素原基因编码框中A11位氨基酸残基与A12位氨基酸残基进行了互换,构建了[CysA11Ser,SerA12Cys]人胰岛素原突变基因.在大肠杆菌原核表达系统中对突变体基因进行了表达,并对表达产物进行了变复性研究及初步的分离纯化,获得了具有稳定结构的突变体蛋白质,探讨了突变体A链链内二硫键的形成状况,为进一步深入揭示A链链内二硫键的角色与功能打下了基础.     

嗜酸氧化亚铁硫杆菌的核糖-5-磷酸异构酶的同源建模研究

采用同源建模技术和分子动力学模拟方法,构建了嗜酸氧化亚铁硫杆菌Acidithiobacillus ferrooxidans(A.f)的核糖-5-磷酸异构酶(rpiA)基因编码的蛋白质三维分子结构模型。将结构模型进行绑定位点搜索并与底物核糖-5-磷酸(R5P)进行柔性分子对接,结果显示,R5P被招募到A.ferrooxidans的RpiA的活性位点并随后被激活;残基Asp81,Thr31,Lys121,Ser30,Glu103,Asp84,Lys94,Asp118,Lys7,Gly97,Gly29,Gly95,Thr28和H2O对底物绑定或催化起重要作用,其中,Gly97,Gly29,Gly95和Thr28是新识别的残基,它们在其他生物体的RpiA中相当保守但未被发现。     

Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide

Peptide bond formation is the principal reaction of protein synthesis. It takes place in the peptidyl transferase centre of the large (50S) ribosomal subunit. In the course of the reaction, the polypeptide is transferred from peptidyl transfer RNA to the alpha-amino group of amino acyl-tRNA. The crystallographic structure of the 50S subunit showed no proteins within 18 A from the active site, revealing peptidyl transferase as an RNA enzyme. Reported unique structural and biochemical features of the universally conserved adenine residue A2451 in 23S ribosomal RNA (Escherichia coli numbering) led to the proposal of a mechanism of rRNA catalysis that implicates this nucleotide as the principal catalytic residue. In vitro genetics allowed us to test the importance of A2451 for the overall rate of peptide bond formation. Here we report that large ribosomal subunits with mutated A2451 showed significant peptidyl transferase activity in several independent assays. Mutations at another nucleotide, G2447, which is essential to render catalytic properties to A2451 (refs 2, 3), also did not dramatically change the transpeptidation activity. As alterations of the putative catalytic residues do not severely affect the rate of peptidyl transfer the ribosome apparently promotes transpeptidation not through chemical catalysis, but by properly positioning the substrates of protein synthesis.