Dissecting the catalytic triad of a serine protease

Serine proteases are present in virtually all organisms and function both inside and outside the cell; they exist as two families, the 'trypsin-like' and the 'subtilisin-like', that have independently evolved a similar catalytic device characterized by the Ser, His, Asp triad, an oxyanion binding site, and possibly other determinants that stabilize the transition state (Fig. 1). For Bacillus amyloliquefaciens subtilisin, these functional elements impart a total rate enhancement of at least 10(9) to 10(10) times the non-enzymatic hydrolysis of amide bonds. We have examined the catalytic importance and interplay between residues within the catalytic triad by individual or multiple replacement with alanine(s), using site-directed mutagenesis of the cloned B. amyloliquefaciens subtilisin gene. Alanine substitutions were chosen to minimize unfavourable steric contacts and to avoid imposing new charge interactions or hydrogen bonds from the substituted side chains. In contrast to the effect of mutations in residues involved in substrate binding, the mutations in the catalytic triad greatly reduce the turnover number and cause only minor effects on the Michaelis constant. Kinetic analyses of the multiple mutants demonstrate that the residues within the triad interact synergistically to accelerate amide bond hydrolysis by a factor of approximately 2 X 10(6).     

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.     

Accelerated evolution in the reactive centre regions of serine protease inhibitors

The serine protease inhibitors (serpins) are a family of proteins that function to control the action of serine proteases in many diverse physiological processes. The functional region or reactive centre of these inhibitors is near the C-terminal end and is an exposed site that acts as a bait for the appropriate serine protease to recognize and covalently bind. The specificity of the inhibitor is determined, at least in part, by a single amino acid that resides in this region at the P1 position. We show here that following a gene duplication event the reactive centres of three related rodent protease inhibitors have diverged from each other at unprecedented rates. This has resulted in proteins with different predicted specificities and we postulate that these changes were fixed by positive darwinian selection and that the most likely selective forces are extrinsic proteases, namely those used by parasites to facilitate their spread throughout the host.     

A gene required for the specification of dorsal-ventral pattern in Drosophila appears to encode a serine protease

The maternal effect gene snake is required for the establishment of the dorsal-ventral axis during the embryonic development of Drosophila. The molecular cloning of the gene and analysis of a complementary DNA sequence suggest that the gene encodes a serine protease which is structurally similar to proteases involved in blood clotting, peptide processing, and complement fixation pathways.     

磁场对脂肪酶催化活性的影响

研究了磁场对发生在液-液两相界面上的酶促反应的影响.4℃时磁化酶溶液,短时间内酶活性显著提高,0.1T的磁场作用1h可使酶活力提高76.1%,随着作用时间的增长,酶活性逐渐降低.pH值、温度均对酶的磁效应有明显的影响;酶的磁效应存在着滞后效应;磁化水也可明显提高酶的催化活性,经0.485T的磁场作用的水可使酶活性提高将近1倍.     

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.     

Plasma protease inhibitors in mouse and man: divergence within the reactive centre regions

The plasma protease inhibitors control a wide variety of physiological functions including blood coagulation, complement activation and aspects of the inflammatory response. The inhibitors function by forming a 1:1 complex with a specific protease within the reactive centre region of the inhibitor. Little is known about the evolutionary relationships of these inhibitors. We report here the sequences of cDNAs which represent the C-terminal halves of the two major murine plasma protease inhibitors. One of these, murine alpha 1-antitrypsin, more appropriately called alpha 1-proteinase inhibitor (alpha 1-PI), has diverged from its human counterpart at a vital position in the reactive centre but this has not led to a physiologically significant change in function. Also, we have determined the partial sequence of a recently characterized protein termed contrapsin, which inhibits trypsin-like proteases. We show, surprisingly, that contrapsin is highly homologous to human alpha 1-antichymotrypsin, an inhibitor of chymotrypsin-like proteases. The reactive centre regions of these two inhibitors have diverged considerably, which may account for the differences in specificity. We propose that the genes for contrapsin and human alpha 1-antichymotrypsin are the descendents of a single gene that have evolved since rodent and primate divergence to encode proteins with different functions.     

Structure of the catalytic domain of the hepatitis C virus NS2-3 protease

Hepatitis C virus is a major global health problem affecting an estimated 170 million people worldwide. Chronic infection is common and can lead to cirrhosis and liver cancer. There is no vaccine available and current therapies have met with limited success. The viral RNA genome encodes a polyprotein that includes two proteases essential for virus replication. The NS2-3 protease mediates a single cleavage at the NS2/NS3 junction, whereas the NS3-4A protease cleaves at four downstream sites in the polyprotein. NS3-4A is characterized as a serine protease with a chymotrypsin-like fold, but the enzymatic mechanism of the NS2-3 protease remains unresolved. Here we report the crystal structure of the catalytic domain of the NS2-3 protease at 2.3 A resolution. The structure reveals a dimeric cysteine protease with two composite active sites. For each active site, the catalytic histidine and glutamate residues are contributed by one monomer, and the nucleophilic cysteine by the other. The carboxy-terminal residues remain coordinated in the two active sites, predicting an inactive post-cleavage form. Proteolysis through formation of a composite active site occurs in the context of the viral polyprotein expressed in mammalian cells. These features offer unexpected insights into polyprotein processing by hepatitis C virus and new opportunities for antiviral drug design.     

1株脂肪酶产生菌的筛选鉴定及其脂肪酶基因的克隆表达

从武汉市郊蓖麻地土壤中分离到1株产脂肪酶菌株,结合形态观察和生理生化鉴定,扩增16S rDNA并测序,运用Blast比对构建了进化树,发现该菌与粘质沙雷氏菌(Serratia marcescens)的同源性高达99％,初步鉴定该菌属于沙雷氏菌属(Serratia),命名为Serratia sp.HS-L5.克隆了脂肪酶...     

Virtual substrates screening model of triacylglycerol lipase from <Emphasis Type="Italic">Bacillus thermocatenulanatus</Emphasis>

A reliable 3-D structure of Triacylglycerol lipase from Bacillus thermocatenulanatus was constructed by homology modeling. Under molecular dynamics simulation, it was refined and checked. The model was further used as a receptor to search binding sites and carry out flexible docking with a range of substrates, whose enzyme activities were already measured. By inputting a series of docking results, virtual substrates screening models were established and assessed. Monadic nonlinear solution demanded less data but was weak in fitting enzyme activity data with little difference; its mean absolute percentage error (MAPE) of regression was 0.67 and mean square error (MSE) was 1.73 U/mg. Both quadratic stepwise regression and BP neural network were good in regression and prediction; however, more data were required. In the cross-validation of 12 groups, overall MAPE of regression and prediction for the former were 0.18 and 0.49, while the latter was 0.55 and 0.36. MSE values for these two methods were 0.95 and 1.20 U/mg, respectively. Therefore, monadic nonlinear regression model can be used as a preliminary screening one; quadratic stepwise regression and BP neural network approach can be applied to precise screening.     

Application of ring-opening metathesis polymerization in study of polymer molecular weight-mediated catalytic properties of immobilized lipase

Recently, significant efforts have been devoted into the study of the effect of hydrophobic supports on the catalytic properties of immobilized lipases. It seems that immobilization lipases on hydrophobic supports is a simple and efficient method to improve the catalytic activity of lipases. In this study, the hydrophobic poly(N-propyl-norbornene-exo-2,3-dicarboximide)s with well-controlled molecular weight were synthesized by the living ring-opening metathesis polymerization, and the lipases from Pseudomonas sp. were then immobilized on these hydrophobic polymer supports through the physical adsorption. The immobilized lipases exhibited higher activity and enantioselectivity for the transesterification of 2-octanol than those of free lipases. Furthermore, we investigated the polymer molecular weight-mediated catalytic properties of immobilized lipases. It was found that the catalytic activity and E value of the immobilized lipases increased with the increase of the polymer molecular weight. At the polymeric molecular weight of about 40kDa, the highest E value (58 at 54.2% of conversion, enantiomeric excess = 99%) was reached. After the molecular weight of polymers getting higher than 40 kDa, catalytic activity and E value of the immobilized lipase decreased. Supported by the Stake Key Development Program of Basic Research of China (Grant No.2007CB808000) and National Natural Science Foundation of China (Grant Nos. 50773028, and 20803028).     

A new A4 amyloid mRNA contains a domain homologous to serine proteinase inhibitors

The amyloid proteins isolated from neuritic plaques and the cerebrovasculature of Alzheimer's disease are self-aggregating moieties termed A4 protein and beta-protein, respectively. A putative A4 amyloid precursor (herein termed A4(695] has been characterized by analysis of a human brain complementary DNA. We report here the sequence of a closely related amyloid cDNA, A4(751), distinguished from A4(695) by the presence of a 168 base-pair (bp) sequence which adds 57 amino acids to, and removes one residue from, the predicted A4(695) protein. The peptide predicted from this insert is very similar to the Kunitz family of serine proteinase inhibitors. The two A4-specific messenger RNAs are differentially expressed: in a limited survey, A4(751) mRNA appears to be ubiquitous, whereas A4(695) mRNA has a restricted pattern of expression which includes cells from neuronal tissue. These data may have significant implications for understanding amyloid deposition in Alzheimer's disease.     

Crystal structure of a retroviral protease proves relationship to aspartic protease family

Retroviral gag, pol and env gene products are translated as precursor polyproteins, which are cleaved by virus-encoded proteases to produce the mature proteins found in virions. On the basis of the conserved Asp-Thr/Ser-Gly sequence at the putative protease active sites, and other biochemical evidence, retroviral proteases have been predicted to be in the family of pepsin-like aspartic proteases. It has been suggested that aspartic proteases evolved from a smaller, dimeric ancestral protein, and a recent model of the human immunodeficiency virus (HIV) protease postulated that a symmetric dimer of this enzyme is equivalent to a pepsin-like aspartic protease. We have now determined the crystal structure of Rous sarcoma virus (RSV) protease at 3-A resolution and find it is dimeric and has a structure similar to aspartic proteases. This structure should provide a useful basis for the modelling of the structures of other retroviral proteases, such as that of HIV, and also for the rational design of protease inhibitors as potential antiviral drugs.     

Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein?

Calcium-dependent protease (calcium protease) is apparently involved in a variety of cellular processes. Here we have attempted to clarify the role and regulatory mechanism of calcium protease by analysing its structure. The complete primary structure of calcium protease (relative molecular mass (Mr) 80,000 (80K), 705 amino acids) was deduced from the nucleotide sequence of cloned complementary DNA. The protein contains four distinct domains, and we have observed a marked similarity between the second and fourth domains and the papain-like thiol proteases and calmodulin-like calcium-binding proteins, respectively. This finding suggests that calcium protease arose from the fusion of genes for proteins of completely different function and evolutionary origin. Further, it provides functional insight into cellular regulatory mechanisms mediated by Ca2+ through calcium-binding proteins.