猪苓糖苷水解酶家族基因及其差异表达

猪苓与蜜环菌建立共生关系时,猪苓菌丝会反侵染并消解蜜环菌菌索,以获取营养物质,糖苷水解酶是参与这一过程的主要酶类之一。本研究从猪苓转录数据库中获得糖苷水解酶家族基因42类、309个;其编码的糖苷水解酶蛋白含各类结构域344个,以糖苷水解酶结构域glyco＿hydro为主,共计35类173个。对猪苓糖苷水解酶进行的gene ontology (GO)功能注释结果表明,这些蛋白参与的生物学过程以物质代谢及分解过程为主,特别是多糖等大分子物质代谢;181个猪苓糖苷水解酶具有水解酶活性,这些水解酶活性呈多样性分布。与未被蜜环菌侵染的猪苓部位相比,43个糖苷水解酶基因在蜜环菌侵染的菌核部位中差异表达,编码包括glyco＿hydro＿48、cellulase和polysacc＿deac＿1等功能结构域,可能发挥水解几丁质、纤维素酶活性及免疫调节等活性,这为猪苓与蜜环菌互作关系的研究提供了候选基因及蛋白。     

纳米水解酶的研究进展

水解酶由至少200种单独的蛋白质组成,可催化一系列独特化学键的水解.但是天然酶的固有缺点,如易变性、成本高、制备费力和回收困难,极大地限制了它们的实际应用.为了克服这些缺点,研究人员长期以来致力于探索人工水解酶模拟物.自从2007年发现Fe₃O₄纳米颗粒可以作为过氧化物酶模拟物,关于纳米酶的研究不断涌现.与天然酶相比,纳米酶具有制备简单、可大规模生产、环境耐受性强、制备及储存成本低廉、可重复使用等优势.纳米水解酶是指具有水解酶活性的纳米材料,金属有机框架材料、碳基纳米材料和金纳米粒子等的水解酶活性均已被报道.近年来,纳米水解酶研究领域进入蓬勃发展期,然而至今尚未见关于纳米水解酶的综述.本文首先根据水解底物的不同对纳米水解酶进行分类并分别讨论其催化机理,之后对影响纳米水解酶活性的因素及纳米水解酶的应用进行总结,最后概述和讨论纳米水解酶的当前挑战和未来前景.     

S-腺苷高半胱氨酸水解酶的晶体结构及其催化机制

AdoHcy水解酶是一重要的广谱抗病毒药物靶标,对其结构,特别是三维空间结构的研究,有助于深入了解和阐述其功能,并为实现基于靶标结构的药物设计和筛选奠定基础。该文介绍近年来有关AdoHcy水解酶晶体结构的研究成果。     

瘤胃细菌GH48家族糖苷水解酶基因多样性

【目的】了解瘤胃细菌第48家族糖苷水解酶基因(GH48)多样性,为木质纤维素高效降解提供新的基因资源。【方法】通过基因序列比对,设计gh48的简并引物;同时提取两个瘤胃样品的总DNA和总RNA,并将总RNA逆转录成cDNA。以总DNA和cDNA为模板,通过PCR扩增分别建立克隆文库并对克隆文库进行测序;对所得序列进行out种类划分和聚类分析。【结果】本研究共得到了455条编码GH48家族蛋白的基因序列,核苷酸序列之间的相似性为58.65%-100%。对序列的进一步分析表明,89%可以作为区分其种类的界定标准。以此为依据确定所得到的基因序列分别编码66种不同的GH48家族蛋白,分别聚为5个相对独立的类群,其中新类群C中OTU65所代表的序列是cDNA克隆文库中的优势序列,分别占两个cDNA克隆文库的36.4%和19.5%。我们的结果揭示瘤胃细菌gh48基因具有丰富的多样性,同时,其中也存在优势表达的GH48家族蛋白。     

右旋糖酐-α-1,6键水解酶的家族、结构及其应用

右旋糖酐（dextran）水解酶种类繁多,其中右旋糖酐-α-1,6键水解酶（D-α-1,6 H）是主要的水解酶类.该类酶包括右旋糖酐酶（EC 3.2.1.11）、葡萄糖右旋糖酐酶（EC 3.2.1.70）、异麦芽糖右旋糖酐酶（EC 3.2.1.94）等,分属不同糖苷水解酶家族.D-α-1,6 H的结构和催化方式多样,分类和进化关系复杂,是糖苷水解酶催化机制研究和酶蛋白分子进化研究的好材料.D-α-1,6H及该类酶的催化产物在工业和医学中均有重要而广泛的应用.近年来对D-α-1,6H的理论和应用研究逐渐增加,但仍缺乏深入的系统性研究.本文对D-α-1,6H的家族、结构和功能进行分析,并对其在工业和医学中的最新应用研究作以总结.     

蜜环菌糖苷水解酶家族基因在菌索与菌丝间的差异表达分析

蜜环菌是一种兼性腐生和寄生的真菌,通过降解伴栽基质并为药用植物(天麻)或菌物(猪苓)提供营养物质,而糖苷水解酶是这一过程的主要酶类.本研究从蜜环菌Armillaria mellea 541菌株转录数据库中共获得糖苷水解酶家族基因170个,分布于39个亚家族.进一步分析发现,这些家族基因编码的糖苷水解酶家族蛋白(glyc...     

糖苷水解酶7家族蛋白在纤维素降解中作用的研究进展

糖苷水解酶7家族（glycoside hydrolase family, GH7）是一类来源于真菌的水解酶,作用于纤维素结晶区或不定形区的β-1,4 键,可用于高效降解纤维素转化为可发酵的糖。GH7的成员具有高度保守序列以及相似三维结构,其催化结构域是由多个loop区围绕反向平行的β 折叠形成的β 三明治结构。目前已有17个GH7成员的结晶结构得到解析,明确了酶的结构与催化功能之间的关联,对GH7的来源及分类、蛋白序列、结构特征与催化纤维素降解功能关系的研究进展进行阐述。     

腈水解酶在羧酸合成中的研究进展

有机羧酸是有机合成中的重要中间体,用腈水解酶催化有机腈实现有机羧酸的合成不仅具有反应条件温和、污染少和易处理等优点,而且更重要的是能实现一般化学法所不能达到的高度化学、区域和立体选择性。综述了腈水解酶的来源、特性和作用机理,介绍了腈水解酶在有机合成中的研究进展以及该酶在工业上的应用前景。     

腈水解酶的来源、结构、作用机制及其应用

综合报道了腈水解酶的来源、结构、作用机制及其工业应用。     

粘细菌产生的水解酶类研究进展

粘细菌隶属于δ变形菌纲(Deltaproteobacteria),是重要的药源微生物类群,但是其分离培养困难,严重限制了粘细菌资源的发掘和开发利用。粘细菌是微生物捕食者,通过产生丰富多样的胞外水解酶,如淀粉酶、蛋白酶、几丁质酶、纤维素酶、磷酸酶、蛋白酶等来裂解其他微生物或分解纤维素等作为营养物质来源。目前,粘细菌分离纯化技术主要是利用被捕食菌或纤维素诱导法。可以说,粘细菌胞外水解酶是研究其分离培养方法的物质基础。然而,目前研究者们对粘细菌产生的水解酶类关注较少。本文主要对粘细菌产生的水解酶种类、性质及其功能进行归纳总结,为今后粘细菌分离培养技术和开发利用等相关研究提供参考。     

Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1

Branching enzymes (BEs) catalyze the formation of branch points in glycogen and amylopectin by cleavage of α-1,4 glycosidic bonds and subsequent transfer to a new α-1,6 position. BEs generally belong to glycoside hydrolase family 13 (GH13); however TK1436, isolated from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, is the first GH57 member, which possesses BE activity. To date, the only BE structure that had been determined is a GH13-type from Escherichia coli. Herein, we have determined the crystal structure of TK1436 in the native state and in complex with glucose and substrate mimetics that permitted mapping of the substrate-binding channel and identification of key residues for glucanotransferase activity. Its structure encompasses a distorted (β/α)(7)-barrel juxtaposed to a C-terminal α-helical domain, which also participates in the formation of the active-site cleft. The active site comprises two acidic catalytic residues (Glu183 and Asp354), the polarizer His10, aromatic gate-keepers (Trp28, Trp270, Trp407, and Trp416) and the residue Tyr233, which is fully conserved among GH13- and GH57-type BEs. Despite TK1436 displaying a completely different fold and domain organization when compared to E. coli BE, they share the same structural determinants for BE activity. Structural comparison with AmyC, a GH57 α-amylase devoid of BE activity, revealed that the catalytic loop involved in substrate recognition and binding, is shortened in AmyC structure and it has been addressed as a key feature for its inability for glucanotransferase activity. The oligomerization has also been pointed out as a possible determinant for functional differentiation among GH57 members.     

Structure of a bacterial α-1,2-glucosidase defines mechanisms of hydrolysis and substrate specificity in GH65 family hydrolases

Glycoside hydrolase family 65 (GH65) comprises glycoside hydrolases (GHs) and glycoside phosphorylases (GPs) that act on α-glucosidic linkages in oligosaccharides. All previously reported bacterial GH65 enzymes are GPs, whereas all eukaryotic GH65 enzymes known are GHs. In addition, to date, no crystal structure of a GH65 GH has yet been reported. In this study, we use biochemical experiments and X-ray crystallography to examine the function and structure of a GH65 enzyme from Flavobacterium johnsoniae (FjGH65A) that shows low amino acid sequence homology to reported GH65 enzymes. We found that FjGH65A does not exhibit phosphorolytic activity, but it does hydrolyze kojibiose (α-1,2-glucobiose) and oligosaccharides containing a kojibiosyl moiety without requiring inorganic phosphate. In addition, stereochemical analysis demonstrated that FjGH65A catalyzes this hydrolytic reaction via an anomer-inverting mechanism. The three-dimensional structures of FjGH65A in native form and in complex with glucose were determined at resolutions of 1.54 and 1.40 Å resolutions, respectively. The overall structure of FjGH65A resembled those of other GH65 GPs, and the general acid catalyst Glu⁴⁷² was conserved. However, the amino acid sequence forming the phosphate-binding site typical of GH65 GPs was not conserved in FjGH65A. Moreover, FjGH65A had the general base catalyst Glu⁶¹⁶ instead, which is required to activate a nucleophilic water molecule. These results indicate that FjGH65A is an α-1,2-glucosidase and is the first bacterial GH found in the GH65 family.     

B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes

The crystal structure of the product of the Bacillus subtilis ykuD gene was solved by the multiwavelength anomalous dispersion (MAD) method and refined using data to 2.0 A resolution. The ykuD protein is a representative of a distinctly prokaryotic and ubiquitous family found among both pathogenic and nonpathogenic Gram-positive and Gram-negative bacteria. The deduced amino acid sequence reveals the presence of an N-terminal LysM domain, which occurs among enzymes involved in cell wall metabolism, and a novel, putative catalytic domain with a highly conserved His/Cys-containing motif of hitherto unknown structure. As the wild-type protein did not crystallize, a double mutant was designed (Lys117Ala/Gln118Ala) to reduce excess surface conformational entropy. As expected, the structure of the LysM domain is similar to the NMR structure reported for an analogous domain from Escherichia coli murein transglycosylase MltD. The molecular model also shows that the 112-residue-long C-terminal domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of the ykuD family may play an important role in cell wall biology.     

Phylogenetic analysis of family 6 glycoside hydrolases

Multiple sequence alignment separates members of glycoside hydrolase Family 6 into eight subfamilies: one of mainly actinobacterial endoglucanases (EGs), one of ascomycotal EGs, one of chytridiomycotal EGs and cellobiohydrolases (CBHs), one of actinobacterial and proteobacterial CBHs, one of chytridiomycotal CBHs, two of ascomycotal CBHs, and one of basidiomycotal CBHs. Each also has some proteins of unknown function. Multiple sequence alignment also extends to all of Family 6 the observation that lengths of loops that form the active-site tunnel in CBHs vary among subfamilies, and along with loop conformations, determine enzyme function.     

Structural and enzymatic characterization of NanS (YjhS), a 9-O-Acetyl N-acetylneuraminic acid esterase from Escherichia coli O157:H7

There is a high prevalence of sialic acid in a number of different organisms, resulting in there being a myriad of different enzymes that can exploit it as a fermentable carbon source. One such enzyme is NanS, a carbohydrate esterase that we show here deacetylates the 9 position of 9-O-sialic acid so that it can be readily transported into the cell for catabolism. Through structural studies, we show that NanS adopts a SGNH hydrolase fold. Although the backbone of the structure is similar to previously characterized family members, sequence comparisons indicate that this family can be further subdivided into two subfamilies with somewhat different fingerprints. NanS is the founding member of group II. Its catalytic center contains Ser19 and His301 but no Asp/Glu is present to form the classical catalytic triad. The contribution of Ser19 and His301 to catalysis was confirmed by mutagenesis. In addition to structural characterization, we have mapped the specificity of NanS using a battery of substrates.     

聚对苯二甲酸乙二醇酯水解酶研究进展

塑料自20世纪首次合成以来给人类生活带来了极大的便利。然而,塑料稳定的高分子结构导致了塑料废弃物的持续堆积,对生态环境和人类健康均造成严重威胁。聚对苯二甲酸乙二醇酯[poly(ethylene terephthalate),PET]是产量最高的一种聚酯类塑料,近年来PET水解酶的相关研究展现出生物酶法对塑料进行降解、回收的巨大潜力,也为塑料生物降解机制研究建立了参考范例。本文综述了不同微生物来源的PET水解酶及其PET降解能力,阐述了最具代表性的PET水解酶—IsPETase降解PET的催化机理,并总结了近年来通过酶工程改造而获得的高效降解酶,为未来的PET降解机制研究、PET高效降解酶的进一步挖掘和改造提供参考。     

Positive selection of three chitinase genes of the family 18 of glycoside hydrolases in mammals

The digestive enzyme chitinase degrades chitin, and is found in a wide range of organisms, from prokaryotes to eukaryotes. Although mammals cannot synthesize or assimilate chitin, several proteins of the glycoside hydrolase (GH) chitinase family GH18, including some with enzymatic activity, have recently been identified from mammalian genomes. Consequently, there is growing interest in molecular evolution of this family of proteins. Here we report on the use of maximum likelihood methods to test for evidence of positive selection in three genes of the chitinase family GH18, all of which are found in mammals. These focal genes are CHIA, CHIT1 and CHI3L1, which encode the chitinase proteins acidic mammalian chitinase, chitotriosidase and cartilage protein 39, respectively. The results of our analyses indicate that each of these genes has undergone independent selective pressure in their evolution. Additionally, we have found evidence of a signature of positive natural selection, with most sites identified as being subject to adaptive evolution located in the catalytic domain. Our results suggest that positive selection on these genes stems from their function in digestion and/or immunity.     

Study of the active site residues of a glycoside hydrolase family 8 xylanase

Site-directed mutagenesis and a comparative characterisation of the kinetic parameters, pH dependency of activity and thermal stability of mutant and wild-type enzymes have been used in association with crystallographic analysis to delineate the functions of several active site residues in a novel glycoside hydrolase family 8 xylanase. Each of the residues investigated plays an essential role in this enzyme: E78 as the general acid, D281 as the general base and in orientating the nucleophilic water molecule, Y203 in maintaining the position of the nucleophilic water molecule and in structural integrity and D144 in sugar ring distortion and transition state stabilization. Interestingly, although crystal structure analyses and the pH-activity profiles clearly identify the functions of E78 and D281, substitution of these residues with their amide derivatives results in only a 250-fold and 700-fold reduction in their apparent k(cat) values, respectively. This, in addition to the observation that the proposed general base is not conserved in all glycoside hydrolase family 8 enzymes, indicates that the mechanistic architecture in this family of inverting enzymes is more complex than is conventionally believed and points to a diversity in the identity of the mechanistically important residues as well as in the arrangement of the intricate microenvironment of the active site among members of this family.     

Kinetic relationships with processivity in Serratia marcescens family 18 glycoside hydrolases

In nature, recalcitrant polysaccharides such as chitin and cellulose are degraded by glycoside hydrolases (GH) that act synergistically through different modes of action including attack from reducing-end and nonreducing-end (exo-mode) and random (endo-mode) on single polysaccharide chains. Both modes can be combined with a processive mechanism where the GH remain bound to the polysaccharide to perform multiple catalytic steps before dissociation into the solution. In this work, we have determined association rate constants and their activation paramaters for three co-evolved GHs from Serratia marcescens (SmChiA, SmChiB, and SmChiC) with an oligomeric substrate. Interestingly, we observe a positive correlation between the association rate constants and processive ability for the GHs. Previously, a positive correlation has been observed between substrate binding affinity and processive ability. SmChiA with highest processive ability of the three GHs bind with a k_on of 11.5 ± 0.2 μM⁻¹s⁻¹, which is five-fold and 130-fold faster than SmChiB (less processive) and SmChiC (nonprocessive), respectively.