Ribonuclease P

The gene coding for the RNA subunit of ribonuclease P (RNase P) is essential in all free-living organisms. The RNA subunit, itself, is an enzyme and, from its evolutionary tree, we can infer that it is a very ancient molecule. The specificity of this enzyme is that it cleaves other RNA molecules at the junction of single-stranded and the 5' end of double-stranded regions of RNA. One can speculate that this molecule was very useful in an ancient world in cleaving long pieces of RNA, which must have contained hairpin regions in it, into shorter molecules with the capability of different functions from the longer parent. Today, the specificity of the enzyme can be used in designing drug therapies.     

多结构域酶的结构域进化关系

近年来随着生命科学新技术、新方法的涌现,酶蛋白结构和功能研究逐渐深入。具有多结构域的酶蛋白中各个结构域常具有独立的催化或结合底物的功能,在重组酶和组合生物合成研究中具有极大的研究和应用价值。这些结构域功能和组织方式的多样性,是研究分子进化的基础。对结构域进行进化分析对于研究多结构域酶的进化过程、功能相近酶之间的关系,以及对酶的分类鉴定等有重要意义。本文从结构域的重复性、结构域的水平基因转移和结构域的重组等方面出发,对多结构域酶中结构域之间进化关系的研究成果进行综述。     

An ensemble of theta class glutathione transferases with novel catalytic properties generated by stochastic recombination of fragments of two mammalian enzymes

The correlation between sequence diversity and enzymatic function was studied in a library of Theta class glutathione transferases (GSTs) obtained by stochastic recombination of fragments of cDNA encoding human GST T1-1 and rat GST T2-2. In all, 94 randomly picked clones were characterized with respect to sequence, expression level, and catalytic activity in the conjugation reactions between glutathione and six alternative electrophilic substrates. Out of these six different compounds, dichloromethane is a selective substrate for human GST T1-1, whereas 1-menaphthyl sulfate and 1-chloro-2,4-dinitrobenzene are substrates for rat GST T2-2. The other three substances serve as substrates for both enzymes. Through this broad characterization, we have identified enzyme variants that have acquired novel activity profiles that differ substantially from those of the original GSTs. In addition, the expression levels of many clones were improved in comparison to the parental enzyme. A library of mutants can thus display a distribution of properties from which highly divergent evolutionary pathways may emerge, resembling natural evolutionary processes. From the GST library, a clone was identified that, by the point mutation N49D in the rat GST T2-2 sequence, has a 1700% increased activity with 1-menaphthyl sulfate and a 60% decreased activity with 4-nitrophenethyl bromide. Through the N49D mutation, the ratio of these activities has thus been altered 40-fold. An extensive characterization of a population of stochastically mutated enzymes can accordingly be used to find variants with novel substrate-activity profiles and altered catalytic properties. Recursive recombination of selected sequences displaying optimized properties is a strategy for the engineering of proteins for medical and biochemical applications. Such sequential design is combinatorial protein chemistry based on remodeling of existing structural scaffolds and has similarities to evolutionary processes in nature.     

How does an enzyme evolved in vitro compare to naturally occurring homologs possessing the targeted function? Tyrosine aminotransferase from aspartate aminotransferase

Aspartate aminotransferase (AATase) and tyrosine aminotransferase (TATase) are Escherichia coli paralogs that share 43% sequence identity. A plausible model posits that TATase arose from a duplication of an ancestral AATase-like enzyme. Directed evolution of AATase to an enzyme having TATase activity was undertaken in order to compare the evolved AATase variants with homologous TATases. Eight rounds of DNA shuffling and in vivo selection followed by a backcross with WT AATase produced enzymes that exhibited 100-270-fold increases in k(cat)/K(m)(Phe) and had as much as 11% of the tyrosine aminotransferase activity of WT E.coli TATase. Amino acid substitutions in 11 clones from rounds 7 and 8 were compared with conserved residues in AATases and TATases. The findings are conveniently and compactly illustrated by the use of Venn diagrams and set theory notation. A statistically significant (0.001or=75% identical) in AATases and variable (<75% identical) in TATases. Very few mutations occur in the intersection (set AAT intersection TAT) of amino acid residues that are conserved in both enzyme types. Seven mutations from set AAT-TAT were combined by site-directed mutagenesis to give a construct that is 60% as active as the best round 8 enzyme, which has 13 amino acid replacements. The Venn diagrams may provide a generally useful tool to highlight the most important specificity determinants for rational redesign. Amino acid replacements were mapped onto the crystal structure of a hydrocinnamate complex of a designed TATase. Five of the seven positions most frequently substituted in the evolved clones are within 15 A of the phenyl side-chain, but only six of the 48 positions that were mutated once or twice are within that radius. Context dependence, neutral mutations, different selective pressures, and stochastic components provide explanations for the observation that many of the substitutions found in the directly evolved enzymes differ from the corresponding amino acids found in the modern natural TATases.     

L-delta-(alpha-Aminoadipoyl)-L-cysteine-D-valine synthetase: production of dipeptides containing valine residue at its C-terminus

L-delta-(alpha-Aminoadipoyl)-L-cysteine-D-valine synthetase (ACVS) has been recently studied as a model enzyme for peptide synthetases. It was found that in the absence of alpha-aminoadipic acid but in the presence of several cysteine analogues it was incorporated into several analogue dipeptides upon incubation of the potential cysteine analogues with ACVS. [(14)C]Cysteine was incorporated into the[(14)C]cysteinyl-valine analogue dipeptides. Notably, [(14)C]valine incorporation in the presence of N-acylated cysteine analogues was observed. The alpha-aminoadipic acid activation site is influential, inhibitory or promotive, on the production of these putative dipeptide products. The production of dipeptide analogues, containing valine or analogues at the C-terminus, leads to the speculation that the biosynthetic direction of ACV could be from the C-terminus to the N-terminus.     

Arginine decarboxylase is a component activity of the multifunctional enzyme putrescine synthase in cucumber seedlings

A homogenous PreParation of Putrescine synthase, the versatile multifunctional enzyme involved in agmatine →Putrescine conversion inCucumis sativus was found to catalyze enzymatic decarboxylation of arginine also. Similarly, the Purified arginine decarboxylase mediated the comPonent as well as the comPlete set of couPled reactions harboured by Putrescine synthase. Both the enzyme PreParations exhibited identical electroPhoretic and chromatograPhic behaviour and were immunologically indistinguishable. All the enzymic activities are stabilized concurrently by feeding arginine to the intact seedlings. Therefore, it is concluded that the multifunctional Putrescine synthase inCucumis sativus seedlings also harbours arginine decarboxylase activity unlike its counterPart inLathyrus sativus.     

L-氨基酸氧化酶的结构、底物谱、家族进化及应用研究进展

L-氨基酸氧化酶(LAAO)是一类生物体内参与氨基酸氧化代谢的重要氧化还原酶,能够以氧分子为电子受体催化L-氨基酸氧化脱氨,生成相应的酮酸、氨(NH₃)和过氧化氢(H₂O₂).近期发现有些LAAO能够专一性识别特定氨基酸,而不受其他种类氨基酸的干扰,因而在手性胺类化合物拆分、α-酮酸生物合成、临床样本、食品及氨基酸发酵过程中氨基酸含量检测等领域都发挥着重要作用.本文重点综述目前研究报道的底物专一性LAAO,总结并比较这些酶的酶学性质、结构功能,以及家族进化规律等,并进一步讨论这些酶在生物催化及氨基酸检测中的应用.本综述将为底物特异性LAAO的分子机制研究及产业应用研究提供重要的素材和指导.     

过氧物酶体多功能酶2中固醇载体蛋白2结构域的功能

过氧物酶体多功能酶 (包括Ⅰ型、Ⅱ型 ,简称MFE1、MFE2 )在哺乳类动物的脂类代谢中发挥其重要作用 .MFE1具有 2 烯酰CoA水合酶 1和 (3S) 羟脂酰CoA脱氢酶的活性 ,而MFE2具有 2 烯酰CoA水合酶 2和 (3R) 羟脂酰CoA脱氢酶的活性 ,两者均催化烯酰CoA在过氧物酶体β 氧化途径中的第 2步和第 3步反应 .MFE1与MFE2的氨基酸序列不具有任何同源性 ,并且它们的底物特异性也不相同 .比较哺乳类MFE1及酵母MFE2发现 ,哺乳类MFE2羧基末端带有由 12 5个残基组成的固醇载体蛋白 2 (简称SCP2 )结构域 ,其功能是未知的 .为了研究SCP2结构域在MFE2中的功能 ,将人MFE2、MFE2ΔSCP2 (删除MFE2中的SCP2 )、脱氢酶结构域、水合酶结构域以及SCP2结构域分别在E .coli中表达 ,并经纯化得到相应的重组蛋白 .通过测定 2 烯酰CoA水合酶 2和 (3R) 羟脂酰CoA脱氢酶对烯酰CoA的催化活性发现 ,带有SCP2结构域的重组蛋白的酶活力及催化效率高于删除SCP2的突变体蛋白 .实验结果表明 ,SCP2结构域可能通过增强MFE2与脂酰CoA的结合力 ,使得MFE2发挥最有效的催化活力     

Spruce budworm elastase precipitates Bacillus thuringiensis δ-endotoxin by specifically recognizing the C-terminal region

A gut juice protein from Choristoneura fumiferana (spruce budworm) larvae that precipitates certain δ-endotoxins shows a unique specificity for the C-terminal amino acid sequence. Using homolog scanning mutants, we have identified a contiguous region of the Cry1Aa toxin which interacts with the 75-kDa toxin precipitating protein (TPP-75)¹ resulting in precipitation. The contiguous region from Cry1Aa can be transferred to Cry1Ac and results in an identical precipitation reaction. The precipitation reaction occurs rapidly and is unique in that the ratio of precipitating protein to toxin is low (estimated at 0.01), unlike antibody–antigen reactions which exhibit mole ratios close to 1. TPP-75 has been characterized as an elastase-like serine protease. We have taken advantage of this serine protease character and incorporated a radiolabel using an irreversible inhibitor. The radiolabel has allowed us to show the coincidence of the catalytically-inhibited TPP-75 with the toxin in a blotting assay and to follow the degradation of TPP-75 during storage. TPP-75 represents the first evidence that gut juice proteins may selectively attenuate the activity of δ-endotoxins, prior to binding to putative receptors on susceptible cells. TPP-75 should be evaluated as a possible resistance mechanism for those larvae that do not exhibit a receptor-based resistance.