生物工程学报  2025, Vol. 41 Issue (1): 131-147
http://dx.doi.org/10.13345/j.cjb.240265
中国科学院微生物研究所、中国微生物学会主办
0

文章信息

刁红娟, 林鑫凡, 郑仁朝, 郑裕国
DIAO Hongjuan, LIN Xinfan, ZHENG Renchao, ZHENG Yuguo
腈水解酶的催化混乱性研究进展
Advances in the catalytic promiscuity of nitrilases
生物工程学报, 2025, 41(1): 131-147
Chinese Journal of Biotechnology, 2025, 41(1): 131-147
CSTR: 32114.14.j.cjb.240265
DOI: 10.13345/j.cjb.240265

文章历史

Received: March 27, 2024
Accepted: May 7, 2024
腈水解酶的催化混乱性研究进展
刁红娟 , 林鑫凡 , 郑仁朝 , 郑裕国     
浙江工业大学 生物工程学院, 浙江 杭州 310014
摘要:腈水解酶作为一种重要的生物催化剂广泛应用于重要医药中间体的合成,它能高效地将腈基转化为酸和氨,其反应具有温和、绿色环保等优点。腈水解酶不仅具有催化腈生成对应羧酸产物的水解活性,即表现出催化专一性,还兼具催化腈生成酰胺的水合活力,即表现出催化混乱性。腈水解酶的催化混乱性具有两面性:酰胺副产物的存在增加了后续羧酸产物分离纯化的难度和成本;但若能精准调控腈水解酶的催化反应路径实现酶功能的重塑,可以拓宽腈水解酶生物催化的反应类型,为高值酰胺类化合物的生物合成提供新思路和工艺,这对人工酶的创制及生物催化均具有重要意义。本文结合近年来相关的研究成果,综述了当前腈水解酶催化混乱性的研究进展,并从腈水解酶的进化起源、催化结构域以及催化机理等方面,探讨可能影响腈水解酶催化混乱性关键调控因子,为腈水解酶在生物催化领域上的应用提供了借鉴和参考。
关键词腈水解酶    催化混乱性    酶催化机理    生物催化    
Advances in the catalytic promiscuity of nitrilases
DIAO Hongjuan , LIN Xinfan , ZHENG Renchao , ZHENG Yuguo     
College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
Abstract: As important biocatalysts, nitrilases can efficiently convert nitrile groups into acids and ammonia in a mild and eco-friendly manner, being widely used in the synthesis of important pharmaceutical intermediates. Early studies reported that nitrilases only had the hydrolysis activity of catalyzing the formation of corresponding carboxylic acid products from nitriles, showing catalytic specificity. However, recent studies have shown that some nitrilases exhibit the hydration activity for catalyzing the formation of amides from nitriles, showing catalytic promiscuity. The catalytic promiscuity of nitrilases has dual effects. On the one hand, the presence of amide by-products increases the difficulties and costs of subsequent separation and purification of carboxylic acid products. On the other hand, however, if the catalytic reaction pathways of nitrilases can be precisely regulated to reshape enzyme functions, the reactions catalyzed by nitrilases can be broadened to provide new ideas for the biosynthesis of high-value amides, which is crucial for the development of artificial enzymes and biocatalysis. This review summarized the research progress in the catalytic promiscuity of nitrilases and discussed the key regulatory factors that may affect the catalytic promiscuity of nitrilases from the evolutionary origin, catalytic domains, and catalytic mechanisms, hoping to provide reference and inspiration for the application of nitrilases in biocatalysis.
Keywords: nitrilase    catalytic promiscuity    catalytic mechanisms of enzymes    biocatalysis    

传统观点认为,酶作为生物催化剂高效专一催化一种反应,即具有严格的催化特异性和专一性(enzyme specificity)。然而,近年来研究发现一些酶还表现出混乱性(enzyme promiscuity)[1-2],也称为杂泛性、宽泛性或多功能性。酶的混乱性可以进一步细分为3类(图 1),分别为条件混乱性(condition promiscuity)、底物混乱性(substrate promiscuity)、催化混乱性(catalytic promiscuity)[3-5]。条件混乱性表现为酶能在不同于天然反应条件下(如无水介质、极端温度或pH值等)进行催化反应,比如脂肪酶在水溶液和有机溶剂中均能催化酯类底物发生反应[6]。底物混乱性表现为酶具有较宽松的底物选择性,酶可以催化非天然底物历经天然底物相同的催化路径发生反应,比如甲烷单加氧酶除甲烷外还可羟基化150种底物[7]。而酶的催化混乱性主要指酶在发挥其本身的催化功能外,还能够催化不同于其“天然”的化学反应,经历不同的过渡态或者中间体生成相对应的产物[3-4, 8-11]

图 1 酶的条件混乱性、底物混乱性以及催化混乱性 Fig. 1 Schematic diagram of conditional, substrate and catalytic promiscuity of enzymes.

酶的催化混乱性被证实在自然界普遍存在,比如烟草来源的马兜铃烯环化酶(5-epi-aristolochene synthase, TEAS)可催化法尼基焦磷酸(farnesyl pyrophosphate, FPP)生成多种倍半萜天然产物[12-13]。来自于酵母的丙酮酸脱羧酶不仅能催化丙酮酸发生脱羧反应,还能催化乙醛和苯甲醛形成R-苯乙酰甲醇,表现出裂解酶活性[14]。借助蛋白质工程等技术对具有催化混乱性的天然酶进行设计改造,可以拓宽其生物催化的反应类型[3, 15],实现一酶多用或者老酶新用,在酶工程及生物催化领域具有重要意义[16-19]。比如,Yang等[20]报道了一种来自海洋细菌的脯氨酸二肽酶同时具有水解对氧磷的活性,通过定点饱和突变和组合突变将天然肽酶进化为对氧磷水解酶,为有机磷类污染物提供了微生物降解的高效催化剂。此外,Farwell等[21]和Coelho等[22]通过定向进化策略实现了工程化P450氧化酶烯烃环氧化反应外的氮杂环丙烷化和环丙烷化等非天然反应类型。

腈水解酶(nitrilase, EC 3.5.5.1)可催化腈类化合物生成相应的羧酸和氨,其催化过程具有反应条件温和、催化速率高效、绿色环保且环境友好等优势,是生物催化领域中重要的催化剂之一,受到学术界和工业界广泛的关注[23-24]。1964年,Thimann等[25]从大麦叶中首次发现了腈水解酶,该酶能够催化3-吲哚乙腈产生吲哚-3-乙酸。迄今为止,腈水解酶在环保[26]、医药[27]和化工[24]等领域均发挥着重要作用,比如腈水解酶催化烟酸和扁桃酸的生产,这充分体现了腈水解酶的应用潜力,因此对于腈水解酶的研究一直是科研和工业界的热点课题[28-29]

一般认为,腈水解酶催化腈类化合物仅能得到对应的羧酸产物,但研究发现一些腈水解酶(尤其是植物来源),同时表现出水合活力生成酰胺产物,即表现出催化混乱性(图 2)[30-31]。腈水解酶的催化混乱性如一把双刃剑,一方面为高值酰胺类化合物的生物合成提供新思路和工艺;另一方面水合途径的存在不仅会影响目标羧酸产物的收率,同时酰胺副产物的存在也增加了后续产物分离纯化的难度和成本。但由于缺乏对腈水解酶催化机制以及关键影响因子的认识,目前很难精准地调控腈水解酶催化反应方向,这无疑限制了腈水解酶的开发和工业应用。针对上述问题,本文对腈水解酶的催化混乱性潜在的进化起源、催化结构域以及催化机理等方面进行了综述,探讨可能影响腈水解酶催化混乱性关键调控因子,并结合近年来与其相关的研究实例,总结当前腈水解酶催化混乱性的研究进展,以期为创制优良工业属性的腈水解酶提供借鉴和参考。

图 2 腈水解酶的催化杂泛性示意图 Fig. 2 Schematic diagram of catalytic promiscuity of the nitrilase.
1 进化起源分析

腈水解酶在自然界中分布广泛,在植物、细菌和真菌等生物中都有发现。整理了文献报道的具有催化混乱性的腈水解酶(表 1),并列出了菌种来源、酶的命名、催化底物、产物中酰胺占比和参考文献出处,需要注意的是,酰胺与羧酸的比例可能会受到实验条件,如温度、pH或其他环境因素影响。多数情况下,自然界存在的天然腈水解酶水合活力不高,其产物中酰胺占比较低,因此在之前研究中常常被忽视[53]。直到近年来一些较高水合活力的腈水解酶被报道,研究人员开始重点关注腈水解酶的催化混乱性。Zhang等[31]筛选到一株来源于草根围副伯克霍尔德氏菌(Paraburkholderia graminis) DSM 17151的腈水解酶,该酶能催化扁桃腈生成约40%的扁桃酰胺。Piotrowski等[30]发现来自植物拟南芥(Arabidopsis thaliana)的腈水解酶催化底物β-氰基-L-丙氨酸分别生成了天冬氨酸及天冬酰胺,且酰胺的占比高达60%以上。根据所催化的底物结构特征,可以将腈水解酶大致分为[54]芳香族腈水解酶(aromatic nitrilase)、脂肪族腈水解酶(aliphatic nitrilase)、芳基乙腈酶(arylacetonitrilases)。不过也有一些腈水解酶具有较广的底物谱,如来源于A. thaliana的腈水解酶AtNit1可催化脂肪族和芳香族腈类。

为了进一步挖掘不同来源的催化混乱性腈水解酶之间的进化关系,从UniPort蛋白数据库中下载了表 1中腈水解酶的蛋白序列信息,进行多序列比对和进化关系分析,分别借助MOE软件[55]进行序列一致性比较并使用MEGA 11软件[56]进行系统进化树构建。从酶的蛋白序列之间一致性分析结果可以看出(图 3),植物来源的腈水解酶之间相似度大于70%,具有高同源性(深蓝色区域),其他物种之间的腈水解酶同源性相对较低(红色区域)。令人感兴趣的是,来源于大豆根瘤菌(Bradyrhizobium japonicum) USDA110和假单胞菌(Pseudomonas sp.) UW4的腈水解酶与植物来源的腈水解酶之间的序列相似度较高(浅蓝色区域),推测其进化关系上也是如此。进一步的进化关系分析发现(图 4),细菌来源的BrjNIT和PsNIT腈水解酶表现出特殊的进化起源,并不是和其他细菌腈水解酶位于同一进化分支,推测是和植物来源的腈水解酶由同一祖先酶共同进化而来。

表 1 文献中报道的催化混乱性腈水解酶 Table 1 The catalytic promiscuity of the nitrilases reported in the literature
Class Organism Substrate Amide ratio (%) References
Plant Arabidopsis thaliana NIT1 (AtNIT1) 2-fluorobenzyl cyanide 70−85 [32-33]
2-fluoro-2-(3-methylphenyl) ethanenitrile
2-fluoro-2-(4-methylphenyl) ethanenitrile
2-fluoro-2-(4-nitrophenyl) ethanenitrile
2-fluoro-2-(3-methoxyphenyl) ethanenitrile
Fumaronitrile 93−95 [33]
3-nitroacrylonitrile
2-butenenitrile ≤5 [33-35]
3-methoxyacrylonitrile
α-fluorobutyronitrile
2-phenylacetonitrile
2-isobutyl-succinonitrile
Arabidopsis thaliana NIT4 (AtNIT4) β-cyano-L-alanine About 60 [30]
Arabis alpina (AaNIT) Isobutylsuccinonitrile About 3 [34-35]
Phenylacetonitrile
Brassica rapa (BrNIT) Isobutylsuccinonitrile 10−15
Phenylacetonitrile
Mandelonitrile 62
Brassica oleracea (BoNIT) Mandelonitrile 45 [34]
Phenylacetonitrile 3
Camelina sativa (CsNIT) Mandelonitrile 61
Phenylacetonitrile 17
Capsella rubella (CrNIT) Mandelonitrile 61
Phenylacetonitrile 18
Eutrema salsugineum (EsNIT) Mandelonitrile 13
Phenylacetonitrile 1
Oryza sativa (OsNIT) Mandelonitrile 72
Phenylacetonitrile 49
Nicotiana tabacum TNIT4 (NtNIT4) β-cyano-L-alanine About 50 [30]
Zea mays NIT2 (ZmNIT2) Benzyl cyanide ≤10 [36]
1, 4-dicyanobutane
Mandelonitrile
n-butyronitrile 19−40
Valeronitrile
Hexanenitrile
Heptanenitrile
β-hydroxynitrile series 63−88
Bacteria Alcaligenes faecalis ATCC 8750 (AlfNIT) Mandelonitrile
2-phenylpropionitrile
< 1 [37]
Acidovorax facilis 72W (AcfNIT-72W) 2-cyanopyridine < 1 [38]
Acidovorax facilis (AcfNIT) 2-chloronicotinonitrile 54 [39]
Bradyrhizobium japonicum strain USDA110 (BrjNIT) 3-aminopropionitrile 23 [40]
Pseudomonas fluorescens EBC191 (PfNIT) 2-(methoxy)-mandelonitrile < 5 [37, 41-46]
2-phenylacetonitrile
2-phenylpropionitrile
(R)-phenylglycinenitrile
(S)-mandelonitrile 10−50 [41-42]
(R)-mandelonitrile
(S)-phenylglycinenitrile
mandelonitrile
(R)-O-acetylmandelonitrile
(R)-2-acetoxy-2-phenylacetonitrile
O-acetylmandelonitrile
(S)-2-acetoxy-2-phenylacetonitrile 60−90 [42]
2-chloro-2-phenylacetonitrile
Paraburkholderia graminis DSM 17151 (PgNIT-17151) Mandelonitrile About 40 [31]
Paraburkholderia graminis (PgNIT) 2-chloronicotinonitrile About 30 [39, 47]
Pseudomonas sp. UW4 (PsNIT) Indole-3-acetonitrile About 81 [48]
Rhodococcus ATCC 39484 (RhNIT-39484) Phenylacetonitrile 2 [49]
Rhodococcus zopfii (RhzNIT) 2-chloronicotinonitrile 88 [39]
Synechocystis sp. PCC 6803 (SsNIT) 2-cyanopyridine 2 [50]
Fungi Gibberella intermedia CA3-1 (GiNIT) 3-cyanopyridine < 5 [51]
Neurospora crassa OR74A (NcNIT) Mandelonitrile 40 [52]
图 3 不同来源腈水解酶之间的蛋白序列一致性对比结果 Fig. 3 Comparative results of protein sequence identity between nitrilases from different sources. Full name of the enzyme name abbreviations in the figure is shown in Table 1. Numerical value represents the similarity of protein sequence. 图酶名称缩写的全称见表 1。数值代表蛋白序列的相似度。
图 4 植物、细菌和真菌来源的腈水解酶的系统进化树 Fig. 4 Phylogenetic tree for nitrilases in bacteria, fungi and plant.
2 催化结构域分析

为了进一步研究腈水解酶功能和结构之间的构效关系,需要对腈水解酶的结构进行解析。研究人员通过X射线晶体学和核磁共振等结构生物学方法解析了酶的三维结构[57-58],收集了目前RCSB PDB数据库已收录的腈水解酶晶体的PDB ID号、来源、基因、分辨率等信息(表 2)。腈水解酶一般以同源二聚体或者多聚体的形式存在,以拟南芥腈水解酶的晶体结构(图 5)为例,其存在形式为同源十二聚体,最小重复单元为四聚体,并且每个单体具有典型的αββα三明治结构特征。催化活性中心具有高度保守的催化三联体半胱氨酸-谷氨酸-赖氨酸(Cys-Glu-Lys),其在腈水解酶发挥催化功能中扮演重要的角色[37],Cys作为亲核试剂,Lys及Glu一般被认为起到稳定反应中间体的作用,此外Glu也作为广义碱,夺取半胱氨酸的质子以活化半胱氨酸。另外,研究表明多聚体相互作用的界面残基(“A” “C” surface)也会影响酶的活性和催化特性[34]。Park等[59]将来源于敏捷食酸菌(Acidovorax facilis) ZJB09122腈水解酶的“A”界面上第201位点苏氨酸替换为苯丙氨酸,可增强底物在蛋白口袋中的稳定性;同时发现将“C”界面的第339和343位点的谷氨酸替换为正电性残基赖氨酸,有利于增强蛋白-蛋白的相互作用;最终获得了45 ℃下的半衰期延长了约14倍的最佳突变体T201F/Q339K/Q343K。

表 2 RCSB PDB数据库收录的腈水解酶基本结构信息 Table 2 Basic structure information of nitrilases in the RCSB PDB database
PDB entry Organism Gene names Resolution (Å) Chains Sequence length (bp) Released (year)
6ZBY Pseudomonas fluorescens nitA 3.10 Homo 12-mer 350 2021
6I00 Arabidopsis thaliana NIT4 3.40 Homo 12-mer 361 2019
6I5T Arabidopsis thaliana NIT4 3.90 Homo 6-mer 361 2019
6I5U Arabidopsis thaliana NIT4 3.90 Homo 6-mer 361 2019
3WUY Syechocystis sp. PCC 6803 merR 3.10 Homo 2-mer 349 2014
3IVZ Pyrococcus abyssi GE5 PAB1449 1.57 Homo 2-mer 262 2010
3KI8 Pyrococcus abyssi GE5 PAB1449 1.60 Homo 2-mer 262 2010
3IW3 Pyrococcus abyssi GE5 PAB1449 1.80 Homo 2-mer 262 2010
3KLC Pyrococcus abyssi GE5 PAB1449 1.76 Homo 2-mer 262 2010
图 5 拟南芥腈水解酶(PDB ID:6I00)的多聚体结构和催化三联体示意图 Fig. 5 Schematic diagram of the multimeric structure and catalytic triad of Arabidopsis thaliana nitrilase (PDB ID: 6I00).

相对于已报道的腈水解酶序列,目前解析的腈水解酶晶体数量仍很少,且腈水解酶与底物的共晶复合物结构尚未解析出来。随着计算生物学技术的快速发展,可借助计算工具构建蛋白质三维结构,分子对接和分子动力学模拟等[34, 38-39, 47, 50, 57, 60]计算手段获得底物和酶的复合物结构模型。基于蛋白质三维结构信息,锚定要改造的候选区域及关键氨基酸位点,通过定点突变等手段获得催化性能更优的人工改造酶。前期本课题组[34]对水稻(Oryza sativa)来源腈水解酶(OsNIT)的催化混乱性进行了深入研究,通过获得合理的复合物模型指导天然OsNIT酶的分子改造,实现对催化反应路径的双向调控。OsNIT酶的晶体结构尚未被解析出来,借助AlphaFold2工具构建了OsNIT酶的空蛋白结构。然后采用MOE软件将底物苯乙腈对接到蛋白活性空腔,获得多个候选的复合物初始模型。由于分子对接得到的是静态结构,为了模拟蛋白在生理状态下动态变化过程,借助分子动力学模拟软件AMBER对初始对接模型进行30 ns时长的动态弛豫。通过对MD模拟轨迹进行聚类分析获得了代表性结构(图 6),并标注了影响酶的催化混乱性的区域如活性口袋、底物进出通道以及“A/C”界面(图 6A),通过对底物的结合特征分析(图 6B),可以看到底物的氰基C原子与催化三联体的Cys196的S原子之间的距离为3.2 Å,Thr220通过氢键作用进一步固定Cys196,此时复合物处于可发生催化反应的“预反应态”(near-attack state)。催化三联体中的Glu71可发挥催化碱的作用,接受碳正中间体的质子氢从而终止催化反应。催化三联体中的Lys163与底物的氰基N原子形成氢键作用从而固定底物的结合姿势。此外,在催化三联体相邻的区域存在1个带负电的Glu169,其负电性可以维持Lys163处于质子化状态。Trp197的芳香侧链与底物苯乙腈形成π-π堆积作用力,对于维持反应构象具有重要的意义。在催化三联体空间相邻区域的Ile136和Asn246,通过空间立体位阻分别固定Cys196和Glu71。对246、136位残基突变调控关键距离从而改变产物中酰胺的占比,最终获得了2株选择性催化生成主产物羧酸(98.49%)的三突变体和选择性催化生成酰胺(96.36%)的六突变体。

图 6 苯乙腈-OsNIT复合物结构中的关键催化域(A)及底物在蛋白活性口袋中的结合特征分析(B) Fig. 6 The key catalytic domains in the phenylacetonitrile-OsNIT complex structure (A) and analysis of substrate binding pose in the protein active pocket (B).
3 腈水解酶催化混乱性的机理研究

腈水解酶的催化活性位点含有高度保守的催化三联体半胱氨酸-谷氨酸-赖氨酸(Cys-Glu-Lys)[23, 61],其中Cys和Glu起关键作用,直接参与催化反应,虽然Lys不直接参与催化过程,但在维持底物在活性口袋中的结合模式以及稳定催化过程中形成的四面体中间体起到了非常重要的作用[62]。腈水解酶虽然具有水解酶超家族经典的催化三联体结构特征,但目前尚未在腈水解酶中发现特定氧阴离子口袋(oxyanion pocket)的存在。其他水解酶的催化三联体中充当亲核试剂的残基多为Ser或者Thr,而腈水解酶是由半胱氨酸Cys作为亲核试剂。已知Cys的pKa数值约为8,Ser和Thr的pKa数值约为13,因此生理状态下(pH 7),Ser和Thr在酶发生催化反应前均处于质子化状态,相反Cys能够以质子化和去质子化状态交替存在,这说明在催化反应前腈水解酶催化三联体中Cys的活化可能会自发进行,表明腈水解酶的催化机制可能与其他水解酶存在差异。

腈水解酶同时产生羧酸和酰胺(催化混乱)的催化机理虽然是研究者的关注重点之一,但由于目前腈水解酶的晶体结构解析较为匮乏,且天然底物腈化合物与腈水解酶结合的复合物晶体尚未见报道,所以腈水解酶的催化机制仍处于研究初期[34, 38, 50, 62-66]。目前相对被认可的一种腈水解酶催化机理假说如图 7所示,底物进入活性位点后,催化三联体之一的Cys残基上的巯基(−SH)作为亲核试剂进攻底物氰基(−CN) α-碳原子,形成硫代亚胺-酶中间体(中间体Ⅰ),接着1分子水加成到中间体Ⅰ得到1个四面体中间体(中间体Ⅱ);从中间体Ⅱ开始发生分歧,通过2种路径反应得到产物:在路径A中,通过水解途径(实线箭头)质子化末端的−NH2基团,得到羧酸产物和氨;而路径B中,中间体Ⅱ发生硫醇消除形成酰胺产物,这步反应称为水合反应途径(虚线箭头)。

图 7 腈水解酶催化混乱性的催化机理假说 Fig. 7 Catalytic mechanism hypothesis of nitrilase catalytic promiscuity.

根据上述所推测腈水解酶催化混乱性的机制,底物氰基N原子与催化三联体Glu羧基O原子之间的距离(氮氧距离DNO)和催化三联体Cys巯基S原子与Glu羧基O原子之间的距离(硫氧距离DSO),可能会影响腈水解酶催化混乱性的程度。当DNO比DSO小,即DSO−DNO > 0 Å,四面体中间体Ⅱ的氨基更容易质子化,此时路径A (水解途径)为主路径,羧酸为主产物;反之即DSO−DNO < 0 Å,则水合途径占主导,产物中酰胺的占比更高。Jiang等[50]通过计算模拟构建了中间体Ⅱ并监测了MD模拟过程中DSO和DNO的差值(DSO−DNO),发现野生型腈水解酶的差值约1.1 Å,仅产生少量的酰胺(占比2.1%);突变体F193A、F193D和F193N差值为−0.4 Å、−0.6 Å和−1.1 Å,分别产生了42%、66.2%和73.4%的酰胺;突变体F193Y和F193K的差值都大于0 (分别是0.6 Å和1.4 Å),其产物分布类似于野生型酶,都只产生少量酰胺。A. facilis 72W来源的野生型腈水解酶催化2-氰基吡啶产生的酰胺/羧酸为0.4,突变体W188M产物中酰胺/羧酸高达78.3。Wang等[38]分别比较了野生型酶和突变体中DSO−DNO差值,在野生型酶中DSO−DNO=0.3 Å,突变体W188M中DSO−DNO=−1.4 Å,因此突变体W188M中酰胺为主产物。Tang等[34]的研究也有类似的结果,水稻来源的腈水解酶催化苯乙腈底物时(图 8),Asn246和Ile136通过空间立体位阻固定Cys196和Glu71,突变246、136残基可以调控催化三联体与底物氰基间的关键距离,进而影响产物的形成。Asn246突变为侧链较小的Val,使得Cys196活动的空间变大并使其与Glu71的距离变大。同时第2个水分子及时传递至反应位点,通过路径A生成主产物苯乙酸;Ile136突变为Gln,空间位阻效应使Glu71向蛋白口袋下方移动,缩短了其与Cys196间的距离,经路径B生成主产物苯乙酰胺。

图 8 水稻来源的腈水解酶催化混乱性调控机制 Fig. 8 The catalytic promiscuity mechanism of nitrilase derived from Oryza sativa.
4 腈水解酶催化混乱性的影响因素研究

酶催化反应条件变化如pH、温度等会影响腈水解酶催化混乱性。Rustler等[67]用荧光假单胞菌(Pseudomonas fluorescens) EBC191来源的腈水解酶进行催化外消旋扁桃腈底物,发现在pH等于5时产生的扁桃酰胺含量最低,随着pH值的升高,产物中酰胺的占比逐渐增加。Effenberger等[32]使用A. thaliana来源的腈水解酶催化2-氟-2-苯基乙腈,当温度为7 ℃、pH 9时,产物中酰胺占比达到84%,而温度升到30 ℃时酰胺占比只有71%。Fernandes等[42]P. fluorescens EBC191来源的腈水解酶催化2-苯乙腈,发现pH在5−9范围内对产物酰胺的形成影响较小,而温度对酶的催化混乱性影响较大,在5−40 ℃范围内,随温度的升高,酰胺的比例明显下降,相对于5 ℃时酰胺的占比为89%,40 ℃时降低至62%。从上述结果可以看到,较高的pH值及较低的温度使腈水解酶的催化方向偏向酰胺产物。不过也有研究[30, 36]发现一些腈水解酶对于外界环境因子不是很敏感。

研究表明催化底物也会对腈水解酶的催化混乱性产生一定影响,如底物的结构特征、取代基的电子效应和空间位阻效应等。Zhang等[31]研究了P. graminis DSM 17151腈水解酶NitPG催化多类底物所呈现的水合活力差异,发现催化苯乙腈类底物相对苯甲腈和3-苯基丙腈产生更多的酰胺产物,证明其类乙腈结构对于酰胺的形成比较重要;此外,实验结果显示NitPG催化4-甲基苯乙腈、苯乙腈、4-硝基苯乙腈分别产生11%、16%和58%的酰胺,酰胺占比逐渐增加。Dai等[39]以佐式红球菌(Rhodococcus zopfii)来源的腈水解酶RzNIT为催化剂,当催化烟腈底物几乎不产生酰胺,但引入卤素取代时即催化底物为2-氯烟腈,反应生成约87.5%的2-氯烟酰胺产物。Osswald等[33]发现A. thaliana来源的腈水解酶催化不同3-取代丙烯腈所产生的酰胺比例有着明显的差异,当取代基团为氰基(−CN)和硝基(−NO2)时,酰胺占比高达93%和95%,相反,取代基为甲基(−CH3)和甲氧基(−OCH3)时酰胺占比不超过5%。以上研究结果表明,取代基的电子效应会影响产物中羧酸和酰胺的比例,增强取代基的电负性有利于酰胺的形成。当取代基为电负性强的原子如−NO2、−CN、−CF3等,其表现出的吸电子效应使催化区域的氰基N原子不易被质子化,反应路径倾向于pathway B,导致酰胺变成主产物。Mukherjee等[36]研究来源于玉米(Zea mays)的腈水解酶ZmNIT2催化脂肪族腈类底物时,发现该酶催化丁腈、戊腈、己腈和庚腈所产生的酰胺占比分别为19%、26%、36%和40%,随着碳链延长,其空间位阻可能会影响关键中间体的水解,造成产物中酰胺的比例升高。此外,P. fluorescens EBC191来源的腈水解酶在催化外消旋底物时所产生的酸和酰胺比例也会不同[53, 41-42, 67],该酶催化R-扁桃腈、R-2-乙酰氧基-2-苯乙腈和R-苯胺基乙腈分别产生约10%、33%和不足1%的酰胺,而催化该3种S构型底物所产生的酰胺占比分别提升至约50%、62%和10%。粗糙脉孢菌(Neurospora crassa) OR74A来源[52]的腈水解酶也有类似的结果,该酶催化R-扁桃腈几乎不产生酰胺,而催化S-扁桃腈产生了约84%的S-扁桃酰胺。从上述结果可以看出,底物的手性也会对腈水解酶的催化混乱性造成一定的影响,但其影响因素尚不明晰。

另外,腈水解酶催化混乱性还受到酶本身结构的影响,尤其是活性位点中催化三联体相邻的氨基酸残基,主要是通过突变相关残基调控底物的结合姿势和相互作用特征。P. fluorescens EBC191来源[37]的腈水解酶催化扁桃腈底物产生约19%的酰胺,而将与催化三联体Cys164直接相邻的Ala165突变为Arg后,产物酰胺比例提高至41%;粪产碱杆菌(Alcaligenes faecalis) ATCC 8750来源的腈水解酶催化扁桃腈仅产生0.7%的酰胺,但将催化域中Trp164突变为Ala时,酰胺比例提高至70%。同样是P. fluorescens EBC191来源的腈水解酶,与催化三联体Cys164直接相邻的另一个位点Cys163的突变也提高了酰胺占比[44]。同时,处于催化三联体附近的188和206位点,其突变体Trp188Leu和Asn206Lys均以酰胺为主产物(80%和60%以上)[68],并且188位点突变为Arg、Lys和Pro,可催化生成90%以上的扁桃酰胺[43];此外,一些突变体的C末端缺失也表现出更强的酰胺形成能力[45]。黑曲霉(Aspergillus niger)来源的腈水解酶催化扁桃腈的产物中未检测到扁桃酰胺,当对催化三联体附近的位点改造,发现W163A突变体产生了33%的酰胺;N. crassa来源的腈水解酶突变体W168A的产物酰胺占比也从40%提高到85%[52]

5 腈水解酶催化混乱性的应用案例

催化混乱性给腈水解酶的应用带来“混乱”的影响:一方面它使得目标羧酸产物中含有一定比例的酰胺,降低了羧酸产物的收率,同时增加了产物后续分离纯化的成本,给腈水解酶的工业应用带来挑战;而另一方面,腈水解酶的催化混乱性也是一个机遇,相对于常规的腈水合酶通常表现出对脂肪族底物的偏好且对氰类化合物敏感[43],而腈水解酶不依赖于金属离子,可耐受高浓度的氰离子,且重组表达更简单,有利于大规模的工业应用。如果能使腈水解酶的反应偏向于生成酰胺,那将为高附加值酰胺类化合物的生物合成提供新工艺。

腈水解酶催化混乱性的两面性,引起了众多学者的关注,其相关应用案例如表 3所示。当羧酸为目标产物,需要消除酰胺副产物。一些小组通过采用双酶一锅两步级联反应策略来消除酰胺副产物,如Tao等[40]将腈水解酶与酰胺酶“串联”,消除腈水解酶产生的酰胺副产物,将β-丙氨酸的产量提高到90%,收率达到15.02 g/(L·h)。Zhang等[35]将高山南芥(Arabis alpina)来源的腈水解酶突变体N258D与泛菌属(Pantoea sp.)来源的酰胺酶“串联”,消除了酰胺副产物(S)-3-氰基-5-甲基己酰胺,催化异丁基琥珀腈转化(S)-3-氰基-5-甲基己酸,转化率达到45%,eep高达99.3%。另一种策略即蛋白质分子改造工程,抑制催化混乱腈水解酶的水合活力,专一地生产目标羧酸产物,如R. zopfii来源[39]的野生型腈水解酶催化2-氯烟腈生成88%的酰胺,目标产物2-氯烟酸仅占12%,而其突变体W167G完全消除了水合活力并将水解活性提高了20倍。Lu等[60]将嵌合型腈水解酶BaNIT所产生的酰胺副产物(S)-3-氰基-5-甲基己酰胺从15.8%降低到了1.9%,同时将酶活力提高了5.4倍。当酰胺作为目标产物时,需要尽可能消除羧酸产物的生成。如Zhang等[69]从蛋白数据库中鉴定出来源于恶疫霉(Phytophthora cactorum)的腈水解酶,该酶催化扁桃腈转化生成89.7%的扁桃酰胺,其突变体W167A将产物中扁桃酰胺的占比提升至99.8%。野生型的集胞藻(Syechocystis sp.) PCC 6803腈水解酶转化2-氰基吡啶生成2.1%的相应酰胺,其突变体F193N将酰胺占比提升至73.4%,Sun等[70]在单突变体F193N上进一步迭代突变,获得的突变体F193N/G101K/Q192H/I201M将酰胺的占比提升至98.5%。如前所述,通过蛋白质工程可将酰胺从副产物转变成主产物(表 3)。此外,也有一些天然腈水解酶(表 1)表现出高的水合活力,显示出腈水解酶具有成为新型“腈水合酶”的潜力,这在生物合成领域中具有重大的意义。

表 3 关于腈水解酶催化混乱性的应用案例 Table 3 Application cases regarding the catalytic promiscuity of nitrilases
Objective Organism Substrate & Product Mutation Result References
Eliminate amide products Arabis alpina Isobutylsuccinonitrile & (S)-3-cyano-5-methylhexanoic acid No mutation The amide byproduct was eliminated and acid was obtained with a conversion of 45.0% and eep of 99.3% [35]
Arabis alpine & Brassica rapa (chimeric nitrilase) Isobutylsuccinonitrile & (S)-3-cyano-5-methylhexanoic acid V82L/M127I/C237S (BaNITM2) 1.5 g/L Escherichia coli cells harboring BaNITM2 as biocatalyst converted 150 g/L Isobutylsuccinonitrile afforded (S)-3-cyano-5-methylhexanoic acid with > 99.0% e.e. and 45.9% conversion [60]
Bradyrhizobium japonicum strain USDA110 3-aminopropionitrile & β-alanine No mutation The isolated yield of β-alanine was 90%, the space-time-yield was 15.02 g/(L·h) [40]
Rhodococcus zopfii 2-chloronicotinonitrile & 2-chloronicotinic acid W167G, W167A, N165C, N165A, N165G W167G converted 100 mmol/L 2-chloronicotinonitrile exclusively into 2-chloronicotinic acid within 16 h [39]
Enhance amide products Alcaligenes faecalis ATCC 8750 Mandelonitrile & (S)-mandeloamide W164A W164A variant formed significantly more (S)-mandeloamide than wide type [37]
Acidovorax facilis 72 W 2-cyanopyridine & 2-picolinamide W188G, W188A, W188C, W188L, W188M, W188S, W188V W188M mutant converted 250 mmol/L 2-cyanopyridine to more than 98% 2-picolin-amide in 12 h with a specific activity of 90 U/mg [38]
Neurospora crassa OR74A 2-phenylpropionitril & 2-phenylpropionamide W168A W168A mutant formed significantly increased amounts of 2-phenylpropionamide [52]
Oryza sativa Phenylacetonitrile & phenylacetamide A87M/I91P/I136Q/M164V/R224S/V226R The phenylacetamide was increased from 49.1% to 96.4% by the hexamutant [34]
Phytophthora cactorum Mandelonitrile & mandeloamide W167A, W167V, W190C, W190R These four variants reduced the acid by-product to less than 1% yield [69]
Pseudomonas fluorescens EBC191 Mandelonitrile & mandeloamide C-terminal deletions, C163A, C163N, Nit(DelC-60)-Cys163Asn nitrilase variant, which produces about 70% of amide from mandelonitrile [44]
mandelonitrile & mandeloamide C-terminal deletions, W188L, W188K, W188P, W188R, N206K These mutants formed increased amounts of mandeloamide from mandelonitrile [43, 45, 68]
Syechocystis sp. PCC 6803 2-cyanopyridine & 2-picolinamide F193A, F193D, F193N, F193E, F193Q F193N improved amide product up to 73%, which was about 35-fold that of wild type [50]
F193N/G101K/Q192H/I201M This mutant retained only 1.5% of the carboxylic acid ratio [70]
eep refers to enantiomeric excess of the product.
6 展望

腈水解酶在生物催化中具有广泛的应用前景,其催化混乱性已成为当前研究的热点之一。然而,目前对于腈水解酶催化混乱性的调控机制和结构基础的认识还相对有限,其具体的催化机制尚未完全阐明,需要进一步深入研究。尽管通过酶工程等手段已获得了一些具有特定催化性能的腈水解酶突变体,但对于如何更精准地设计和优化腈水解酶仍需要更多的努力。未来,随着对腈水解酶催化机制的深入研究,有望发现和设计更多具有特定催化性能的腈水解酶,为工业生产中的废物处理、有机合成和医药行业等领域提供更多的可能性。此外,对腈水解酶混乱性的深入理解还将促进对生物催化的发展,为生物工程领域提供更多的新思路和方法,从而为环境保护和可持续发展作出更大的贡献。

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