Thermostable cyclodextrinase (Tk1770 CDase) from hyperthermophilic archaeon Thermococcus kodakarensis (KOD1) hydrolyzes cyclodextrins into linear dextrins. The sequence of Tk1770 CDase retrieved from UniProt was aligned with sequences of sixteen CD hydrolyzing enzymes and a phylogenetic tree was constructed using Bayesian inference. The homology model of Tk1770 CDase was constructed and optimized with Modeller v9.14 program. The model was validated with ProSA server and PROCHECK analysis. Four conserved regions and the catalytic triad consisting of Asp411, Glu437, and Asp502 of GH13 family were identified in catalytic site. Also an additional fifth conserved region downstream to the fourth region was also identified. The structure of Tk1770 CDase consists of an additional N′-domain and a helix-loop-helix motif that is conserved in all archaeal CD hydrolyzing enzymes. The N′-domain contains an extended loop region that forms a part of catalytic domain and plays an important role in stability and substrate binding. The docking of substrate into catalytic site revealed the interactions with different conserved residues involved in substrate binding and formation of enzyme-substrate complex.

中文翻译：

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使用计算机模拟方法对来自柯达喀尔木霉（KOD1）的环糊精酶（TK1770）进行序列，结构和结合分析。

嗜热古细菌Thermococcus kodakarensis的热稳定环糊精酶（Tk1770 CDase）（KOD1）将环糊精水解为线性糊精。从UniProt检索到的Tk1770 CDase的序列与16种CD水解酶的序列比对，并使用贝叶斯推论构建了系统树。用Modeller v9.14程序构建并优化了Tk1770 CDase的同源性模型。该模型已通过ProSA服务器和PROCHECK分析进行了验证。在催化位点鉴定了四个保守区域和由GH13家族的Asp411，Glu437和Asp502组成的催化三联体。还确定了第四区域下游的另一个第五保守区域。Tk1770 CDase的结构由一个额外的N'结构域和一个螺旋-环-螺旋基序组成，该基序在所有古细菌CD水解酶中都保守。N'-结构域包含形成催化结构域一部分的延伸环区，并且在稳定性和底物结合中起重要作用。底物对接至催化位点揭示了与参与底物结合和酶-底物复合物形成的不同保守残基的相互作用。