Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India.
Biochemistry (Mosc). 2009 Sep;74(9):1049-55. doi: 10.1134/s0006297909090144.
A total of 48 full-length protein sequences of pectin lyases from different source organisms available in NCBI were subjected to multiple sequence alignment, domain analysis, and phylogenetic tree construction. A phylogenetic tree constructed on the basis of the protein sequences revealed two distinct clusters representing pectin lyases from bacterial and fungal sources. Similarly, the multiple accessions of different source organisms representing bacterial and fungal pectin lyases also formed distinct clusters, showing sequence level homology. The sequence level similarities among different groups of pectinase enzymes, viz. pectin lyase, pectate lyase, polygalacturonase, and pectin esterase, were also analyzed by subjecting a single protein sequence from each group with common source organism to tree construction. Four distinct clusters representing different groups of pectinases with common source organisms were observed, indicating the existing sequence level similarity among them. Multiple sequence alignment of pectin lyase protein sequence of different source organisms along with pectinases with common source organisms revealed a conserved region, indicating homology at sequence level. A conserved domain Pec_Lyase_C was frequently observed in the protein sequences of pectin lyases and pectate lyases, while Glyco_hydro_28 domains and Pectate lyase-like beta-helix clan domain are frequently observed in polygalacturonases and pectin esterases, respectively. The signature amino acid sequence of 41 amino acids, i.e. TYDNAGVLPITVNSNKSLIGEGSKGVIKGKGLRIVSGAKNI, related with the Pec_Lyase_C is frequently observed in pectin lyase protein sequences and might be related with the structure and enzymatic function.
共有 48 个来自不同生物源的完整果胶裂解酶蛋白序列可在 NCBI 中获得，我们对其进行了多序列比对、结构域分析和系统发育树构建。基于蛋白序列构建的系统发育树揭示了两个不同的聚类，分别代表细菌和真菌来源的果胶裂解酶。同样，不同生物源的不同接入点的细菌和真菌果胶裂解酶也形成了不同的聚类，显示出序列水平的同源性。通过将每个组的单个蛋白序列与具有共同生物源的其他组进行序列比对，分析了不同果胶酶组（即果胶裂解酶、果胶酸裂解酶、多聚半乳糖醛酸酶和果胶酯酶）之间的序列水平相似性。观察到四个不同的聚类，分别代表具有共同生物源的不同果胶酶组，表明它们之间存在序列水平的相似性。对不同生物源的果胶裂解酶蛋白序列与具有共同生物源的果胶酶进行多序列比对，揭示了一个保守区域，表明它们在序列水平上具有同源性。在果胶裂解酶和果胶酸裂解酶的蛋白序列中经常观察到 Pec_Lyase_C 保守结构域，而 Glyco_hydro_28 结构域和 Pectate lyase-like beta-helix clan 结构域分别在多聚半乳糖醛酸酶和果胶酯酶中经常观察到。41 个氨基酸的特征氨基酸序列，即 TYDNAGVLPITVNSNKSLIGEGSKGVIKGKGLRIVSGAKNI，与 Pec_Lyase_C 相关，在果胶裂解酶蛋白序列中经常观察到，可能与结构和酶功能有关。
