National Bureau of Agriculturally Important Microorganisms (ICAR), Kusmaur, Kaithauli, Mau Nath Bhanjan, 275101, Uttar Pradesh, India.
J Mol Model. 2012 Sep;18(9):4101-11. doi: 10.1007/s00894-012-1389-0. Epub 2012 Apr 17.
As part of an effort to obtain a fungal 1-aminocyclopropane-1-carboxylate deaminase encoding gene from Phytophthora sojae expressed sequence Tag database, we identify and characterize the ACCD from P. sojae using bioinformatics data mining tools and techniques. Computed structural model of P. sojae ACCD was found to consist of mixed α/β motifs and probable loops. The predicted model resembles the structure of Pseudomonas ACCD (RMSD-0.44 Å). The main differences observed between them are the presence of partial length of domain one, and longer helix α4. Ramachandran plot analysis revealed that portion of all residues falling into the most favorable regions was 95.0%. The substrate - and geometrical- docking of developed structure postulated functional capability of ACCD to carry out ACC cleavage reaction. The catalytic site in homo-tetrameric structure open to opposite directions separated by ∼37.97 Å distance arranged around central axis. This study provides a comprehensive identification and characterization of the ACCD in P. sojae and it may be helpful in the transcriptional and expression based study of P. sojae pathogenesis.
为了从大豆疫霉表达序列标签数据库中获得一种真菌 1-氨基环丙烷-1-羧酸脱氨酶编码基因，我们使用生物信息学数据挖掘工具和技术，对大豆疫霉 ACCD 进行了鉴定和特性分析。计算出的大豆疫霉 ACCD 结构模型由混合的α/β基元和可能的环组成。预测模型与假单胞菌 ACCD 的结构相似（RMSD-0.44Å）。观察到的主要区别是存在部分结构域一和更长的α4 螺旋。Ramachandran 图谱分析表明，所有残基中处于最有利区域的部分为 95.0%。开发的结构的底物和几何对接假设了 ACCD 进行 ACC 裂解反应的功能能力。在由中央轴围绕的约 37.97Å 距离处，以相反方向排列的同源四聚体结构中的催化位点。本研究全面鉴定和分析了大豆疫霉中的 ACCD，这可能有助于大豆疫霉发病机制的转录和表达研究。
