Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.
Arch Biochem Biophys. 2018 Mar 1;641:39-49. doi: 10.1016/j.abb.2018.01.015. Epub 2018 Jan 31.
Pectin methylesterase (CtPME) from Clostridium thermocellum of family 8 carbohydrate esterase (CE8) belongs to pectin methylesterase super family (E.C.3.1.1.11). BLAST analysis of CtPME showed 38% sequence identity with PME from Erwinia chrysanthemi. Multiple sequence alignment of CtPME with other known structures of pectin methylesterase revealed the conserved and semi-conserved amino acid residues. Homology modelling of CtPME structure revealed a characteristic right handed parallel β-helices. The energy of modelled structure was minimized by using YASARA software. The Ramachandran plot of CtPME shows 83.7% residues in non-glycine and non-proline residues in most-favorable region, 13.8% in additional allowed region and 1.4% in generously allowed region, indicating that CtPME has a stable conformation. The secondary structure of CtPME predicted using PSI-Pred software and confirmed by the circular dichroism (CD) showed α-helices (3.1%), β-sheets (40.1%) and random coils (56.9%). Small Angle X-ray Scattering (SAXS) analysis demonstrated the overall shape and structural characterization of CtPME in solution form. Guinier analysis gave the radius of gyration (R) 2.28 nm for globular shape and 0.74 nm for rod shape. Kratky plot gave the indication that protein is fully folded in solution. The ab initio derived dummy atom model of CtPME superposed well on modelled CtPME structure.
热纤梭菌果胶甲基酯酶（CtPME）属于家族 8 碳水化合物酯酶（CE8），属于果胶甲基酯酶超家族（E.C.3.1.1.11）。CtPME 的 BLAST 分析显示与菊欧文氏菌的 PME 具有 38%的序列同一性。CtPME 与其他已知果胶甲基酯酶结构的多重序列比对显示出保守和半保守的氨基酸残基。CtPME 结构的同源建模揭示了特征性的右手平行β-螺旋。使用 YASARA 软件最小化建模结构的能量。CtPME 的 Ramachandran 图显示 83.7%的残基位于最适区域的非甘氨酸和非脯氨酸残基，13.8%位于附加允许区域，1.4%位于慷慨允许区域，表明 CtPME 具有稳定的构象。PSI-Pred 软件预测的 CtPME 二级结构，并通过圆二色性（CD）得到证实，显示α-螺旋（3.1%）、β-折叠（40.1%）和无规卷曲（56.9%）。小角度 X 射线散射（SAXS）分析证明了 CtPME 在溶液形式下的整体形状和结构特征。Guinier 分析给出了旋转半径（R）为 2.28nm 的球形和 0.74nm 的棒形。Kratky 图表明蛋白质在溶液中完全折叠。从头计算得到的 CtPME 虚拟原子模型与建模的 CtPME 结构很好地叠加。
