Delbaere L T, Vandonselaar M, Prasad L, Quail J W, Wilson K S, Dauter Z
Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada.
J Mol Biol. 1993 Apr 5;230(3):950-65. doi: 10.1006/jmbi.1993.1212.
The structures of the fourth lectin isolated from Griffonia simplicifolia (GS4) and its complex with the methyl-glycoside of the Lewis b human blood group determinant (Le(b)-OMe) are reported at high resolution. The native GS4 crystal is isomorphous with the complexed GS4 crystal. The space group is P4(2)2(1)2 with unit cell dimensions a = 78.9 A, c = 89.1 A with one subunit of the lectin (bound to 1 Le(b)-OMe in the complex) in the crystallographic asymmetric unit. The native GS4 structure was solved by the molecular replacement technique and least-squares refined (PROLSQ and X-PLOR). The orientation of the Le(b)-OMe tetrasaccharide in the complex was established from a 2.8 A difference map with coefficients (Fcomplex--Fnative) and calculated phase angles from the native model. Both the final native and complex GS4 models consist of 1904 protein non-hydrogen atoms, one sulfate ion, one Ca ion, one Mn ion and three covalently-bound sugar residues N-linked to Asn18. In addition, the complex model has 47 Le(b)-OMe non-hydrogen atoms. The two structures have 135 water molecules in common in addition to eight and nine unique water molecules in the native and complex structures, respectively. The root-mean-square deviations from ideal bond distances and angles are 0.016 A, 3.2 degrees and 0.016 A, 3.0 degrees, for the native and complexed GS4, respectively. The R index for all unique data from 8 to 2.0 A is 0.187 for the native (19,204 reflections) and 0.181 for the complex (19,212 reflections). The tertiary structure of each subunit is similar to that of other leguminous lectins but the quaternary structure of the molecular dimer is different from that of any other lectin reported to date. The co-ordination about the Ca ion is pentagonal bipyramidal (with 1 long Ca(2+)-oxygen bond) and the co-ordination about the Mn ion is octahedral. Two conserved residues (Asp149 and Ser155) appear to be important because they are hydrogen-bonded to each other and to groups that co-ordinate the Mn ion. There are three cis-peptides in the polypeptide chain; two involve non-proline residues, one of which is homologous with other leguminous lectins and the other is unique to GS4. The two non-proline cis-peptides are located in the carbohydrate-binding site and are important for the specificity of the lectin. The molecular recognition of Le(b)-OMe by GS4 involves both polar and extensive non-polar interactions.(ABSTRACT TRUNCATED AT 400 WORDS)
本文报道了从西非豆科植物种子中分离得到的第四种凝集素（GS4）及其与Lewis b人类血型决定簇甲基糖苷（Le(b)-OMe）复合物的高分辨率结构。天然GS4晶体与复合物晶体同晶型。空间群为P4(2)2(1)2，晶胞参数a = 78.9 Å，c = 89.1 Å，晶体学不对称单元中有一个凝集素亚基（复合物中结合1个Le(b)-OMe）。天然GS4结构通过分子置换技术解析并进行了最小二乘法精修（PROLSQ和X-PLOR）。复合物中Le(b)-OMe四糖的取向通过2.8 Å的差值图确定，该图由系数（F复合物 - F天然）和天然模型计算的相角构成。最终的天然和复合物GS4模型均由1904个蛋白质非氢原子、一个硫酸根离子、一个钙离子、一个锰离子以及三个与Asn18共价连接的糖残基组成。此外，复合物模型还有47个Le(b)-OMe非氢原子。两种结构除了分别有8个和9个独特水分子外，还有135个共有水分子。天然和复合物GS4与理想键长和键角的均方根偏差分别为0.016 Å、3.2°和0.016 Å、3.0°。天然GS4（19,204个反射）和复合物（19,212个反射）在8至2.0 Å范围内所有独特数据的R指数分别为0.187和0.181。每个亚基的三级结构与其他豆科凝集素相似，但分子二聚体的四级结构与迄今报道的任何其他凝集素不同。钙离子的配位为五角双锥（有1个长的Ca(2 +)-氧键），锰离子的配位为八面体。两个保守残基（Asp149和Ser155）似乎很重要，因为它们相互之间以及与配位锰离子的基团形成氢键。多肽链中有三个顺式肽段；两个涉及非脯氨酸残基，其中一个与其他豆科凝集素同源，另一个是GS4特有的。这两个非脯氨酸顺式肽段位于碳水化合物结合位点，对凝集素的特异性很重要。GS4对Le(b)-OMe的分子识别涉及极性和广泛的非极性相互作用。（摘要截断于400字）
