Schäfer M, Schneider T R, Sheldrick G M
Institut für Anorganische Chemie, Universität Göttingen, Germany.
Structure. 1996 Dec 15;4(12):1509-15. doi: 10.1016/s0969-2126(96)00156-6.
Vancomycin and other related glycopeptide antibiotics are clinically very important because they often represent the last line of defence against bacteria that have developed resistance to antibiotics. Vancomycin is believed to act by binding nascent cell wall mucopeptides terminating in the sequence D-Ala-D-Ala, weakening the resulting cell wall. Extensive NMR and other studies have shown that the formation of asymmetric antibiotic dimers is important in peptide binding. Despite intensive efforts the crystal structure of vancomycin has been extremely difficult to obtain, partly because high-resolution data were unavailable, and partly because the structure was too large to be solved by conventional "direct methods'.
Using low-temperature synchrotron X-ray data combined with new ab initio techniques for solving the crystallographic phase problem, we have succeeded in determining the crystal structure of vancomycin at atomic resolution. The structure provides much detailed information that should prove invaluable in modelling and mechanistic studies.
Our structure confirms that vancomycin exists as an asymmetric dimer. The dimer conformation allows the docking of two D-Ala-D-Ala peptides in opposite directions; these presumably would be attached to different glycopeptide strands. In the crystal, one of the binding pockets is occupied by an acetate ion that mimics the C terminus of the nascent cell wall peptide; the other is closed by the asparagine sidechain, which occupies the place of a ligand. The occupied binding pocket exhibits high flexibility but the closed binding pocket is relatively rigid. We propose that the asparagine sidechain may hold the binding pocket in a suitable conformation for peptide docking, swinging out of the way when the peptide enters the binding pocket.
万古霉素及其他相关糖肽类抗生素在临床上非常重要，因为它们常常是抵御已对抗生素产生耐药性的细菌的最后一道防线。据信万古霉素通过与以D - Ala - D - Ala序列结尾的新生细胞壁粘肽结合来发挥作用，从而削弱由此产生的细胞壁。广泛的核磁共振及其他研究表明，不对称抗生素二聚体的形成在肽结合中很重要。尽管付出了巨大努力，但万古霉素的晶体结构极难获得，部分原因是无法获得高分辨率数据，部分原因是该结构太大，无法通过传统的“直接法”求解。
利用低温同步加速器X射线数据并结合新的从头算技术来解决晶体学相位问题，我们成功地在原子分辨率下确定了万古霉素的晶体结构。该结构提供了许多详细信息，在建模和机理研究中应会被证明具有极高价值。
我们的结构证实万古霉素以不对称二聚体形式存在。二聚体构象允许两个D - Ala - D - Ala肽以相反方向对接；这些肽大概会附着在不同的糖肽链上。在晶体中，其中一个结合口袋被一个模拟新生细胞壁肽C末端的醋酸根离子占据；另一个被天冬酰胺侧链封闭，该侧链占据了配体的位置。被占据的结合口袋表现出高灵活性，但封闭的结合口袋相对刚性。我们提出天冬酰胺侧链可能将结合口袋保持在适合肽对接的构象，当肽进入结合口袋时它会摆动让开。
