BACKGROUND & AIMS:
:Iminodisuccinate (IDS) epimerase catalyzes the epimerisation of R,R-, S,S- and R,S- iminodisuccinate, one step in the biodegradation of the chelating agent iminodisuccinate by Agrobacterium tumefaciens BY6. The enzyme is a member of the MmgE/PrpD protein family, a diverse and little characterized class of proteins of prokaryotic and eukaryotic origin. IDS epimerase does not show significant overall amino acid sequence similarity to any other protein of known three-dimensional structure. The crystal structure of this novel epimerase has been determined by multi-wavelength diffraction to 1.5 A resolution using selenomethionine-substituted enzyme. In the crystal, the enzyme forms a homo-dimer, and the subunit consists of two domains. The larger domain, not consecutive in sequence and comprising residues Met1-Lys266 and Leu400-Pro446, forms a novel all alpha-helical fold with a central six-helical bundle. The second, smaller domain folds into an alpha+beta domain, related in topology to chorismate mutase by a circular permutation. IDS epimerase is thus not related in three-dimensional structure to other known epimerases. The fold of the IDS epimerase is representative for the whole MmgE/PrpD family. The putative active site is located at the interface between the two domains of the subunit, and is characterized by a positively charged surface, consistent with the binding of a highly negatively charged substrate such as iminodisuccinate. Docking experiments suggest a two-base mechanism for the epimerisation reaction.
背景与目标:
:亚氨基二琥珀酸酯(IDS)差向异构酶催化R,R-,S,S-和R,S-亚氨基二琥珀酸酯的差向异构化,这是根癌农杆菌BY6对螯合剂亚氨基二琥珀酸酯的生物降解的一个步骤。该酶是MmgE / PrpD蛋白质家族的成员,MmgE / PrpD蛋白质家族是原核和真核来源的多种多样且鲜为特征的蛋白质。 IDS差向异构酶与已知三维结构的任何其他蛋白质均未显示出明显的总体氨基酸序列相似性。该新型差向异构酶的晶体结构已通过硒代蛋氨酸取代的酶通过多波长衍射确定为1.5 A的分辨率。在晶体中,酶形成同型二聚体,该亚基由两个结构域组成。较大的结构域,顺序不连续,包含残基Met1-Lys266和Leu400-Pro446,形成带有中心六螺旋束的新型全α螺旋折叠。第二个较小的域折叠成一个alpha beta域,该域在拓扑结构上与通过循环排列分支变异酶有关。因此,IDS差向异构酶在三维结构上与其他已知的差向异构酶无关。 IDS差向异构酶的折叠代表整个MmgE / PrpD家族。推定的活性位点位于亚基的两个结构域之间的界面处,其特征是带正电的表面,与带负电的底物(如亚氨基二琥珀酸酯)的结合相一致。对接实验提出了差向异构反应的两碱基机制。