Buetow Lori, Dawson Alice, Hunter William N
Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Nov 1;62(Pt 11):1082-6. doi: 10.1107/S1744309106041893. Epub 2006 Oct 25.
The structure of recombinant Aquifex aeolicus UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) in complex with UDP has been determined to a resolution of 2.2 A. Previous studies have characterized the binding sites of the fatty-acid and sugar moieties of the substrate, UDP-(3-O-hydroxymyristoyl)-N-acetylglucosamine, but not that of the nucleotide. The uracil-binding site is constructed from amino acids that are highly conserved across species. Hydrophobic associations with the Phe155 and Arg250 side chains in combination with hydrogen-bonding interactions with the main chain of Glu154 and the side chains of Tyr151 and Lys227 position the base. The phosphate and ribose groups are directed away from the active site and interact with Arg137, Lys156, Glu186 and Arg250. The orientation of the phosphate-ribose tail is not conducive to catalysis, perhaps owing to the position of an inhibitory Zn(2+). However, based on the position of uracil revealed in this study and on the previously reported complex of LpxC with an inhibitor, a model is proposed for substrate binding.
已确定重组嗜热栖热菌UDP - 3 - O - 酰基 - N - 乙酰葡糖胺脱乙酰酶（LpxC）与UDP复合物的结构，分辨率为2.2埃。先前的研究已对底物UDP -（3 - O - 羟基肉豆蔻酰）- N - 乙酰葡糖胺的脂肪酸和糖部分的结合位点进行了表征，但未对核苷酸的结合位点进行表征。尿嘧啶结合位点由物种间高度保守的氨基酸构成。与Phe155和Arg250侧链的疏水缔合，以及与Glu154主链、Tyr151和Lys227侧链的氢键相互作用确定了碱基的位置。磷酸基团和核糖基团远离活性位点，并与Arg137、Lys156、Glu186和Arg250相互作用。磷酸 - 核糖尾部的方向不利于催化，这可能是由于抑制性Zn(2+)的位置所致。然而，基于本研究中揭示的尿嘧啶位置以及先前报道的LpxC与抑制剂的复合物，提出了一种底物结合模型。
