Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain.
Oxford Glycobiology Institute, Dept. of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, England, UK.
Biochim Biophys Acta Gen Subj. 2018 Sep;1862(9):1948-1955. doi: 10.1016/j.bbagen.2018.06.013. Epub 2018 Jun 15.
Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.
人卟胆原脱氨酶（PBGD）是血红素途径中的第三酶，催化单次反应将卟胆原转化为羟甲基胆烷。值得注意的是，PBGD 在该过程中仅使用一个活性部位，每次形成独特但化学等价的键。该酶的四个中间复合物已通过生物化学方法得到验证，可以分离，但除了与辅因子结合的apo 和 holo 酶之外，从未进行过结构表征。我们展示了两种人 PBGD 中间体的晶体结构：加载辅因子的 PBGD 和含有两个额外底物吡咯环的反应中间体。这些结果与 SAXS 和 NMR 实验相结合，使我们能够提出一种比以前建议的更少结构重排的反应进展机制：该酶将一个灵活的环滑过不断增长的产物活性部位腔。为该基本反应提出的结构和机制解释了一组错义突变如何导致急性间歇性卟啉症。
