Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
J Am Chem Soc. 2010 Sep 1;132(34):11993-2005. doi: 10.1021/ja103530v.
Unique heme-containing tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) catalyze oxidative cleavage of the pyrrole ring of L-tryptophan (Trp). Although these two heme dioxygenases were discovered more than 40 years ago, their reaction mechanisms were still poorly understood. Encouraged by recent X-ray crystal structures, new mechanistic pathways were proposed. We performed ONIOM(B3LYP:Amber) calculations with explicit consideration of the protein environment to study various possible reaction mechanisms for bacterial TDO. The ONIOM calculations do not support the proposed mechanisms (via either formation of the dioxetane intermediate or Criegee-type rearrangement); a mechanism that is exceptional in the hemes emerges. It starts with (1) direct radical addition of a ferric-superoxide intermediate with C2 of the indole of Trp, followed by (2) ring-closure via homolytic O-O cleavage to give epoxide and ferryl-oxo (Cpd II) intermediates, (3) acid-catalyzed regiospecific ring-opening of the epoxide, (4) oxo-attack, and (5) finally C-C bond cleavage concerted with back proton transfer. The involvement of dual oxidants, ferric-superoxide and ferryl-oxo (Cpd II) intermediates, is proposed to be responsible for the dioxygenase reactivity in bacterial TDO. In particular, the not-well-recognized ferric-superoxide porphyrin intermediate is found to be capable of reacting with pi-systems via direct radical addition, an uncommon dioxygen activation in the hemes. The comparison between Xanthomonas campestris TDO and some heme as well non-heme oxygenases is also discussed.
独特的血红素色氨酸 2,3-双加氧酶(TDO)和吲哚胺 2,3-双加氧酶(IDO)催化 L-色氨酸(Trp)吡咯环的氧化裂解。尽管这两种血红素加氧酶在 40 多年前就被发现了,但它们的反应机制仍不清楚。最近的 X 射线晶体结构的发现,提出了新的机制途径。我们使用考虑了蛋白质环境的 ONIOM(B3LYP:Amber)计算来研究细菌 TDO 的各种可能的反应机制。ONIOM 计算不支持所提出的机制(通过二氧杂环丁烷中间体或 Criegee 型重排形成);出现了血红素中特殊的机制。它从(1)铁超氧化物中间体与 Trp 吲哚的 C2 的直接自由基加成开始,然后(2)通过均裂 O-O 裂解进行环闭合,得到环氧化物和铁酰氧基(Cpd II)中间体,(3)环氧化物的酸催化区域特异性开环,(4)氧进攻,(5)最后与回位质子转移协同进行 C-C 键断裂。提出双氧化剂,铁超氧化物和铁酰氧基(Cpd II)中间体的参与,是细菌 TDO 中双加氧酶反应性的原因。特别是,发现不太被认可的铁超氧化物卟啉中间体能够通过直接自由基加成与π体系反应,这在血红素中是一种不常见的双氧活化。还讨论了黄单胞菌 TDO 与一些血红素和非血红素加氧酶的比较。