東京大学 生物生産工学研究センター
環境保全工学研究室

図2-1. Carbazole binding to the substrate-binding pocket of CARDO-O. Panel A illustrates the closure of the entrance of the substrate-binding pocket (white arrows) upon carbazole binding. Conformational changes are obvious for amino acid residues Leu202-Thr214 (shown as cyan [before binding] and orange [after binding]) and Asp229-Val238 (shown as lime [before binding] and magenta [after binding]). Phe204 and Ile231, which had large conformational changes, are shown as stick models. Panel B shows the binding manner of carbazole and oxygen (peroxide ligand) at the substrate-binding pocket (Ashikawa et al. 2006; part of this figure includes unpublished results). The iron ion ligands and amino acid residues that constitute the substrate are shown in stick models and are salmon in color. Carbazole is also shown as a stick model (white for carbon). The iron ions and oxygen (peroxide) ligands are shown as green and small red spheres, respectively. The hydrogen bond interaction between the imino nitrogen of carbazole and the carbonyl oxygen of Gly178 is indicated by a red broken line.

図2-2. (A) Overall structures of the binary complex of CARDO-OJ3 with CARDO-FCA10, (B) superposed view of the three CARDO-FCA10 molecules, and (C) hypothetical electron-transport routes between CARDO-FCA10 and CARDO-OJ3. In panel A, the three CARDO-O subunits (chain A, slate blue; chain B, forest green; and chain C, red) and the three CARDO-F molecules (chain D, cyan; chain E, yellow; and chain F, salmon) are shown. The [2Fe-2S]R and the non-heme iron are shown as spheres (iron ions, green; sulfide ions, yellow). In panel B, the distances between the electron-transfer centers are shown. In panel C, the active-site iron and its coordinated residues of CARDO-O chain A, the [2Fe-2S]R and the coordinated residues of CARDO-O chain B and CARDO-F, and the amino acid residues and water molecules possibly involved in electron transfer in the complex are shown. Each chain is colored as in panel A. The magenta and brown dotted lines indicate the two hypothetical electron-transfer pathways (routes 1 and 2) between the two [2Fe-2S]R. The possible electron-transfer pathway from the [2Fe-2S]R to the active-site iron in CARDO-O is shown as an orange dotted line.

図2-3. The circular gene maps of pCAR1 (left) and pCAR3 (right). Genes or ORFs outside the circle are coded clockwise; those inside are coded counterclockwise. The (putative) functions of genes or ORFs are shown by color as follows: orange, maintenance or DNA processing; dark green, conjugative transfer; blue, transposition or integration; red, degradation; light green, transport; black, regulation; magenta, other known function; gray, unknown function (homologous to hypothetical protein); and yellow, unknown function (no homology). Bars inside the circular gene map indicate the G+C contents of ORFs shown in same color. The broken circle indicates the average G+C content of the entire pCAR1 (56%) and pCAR3 (62.5%). In pCAR3, bold purple lines show the regions homologous to pNL1 (Romine et al. J. Bacteriol., 181, 1585-1602, 1999).

図2-4. Overview of the project entitled ‘Functional Analysis of behavior of Degradative Plasmid in Natural Environment’ [see this page].

図2-5. Interaction between IncP-7 carbazole degradative plasmid pCAR1 and P.putida KT2440 chromosome detected by transcriptome and biochemical analyses.