Mapping the key residues of SufB and SufD essential for biosynthesis of iron-sulfur clusters

Eiki Yuda; Naoyuki Tanaka; Takashi Fujishiro; Nao Yokoyama; Kei Hirabayashi; Keiichi Fukuyama; Kei Wada; Yasuhiro Takahashi

doi:10.1038/s41598-017-09846-2

Mapping the key residues of SufB and SufD essential for biosynthesis of iron-sulfur clusters

Sci Rep. 2017 Aug 24;7(1):9387. doi: 10.1038/s41598-017-09846-2.

Authors

Eiki Yuda¹, Naoyuki Tanaka^{1

2}, Takashi Fujishiro¹, Nao Yokoyama¹, Kei Hirabayashi^{3

4}, Keiichi Fukuyama⁵, Kei Wada³, Yasuhiro Takahashi⁶

Affiliations

¹ Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan.
² Innovation Medical Research Institute, University of Tsukuba, Ibaraki, 305-8577, Japan.
³ Department of Medical Sciences, University of Miyazaki, Miyazaki, 889-1692, Japan.
⁴ Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
⁵ Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, 565-0871, Japan.
⁶ Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan. ytaka@mail.saitama-u.ac.jp.

Abstract

Biogenesis of iron-sulfur (Fe-S) clusters is an indispensable process in living cells. In Escherichia coli, the SUF biosynthetic system consists of six proteins among which SufB, SufC and SufD form the SufBCD complex, which serves as a scaffold for the assembly of nascent Fe-S cluster. Despite recent progress in biochemical and structural studies, little is known about the specific regions providing the scaffold. Here we present a systematic mutational analysis of SufB and SufD and map their critical residues in two distinct regions. One region is located on the N-terminal side of the β-helix core domain of SufB, where biochemical studies revealed that Cys254 of SufB (SufB^C254) is essential for sulfur-transfer from SufE. Another functional region resides at an interface between SufB and SufD, where three residues (SufB^C405, SufB^E434, and SufD^H360) appear to comprise the site for de novo cluster formation. Furthermore, we demonstrate a plausible tunnel in the β-helix core domain of SufB through which the sulfur species may be transferred from SufB^C254 to SufB^C405. In contrast, a canonical Fe-S cluster binding motif (CxxCxxxC) of SufB is dispensable. These findings provide new insights into the mechanism of Fe-S cluster assembly by the SufBCD complex.

Publication types

Research Support, Non-U.S. Gov't