Anaerobic and Aerobic Structures of Ferredoxin II from Desulfovibrio Gigas at Ultrahigh Resolution

Life Science Group, National Synchrotron Radiation Research Center* Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Taiwan**
â—‹Chun-Jung Chen* Yin-Cheng Hsieh** Yi-Hung Lin* Yen-Chieh Huang* Ming-Yih Liu*

Ferredoxin II (Fd II) is a small electron transfer protein isolated from the strict anaerobic sulfate-reducing bacterium, Desulfovibrio gigas. The protein contains 58 amino acids and an iron-sulfur cluster. The cluster [3Fe-4S] spontaneously undergoes conversion to [4Fe-4S] when it is used as an electron mediator in the phosphoroclastic reaction. This two-form interconversion appears to have physiological significance. We have obtained both aerobic and anaerobic Fd II crystals in the high-resolution quality and determined structures independently by the iron single-wavelength anomalous dispersion (Fe-SAD) method using synchrotron radiation X-ray. The structure of aerobic Fd II has been refined to 0.9 Å ultrahigh resolution in space group P21212. Its [3Fe-4S] cluster is bound with Cys8, Cys14, and Cys50, whereas Cys11 extends away from cluster. Cys18 and Cys42 form a disulfide bridge to maintain the protein folding. Multiple-conformations of residues are also observed in ultrahigh-resolution density map. Five isolated Zn2+ ions around the protein are bound with Glu, Asn and Asp residues, respectively, which indicates the transition metals, other than iron, could be incorporated into [3Fe-4S] center. On the other hand, the anaerobic Fd II structure from the crystals grown under anaerobic condition has also been refined in different space group C222. The anaerobic structure shows the different iron-sulfur cluster, disulfide bridge conformations, water structures, crystal packing and electron density distribution among activity site. Here we present the structure comparison between aerobic and anaerobic Fd II at ultrahigh resolution which reveals the unique iron storage function and electron transfer mechanism of ferredoxin II from Desulfovibrio gigas.