Hybrid cluster protein

An iron protein with a strange iron–sulfur–oxygen cluster, and the heart of my PhD.

Left: the whole protein, coloured from the start (orange) to the end (plum) of its chain, with the two iron clusters in the middle. Right: a close-up of the clusters, iron in brown, sulfur in yellow and oxygen in red, with the side chains that hold them.

The hybrid cluster protein (HCP) from Desulfovibrio bacteria holds an unusual cluster of iron, sulfur and oxygen atoms whose job is still debated. During my PhD, between ITQB NOVA and the ESRF, we solved it in different oxidation states: reduced forms from two species at 1.25 and 1.55 Å (1OA0, 1OA1), and the protein from D. vulgaris purified and crystallised entirely without oxygen, solved by MAD at the iron edge at 1.35 Å (1W9M). The cluster’s atoms shift as it changes redox state, and its similarity to carbon monoxide dehydrogenase gave clues to its chemistry.

Both papers made journal covers: the Journal of Biological Inorganic Chemistry in 2003 and Acta Crystallographica D in June 2008 (2003 paper, 2008 paper).

PDB entry: 1W9M at PDBe (also at RCSB PDB)
Released: 2005-02-04
Resolution: 1.35 Å
Paper: Structural and Functional Relationships in the Hybrid Cluster Protein Family:Structure of the Anaerobically Purified Hybrid Cluster Protein from Desulfovibrio Vulgaris at 1.35 A Resolution (Acta Crystallogr.,Sect.D, 2008)
More: Technical details, links and electron density

Pictures and video rendered with UCSF ChimeraX; the 3D view is PDBe Mol*.