High-resolution crystal structure of the recombinant diheme cytochrome c from Shewanella baltica (OS155)

Abstract

Multiheme cytochromes c (cyts c) are c-type cyts characterized by non-standard structural and spectroscopic properties. The relative disposition of the heme cofactors in the core of these proteins is conserved and they can be classified from their geometry in two main groups. In one group the porphyrin planes are arranged in a perpendicular fashion, while in the other they are parallel. Orientation of the heme groups is a key factor that regulates the intramolecular electron transfer pathway. A 16.5 kDa diheme cyt c, isolated from the bacterium Shewanella baltica OS155 (Sb-DHC), was cloned and expressed in E. coli and its structure was investigated by X-ray crystallography. Using high-resolution data (1.14 Å) collected at ELETTRA (Trieste), the crystal structure, with an orthorhombic cell (a = 40.81, b = 42.97, c = 82.07 Å), was solved using the homologous diheme from Rhodobacter sphaeroides (Rs-DHC) as the initial model. The electron density map of the refined structure (R_fact of 13.8% and R_free of 15.4%) shows a two domain structure connected by a central unstructured region (N72-G87). The Sb-DHC, like its homologue (Rs-DHC), folds into a new cyt c class: the N-terminal globular domain, with its three α-helices, belongs to class I of c-type cyts, while the C-terminal domain includes a rare π-helix. The metal centre of the c-type heme groups is axially coordinated by two His residues and it is covalently bound to the protein through two Cys bonds.

Keywords:

• cytochrome c
• diheme
• electron transfer
• biocrystallography
• edge to edge

Acknowledgments

We thank the University Federico II–IBB of Naples (Italy), MIUR (PRIN-2009A5Y3N project), CIRCMSB, Friuli-Venezia-Giulia region (DPReg. 120/2007/Pres.) and University of Trieste FRA2012 for financial support and the XRD1 beamline scientists at Elettra Synchrotron for their technical assistance.