1DW3

STRUCTURE OF A REDUCED OXYGEN BINDING CYTOCHROME C

Summary for 1DW3

• Entry DOI: 10.2210/pdb1dw3/pdb
• Related: 1DW0 1DW1 1DW2
• Descriptor: CYTOCHROME C, HEME C (3 entities in total)
• Functional Keywords: cytochrome c, reduced, disulfide bridge, asparagine ligation, oxygen storage-transport complex, oxygen storage/transport
• Biological source: Rhodobacter sphaeroides
• Total number of polymer chains: 3
• Total formula weight: 36564.88

Authors

Leys, D.,Backers, K.,Meyer, T.E.,Hagen, W.R.,Cusanovich, M.A.,Van Beeumen, J.J. (deposition date: 2000-01-24, release date: 2000-06-28, Last modification date: 2021-03-03)

Primary citation

Leys, D.,Backers, K.,Meyer, T.E.,Hagen, W.R.,Cusanovich, M.A.,Van Beeumen, J.J.
Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.
J.Biol.Chem., 275:16050-16056, 2000

PubMed Abstract: The photosynthetic bacterium Rhodobacter sphaeroides produces a heme protein (SHP), which is an unusual c-type cytochrome capable of transiently binding oxygen during autooxidation. Similar proteins have not only been observed in other photosynthetic bacteria but also in the obligate methylotroph Methylophilus methylotrophus and the metal reducing bacterium Shewanella putrefaciens. A three-dimensional structure of SHP was derived using the multiple isomorphous replacement phasing method. Besides a model for the oxidized state (to 1.82 A resolution), models for the reduced state (2.1 A resolution), the oxidized molecule liganded with cyanide (1. 90 A resolution), and the reduced molecule liganded with nitric oxide (2.20 A resolution) could be derived. The SHP structure represents a new variation of the class I cytochrome c fold. The oxidized state reveals a novel sixth heme ligand, Asn(88), which moves away from the iron upon reduction or when small molecules bind. The distal side of the heme has a striking resemblance to other heme proteins that bind gaseous compounds. In SHP the liberated amide group of Asn(88) stabilizes solvent-shielded ligands through a hydrogen bond.

PubMed: 10821858
DOI: 10.1074/jbc.275.21.16050

Experimental method

X-RAY DIFFRACTION (2.1 Å)