NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c(556).
The structure of oxidized Rhodopseudomonas palustris cytochrome c(556) has been modeled after that of high-spin cytochrome c' from the same bacterium, the latter being the protein with the greatest sequence identity (35%) among all sequenced proteins in the genomes. The two proteins differ in the number of ligands to iron and in spin state, the former being six-coordinate low-spin and the latter five-coordinate high-spin. In order to validate this modeled structure, several structural restraints were obtained by performing a restricted set of NMR experiments, without performing a complete assignment of the protein signals. The aim was to exploit the special restraints arising from the paramagnetism of the metal ion. A total of 43 residual-dipolar-coupling and 74 pseudocontact-shift restraints, which together sampled all regions of the protein, were used in conjunction with over 40 routinely obtained NOE distance restraints. A calculation procedure was undertaken combining the program MODELLER and the solution structure determination program PARAMAGNETIC DYANA, which includes paramagnetism-based restraints. The directions and magnitude of the magnetic susceptibility anisotropy tensor were also calculated. The approach readily provides useful results, especially for paramagnetic metalloproteins of moderate to large dimensions.
Bertini
Ivano
I
CERM and Department of Chemistry, University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. bertini@cerm.unifi.it
Faraone-Mennella
Jasmin
J
Gray
Harry B
HB
Luchinat
Claudio
C
Parigi
Giacomo
G
Winkler
Jay R
JR
D000465:Algorithms; D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D003574:Cytochrome c Group / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D011487:Protein Conformation; D015203:Reproducibility of Results; D012241:Rhodopseudomonas / Q000201:enzymology*
D003574:Cytochrome c Group; C020267:cytochrome c556