Modeling the structure of Pyrococcus furiosus rubredoxin by homology to other X-ray structures.
The three-dimensional structure of rubredoxin from the hyperthermophilic archaebacterium, Pyrococcus furiosus, has been modeled from the X-ray crystal structures of three homologous proteins from Clostridium pasteurianum, Desulfovibrio gigas, and Desulfovibrio vulgaris. All three homology models are similar. When comparing the positions of all heavy atoms and essential hydrogen atoms to the recently solved crystal structure (Day, M. W., et al., 1992, Protein Sci. 1, 1494-1507) of the same protein, the homology model differ from the X-ray structure by 2.09 A root mean square (RMS). The X-ray and the zinc-substituted NMR structures (Blake, P. R., et al., 1992b, Protein Sci. 1, 1508-1521) show a similar level of difference (2.05 A RMS). On average, the homology models are closer to the X-ray structure than to the NMR structures (2.09 vs. 2.42 A RMS).
Wampler
J E
JE
Department of Biochemistry, University of Georgia, Athens 30602.
Bradley
E A
EA
Stewart
D E
DE
Adams
M W
MW
D000595:Amino Acid Sequence; D001105:Archaea / Q000737:chemistry*; D003013:Clostridium / Q000737:chemistry; D003901:Desulfovibrio / Q000737:chemistry; D016969:Desulfovibrio vulgaris / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D012416:Rubredoxins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D014961:X-Ray Diffraction
D012416:Rubredoxins