Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum.
Structures of the Bradyrhizobium japonicum FixL heme domain have been determined in the absence and presence of specific ligands to elucidate the detailed features of its O2 sensing mechanism. The putative roles of spin-state and steric hindrance were evaluated by the structure determination of ferrous CO-bound BjFixLH and correlating its features with other ligand-bound structures. As found for NO-BjFixLH, no protein conformational change was observed in CO-BjFixLH, suggesting a more complicated mechanism than solely spin state or ligand sterics. To evaluate the role of oxidation state, the structure of the ferrous deoxy-BjFixLH was determined. The structure of deoxy-BjFixLH was found to be virtually identical to the structure of the ferric met-BjFixLH. The role of hydrogen bonding of substrates to a heme-pocket water was evaluated by determining the structure of BjFixLH bound to 1-methyl-imidazole that cannot form a hydrogen bond with this water. In this case, the heme-mediated conformational change was observed, limiting the potential importance of this interaction. Finally, the structure of cyanomet-BjFixLH was revisited to rule out concerns regarding the partial occupancy of the cyanide ligand in a previous structure. In the revised structure, Arg 220 was found to move into the heme pocket to form a hydrogen bond to the bound cyanide ligand. The implications of these results on FixL's sensing mechanism are discussed.
Hao
Bing
B
Department of Biochemistry, and The Ohio State Biophysics Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.
Isaza
Clara
C
Arndt
Joseph
J
Soltis
Michael
M
Chan
Michael K
MK
D001120:Arginine / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D020369:Bradyrhizobium / Q000737:chemistry*; D002248:Carbon Monoxide / Q000737:chemistry; D018360:Crystallography, X-Ray; D003486:Cyanides / Q000737:chemistry; D005290:Ferric Compounds / Q000737:chemistry; D005296:Ferrous Compounds / Q000737:chemistry; D006418:Heme / Q000737:chemistry*; D006420:Hemeproteins / Q000737:chemistry*; D000071677:Histidine Kinase; D006860:Hydrogen Bonding; D007093:Imidazoles / Q000737:chemistry; D007536:Isomerism; D008024:Ligands; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship
D001426:Bacterial Proteins; D003486:Cyanides; D005290:Ferric Compounds; D005296:Ferrous Compounds; D006420:Hemeproteins; D007093:Imidazoles; D008024:Ligands; D006418:Heme; D002248:Carbon Monoxide; D001120:Arginine; C067929:FixL protein, Bacteria; D000071677:Histidine Kinase; C018100:1-methylimidazole; D010100:Oxygen