(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > Proteobacteria: NE > Alphaproteobacteria: NE > Rhizobiales: NE > Bradyrhizobiaceae: NE > Bradyrhizobium: NE > Bradyrhizobium japonicum: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acid identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Bradyrhizobium japonicum USDA 6: N, E.
Bradyrhizobium japonicum SEMIA 5079: N, E.
Bradyrhizobium diazoefficiens USDA 110: N, E.
Molecular evidence
Database
No mutation 4 structures(e.g. : 3A2L, 3A2M, 3A2N... more)(less) 3A2L: Crystal structure of DBJA (HIS-DBJA) Bradyrhizobium japonicum haloalkane dehalogenase (mutant dbja delta), 3A2M: Crystal structure of DBJA (HIS-DBJA) Bradyrhizobium japonicum haloalkane dehalogenase (WILD TYPE Type I), 3A2N: Crystal structure of DBJA (HIS-DBJA) Bradyrhizobium japonicum haloalkane dehalogenase (Wild Type Type II P21), 3AFI: Crystal structure of DBJA (HIS-DBJA) Bradyrhizobium japonicum haloalkane dehalogenase No kinetic
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MSKPIEIEIRRAPVLGSSMAYRETGAQDAPVVLFLHGNPTSSHIWRNILP LVSPVAHCIAPDLIGFGQSGKPDIAYRFFDHVRYLDAFIEQRGVTSAYLV AQDWGTALAFHLAARRPDFVRGLAFMEFIRPMPTWQDFHHTEVAEEQDHA EAARAVFRKFRTPGEGEAMILEANAFVERVLPGGIVRKLGDEEMAPYRTP FPTPESRRPVLAFPRELPIAGEPADVYEALQSAHAALAASSYPKLLFTGE PGALVSPEFAERFAASLTRCALIRLGAGLHYLQEDHADAIGRSVAGWIAG IEAVRPQLAA
An enzyme's substrate specificity is one of its most important characteristics. The quantitative comparison of broad-specificity enzymes requires the selection of a homogenous set of substrates for experimental testing, determination of substrate-specificity data and analysis using multivariate statistics. We describe a systematic analysis of the substrate specificities of nine wild-type and four engineered haloalkane dehalogenases. The enzymes were characterized experimentally using a set of 30 substrates selected using statistical experimental design from a set of nearly 200 halogenated compounds. Analysis of the activity data showed that the most universally useful substrates in the assessment of haloalkane dehalogenase activity are 1-bromobutane, 1-iodopropane, 1-iodobutane, 1,2-dibromoethane and 4-bromobutanenitrile. Functional relationships among the enzymes were explored using principal component analysis. Analysis of the untransformed specific activity data revealed that the overall activity of wild-type haloalkane dehalogenases decreases in the following order: LinB~DbjA>DhlA~DhaA~DbeA~DmbA>DatA~DmbC~DrbA. After transforming the data, we were able to classify haloalkane dehalogenases into four SSGs (substrate-specificity groups). These functional groups are clearly distinct from the evolutionary subfamilies, suggesting that phylogenetic analysis cannot be used to predict the substrate specificity of individual haloalkane dehalogenases. Structural and functional comparisons of wild-type and mutant enzymes revealed that the architecture of the active site and the main access tunnel significantly influences the substrate specificity of these enzymes, but is not its only determinant. The identification of other structural determinants of the substrate specificity remains a challenge for further research on haloalkane dehalogenases.
The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Gottfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.
Bradyrhizobium japonicum; Bradyrhizobium diazoefficiens, haloalkane dehalogenase (EC 3.8.1.5) DhaA DbjA
