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1.  Regulatory System of the Protocatechuate 4,5-Cleavage Pathway Genes Essential for Lignin Downstream Catabolism ▿ §  
Journal of Bacteriology  2010;192(13):3394-3405.
Sphingobium sp. strain SYK-6 converts various lignin-derived biaryls with guaiacyl (4-hydroxy-3-methoxyphenyl) and syringyl (4-hydroxy-3,5-dimethoxyphenyl) moieties to vanillate and syringate. These compounds are further catabolized through the protocatechuate (PCA) 4,5-cleavage (PCA45) pathway. In this article, the regulatory system of the PCA45 pathway is described. A LysR-type transcriptional regulator (LTTR), LigR, activated the transcription of the ligK-orf1-ligI-lsdA and ligJABC operons in the presence of PCA or gallate (GA), which is an intermediate metabolite of vanillate or syringate, respectively, and repressed transcription of its own gene. LigR bound to the positions −77 to −51 and −80 to −48 of the ligK and ligJ promoters, respectively, and induced DNA bending. In the presence of PCA or GA, DNA bending on both promoters was enhanced. The LigR-binding regions of the ligK and ligJ promoters in the presence of inducer molecules were extended and shortened, respectively. The LTTR consensus sequences (Box-K and Box-J) in the ligK and ligJ promoters were essential for the binding of LigR and transcriptional activation of both operons. In addition, the regions between the LigR binding boxes and the −35 regions were required for the enhancement of DNA bending, although the binding of LigR to the −35 region of the ligJ promoter was not observed in DNase I footprinting experiments. This study shows the binding features of LigR on the ligK and ligJ promoters and explains how the PCA45 pathway genes are expressed during degradation of lignin-derived biaryls by this bacterium.
PMCID: PMC2897667  PMID: 20435721
2.  Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110 
A haloalkane dehalogenase, DbjA, was crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystal belongs to the orthorhombic system, space group P21212 and diffracts to 1.75 Å resolution.
Haloalkane dehalogenases are key enzymes for the degradation of halogenated aliphatic pollutants. The haloalkane dehalogenase DbjA constitutes a novel substrate-specificity class with high catalytic activity for β-methylated haloalkanes. In order to reveal the mechanism of its substrate specificity, DbjA has been crystallized using the hanging-drop vapour-diffusion method. The best crystals were obtained using the microseeding technique with a reservoir solution consisting of 17–19.5%(w/v) PEG 4000, 0.2 M calcium acetate and 0.1 M Tris–HCl pH 7.7–8.0. The space group of the DbjA crystal is P21212, with unit-cell parameters a = 212.9, b = 117.8, c = 55.8 Å. The crystal diffracts to 1.75 Å resolution.
PMCID: PMC2330215  PMID: 17401198
haloalkane dehalogenases; biodegradation; α/β hydrolases; rhizobia
3.  Crystallization and preliminary crystallographic analysis of DtsR1, a carboxyltransferase subunit of acetyl-CoA carboxylase from Corynebacterium glutamicum  
DtsR1, a carboxyltransferase subunit of acetyl-CoA carboxylase from C. glutamicum, was crystallized and phases were obtained by molecular replacement.
DtsR1, a carboxyltransferase subunit of acetyl-CoA carboxylase derived from Corynebacterium glutamicum, was crystallized by the sitting-drop vapour-diffusion method using polyethylene glycol 6000 as a precipitant. The crystal belongs to the trigonal system with space group R32 and contains three subunits in the asymmetric unit. A molecular-replacement solution was found using the structure of transcarboxylase 12S from Propionibacterium shermanii as a search model.
PMCID: PMC2330119  PMID: 17277455
acetyl-CoA carboxylase; carboxyltransferases; metabolic engineering

Results 1-3 (3)