Journal of Microbiology

Joong-Su Kim

2 Articles

Structural insight for substrate tolerance to 2-deoxyribose-5-phosphate aldolase from the pathogen Streptococcus suis: Thinh-Phat Cao , Joong-Su Kim , Mi-Hee Woo , Jin Myung Choi , Youngsoo Jun , Kun Ho Lee , Sung Haeng Lee; J. Microbiol. 2016;54(4):311-321. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-6029-4

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2-deoxyribose-5-phosphate aldolase (DERA) is a class I aldolase that catalyzes aldol condensation of two aldehydes in the active site, which is particularly germane in drug manufacture. Structural and biochemical studies have shown that the active site of DERA is typically loosely packed and displays broader substrate specificity despite sharing conserved folding architecture with other aldolases. The most distinctive structural feature of DERA compared to other aldolases is short and flexible C-terminal region. This region is also responsible for substrate recognition. Therefore, substrate tolerance may be related to the C-terminal structural features of DERA. Here, we determined the crystal structures of full length and C-terminal truncated DERA from Streptococcus suis (SsDERA). In common, both contained the typical (α/β)8 TIM-barrel fold of class I aldolases. Surprisingly, C-terminal truncation
result
ing in missing the last α9 and β8 secondary elements, allowed DERA to maintain activity comparable to the fulllength enzyme. Specifically, Arg186 and Ser205 residues at the C-terminus appeared mutually supplemental or less indispensible for substrate phosphate moiety recognition. Our results suggest that DERA might adopt a shorter C-terminal region than conventional aldolases during evolution pathway, resulting in a broader range of substrate tolerance through active site flexibility.

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Bacillus manliponensis sp. nov., a New Member of the Bacillus cereus Group Isolated from Foreshore Tidal Flat Sediment: Min Young Jung , Joong-Su Kim , Woon Kee Paek , Jeongheui Lim , Hansoo Lee , Pyoung Il Kim , Jin Yeul Ma , Wonyong Kim , Young-Hyo Chang; J. Microbiol. 2011;49(6):1027-1032. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1049-6

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A Gram-positive, endospore-forming, new Bacillus species, strain BL4-6T, was isolated from tidal flat sediment of the Yellow Sea. Strain BL4-6T is a straight rod, with motility by peritrichate flagella. The cell wall contains meso-diaminopimelic acid, and the major respiratory quinone is menaquinone-7. The major fatty acids are iso-C15:0 and summed feature 3 (containing C16:1 ω7c/ iso-C15:0 2OH, and/or iso-C15:0 2OH/C16:1 ω7c). Cells are catalase-positive and oxidase-negative. The G+C content of the genomic DNA is 38.0 mol%. Based on a comparative 16S rRNA gene sequence analysis, the isolate belongs to the genus Bacillus, forms a clade with the Bacillus cereus group, and is closely related to Bacillus mycoides (98.5%), Bacillus cereus (98.5%), Bacillus anthracis (98.4%), Bacillus thuringiensis (98.4%), Bacillus weihenstephanensis (98.1%), and Bacillus pseudomycoides (97.5%). The isolate showed less than 85% similarity of the gyrA gene sequence and below 95% similarity of the rpoB gene sequence to the members of this group. DNA-DNA relatedness between strain BL4-6T and B. cereus group was found to be in a range of 22.8-42.3%, and thus BL4-6T represents a unique species. On the basis of these studies, strain BL4-6T (=KCTC 13319T =JCM 15802T) is proposed to represent the type strain of a novel species, Bacillus manliponensis sp. nov.

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