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( Priyadarshi Amit ),( Eun Hye Lee ),( Min Woo Sung ),( Jae Hee Kim ),( Min Je Ku ),( Eunice Eun Kyeong Kim ),( Kwang Yeon Hwang ) 한국미생물 · 생명공학회 2008 Journal of microbiology and biotechnology Vol.18 No.1
Alanine racemase, a bacterial enzyme belonging to the fold-type III group of pyridoxal 5`-phosphate (PLP)-dependent enzymes, has been shown to catalyze the interconversion between L- and D-alanine. The alanine racemase from the pathogenic bacterium Enterococcus faecalis v583 has been overexpressed in E. coli and was shown to crystallize an enzyme at 295 K, using polyethylene glycol (PEG) 8000 as a precipitant. X-ray diffraction data to 2.5 Å has been collected using synchrotron radiation. The crystal is a member of the orthorhombic space group, C222₁, with unit cell parameter of a=94.634, b=156.516, c=147.878Å, and α=β=γ=90˚. Two or three monomers are likely to be present in the asymmetric unit, with a corresponding Vm of 3.38Å3 Da-1 and 2.26 Å3 Da-1¹ and a solvent content of 63.7% and 45.5%, respectively.
( Kook Han Kim ),( Jung Jung Eun ),( Hana Im ),( Daniel Van Der Lelie ),( Eunice Eun Kyeong Kim ) 한국미생물 · 생명공학회 2008 Journal of microbiology and biotechnology Vol.18 No.1
The nickel and cobalt resistance of Cupriavidus metallidurans CH34 is mediated by the CnrCBA efflux pump encoded by the cnrYHXCBAT metal resistance determinant. The products of the three genes cnrYXH transcriptionally regulate expression of cnr. CnrY and CnrX are membranebound proteins, probably functioning as anti-sigma factors, whereas CnrH is a cnr-specific extracytoplasmic functions (ECF) sigma factor. The periplasmic domain of CnrX (residues 29-148) was cloned as a N-terminal His-tagged protein, expressed in Escherichia coli, and purified using affinity chromatography and gel filtration. The molecular mass was estimated to be about 13.6 kDa by size exclusion chromatography, corresponding to a monomer. The tetragonal bipyramid crystals were obtained by mixing an equal volume of protein in 50 mM Tris-HCl, pH 7.5, 1% glycerol, 100 mM NaCl, 1 mM DTT, and the reservoir solution of 15% w/v PEG 2000, 100 mM lithium chloride at 277 K in 2-4 days using hanging drop vapor diffusion. The protein concentration was 24 mg/ml. The crystal that diffracted to 2.42 Å resolution belongs to space group P41 or P43 with unit cell parameters of a=b=32.14 Å, c=195.31 Å, α=β=γ=90°, with one molecule of CnrX in the asymmetric unit.
Characterization of Peptide Deformylase2 from B. cereus
Park, Joon-Kyu,Kim, Kook-Han,Moon, Jin-Ho,Kim, Eunice Eun-Kyeong Korean Society for Biochemistry and Molecular Biol 2007 Journal of biochemistry and molecular biology Vol.40 No.6
Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, some bacteria including medically relevant pathogens possess two or more def-like genes. Here we have examined two PDFs from Bacillus cereus. The two share only 32% sequence identity and the crystal structures show overall similarity with PDF2 having a longer C-terminus. However, there are differences at the two active sites, and these differences appear to contribute to the activity difference seen between the two. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface.
Synthesis and Antibacterial Activity of Novel 2-Oxo-pyrrolidinyl Oxazolidinones
Bhattarai, Deepak,Lee, Sun-Hee,Kim, Hyeong-Kyu,Kang, Soon-Bang,Pae, Ae-Nim,Kim, Eunice Eun-Kyeong,Oh, Taeg-Won,Cho, Sang-Nae,Keum, Gyo-Chang Korean Chemical Society 2012 Bulletin of the Korean Chemical Society Vol.33 No.4
Novel antibacterial oxazolidinones bearing pyrrolidinone ring system at the C-5 side chain were synthesized and their in vitro antibacterial activities were evaluated. Most of the synthesized oxazolidinones showed good antibacterial activity against the Gram-positive and Gram-negative bacteria tested.
Structural basis for Ufm1 processing by UfSP1.
Ha, Byung Hak,Ahn, Hee-Chul,Kang, Sung Hwan,Tanaka, Keiji,Chung, Chin Ha,Kim, Eunice Eun Kyeong American Society for Biochemistry and Molecular Bi 2008 The Journal of biological chemistry Vol.283 No.21
<P>Ubiquitin-fold modifier 1 (Ufm1) is a newly identified ubiquitin-like protein. Like ubiquitin and other ubiquitin-like proteins, Ufm1 is synthesized as a precursor that needs to be processed to expose the conserved C-terminal glycine prior to its conjugation to target proteins. Two novel proteases, named UfSP1 and UfSP2, have been shown to be responsible for the release of Ufm1 from Ufm1-conjugated cellular proteins as well as for the processing of its precursor. They show no sequence homology with known proteases. Here, we describe the 1.7A resolution crystal structure of mouse UfSP1, consisting of 217 amino acids. The structure reveals that it is a novel cysteine protease having a papain-like fold, with Cys(53), Asp(175), and His(177) that form a catalytic triad, and Tyr(41) that participates in the formation of the oxyanion hole. This differs from the canonical catalytic triad of papain-like proteases in that the aspartate and the histidine residues are from the 'Asp-Pro-His' box. The Asp-Pro-His configuration seen in UfSP1, together with Atg4B and M48(USP), seem to form a new subfamily of the cysteine protease superfamily. The mutagenesis study of the active site residues confirms structural basis for catalysis. The interaction between UfSP1 and Ufm1 appears quite substantial, since the K(D) value was estimated to be 1.6 mum by the isothermal titration calorimetry analysis. Furthermore, the NMR data shows that the loop between beta3 and alpha2 in addition to the C-terminal region of Ufm1 plays a role in binding to UfSP1.</P>