https://repository.kopri.re.kr/handle/201206/11600 Thu, 05 Mar 2026 07:31:46 GMT 2026-03-05T07:31:46Z https://repository.kopri.re.kr/handle/201206/12983 Title: Structural basis of the cooperative activation of type II citrate synthase (HyCS) from Hymenobacter sp. PAMC 26554 Authors: Park, Sun-Ha; Lee, Chang Woo; Bae, Da-Woon; Do, Hackwon; Jeong, Chang-Sook; Hwang, Jisub; Cha, Sun-Shin; Lee, Jun Hyuck Abstract: Citrate synthase (CS) catalyzes the formation of citrate and coenzyme A from acetyl-CoA and oxaloacetate. CS exists in two forms: type I and type II. We determined the citrate-bound crystal structure of type II CS from the Hymenobacter sp. PAMC 26554 bacterium (HyCS; isolated from Antarctic lichen). Citrate molecules bound to a cleft between the large and small domains of HyCS. Structural comparison of HyCS with other type II CSs revealed that type II CSs have a highly conserved flexible hinge region (residues G264-P265 in HyCS), enabling correct positioning of active site residues. Notably, the catalytic His266 residue of HyCS interacted with Trp262 in the inactive (unliganded open) state of other type II CSs, whereas the His266 residue moved to the active site via a small-domain swing motion, interacting with the bound citrate in the closed conformation of HyCS. However, type I CSs lack this tryptophan residue and face-to-edge interactions. Thus, type II CSs might have a unique domain-motion control mechanism enabling a tight allosteric regulation. An activity assay using a W262A mutant showed a Hill coefficient of 2.4; thus, the interaction between Trp262 and His266 was closely related to the positive cooperative ligand binding of type II CS. (c) 2021 Published by Elsevier B.V. Sat, 31 Jul 2021 00:00:00 GMT https://repository.kopri.re.kr/handle/201206/12983 2021-07-31T00:00:00Z https://repository.kopri.re.kr/handle/201206/12182 Title: Identification of xylanase and acetyl xylan esterase for effective bioenergy Authors: Kim, T. Doohun Mon, 01 Mar 2021 00:00:00 GMT https://repository.kopri.re.kr/handle/201206/12182 2021-03-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/11851 Title: Evaluation of assembly methods combining long-reads and short-reads to obtain Paenibacillus sp. R4 high-quality complete genome Authors: Shin, Seung Chul; Choi, Woong; Lee, Jun Hyuck; Kim, Hyo Jin; Kim, Han-Woo Abstract: We sequenced the Paenibacillus sp. R4 using Oxford Nanopore Technology (ONT), single molecule real-time (SMRT) technology from Pacific Biosciences (PacBio), and Illumina technologies to investigate the application of nanopore reads in de novo sequencing of bacterial genomes. We compared the differences in both genome sequences between genome assemblies using nanopore and PacBio reads and focused on the difference in the prediction of coding sequences. The results indicated that for more accurate predictions of open reading frames, contigs in the assemblies using only PacBio reads also needed to be corrected using short reads with highquality bases, and repeat regions in genomes did not affect the increase of mispredicted coding sequences via genome polishing significantly. In assemblies using only nanopore reads, genome polishing was essential, but many repeat regions in genomes might increase the number of mispredicted coding sequences via genome polishing. The hybrid assembly combining the long reads and short reads represents the best result for coding sequence predictions in genome assemblies using nanopore reads. Thu, 01 Oct 2020 00:00:00 GMT https://repository.kopri.re.kr/handle/201206/11851 2020-10-01T00:00:00Z