BioLab
경북대학교 생명과학부 Structural & Molecular Biology Lab.
김경진 교수
연구실 소개
연구실 홈페이지연구분야
1. Biological decomposition of non-biodegradable plastics
“Is it possible to decompose the non-biodegradable plastics, such as PE, PP, and PET at environments?”
Plastics, including poly(ethylene terephthalate) (PET), have become a necessity for our lives due to their versatile properties such as low-price, lightness, castability and non-degradability. The mass production and use of plastics, however, has led to the accumulation of plastic waste in landfills and the ocean.
Recently, the PET-degrading bacterium Ideonella sakaiensis 201-F6 was isolated by Kohei Oda group from PET debris-contaminated environmental samples. The bacterium degrades PET using PET hydrolase (PETase), monohydroxyethyl terephthalate (MHET) hydrolase (MHETase), and terephthalic acid (TPA)-degrading enzymes. Although the complete degradation of a chip of amorphous PET film (1.9% crystallinity) by the microbe took 6 weeks, it was the first case of bacteria evolved in anthropogenic environments within a hundred of years, showing the possibility of PET degradation using microorganisms at 30°C.
PET degradation under ambient temperatures is highly desirable, and therefore, PET waste management using PETase and MHETase is promising. We have performed structural studies and enzyme engineering with these two enzymes.
Still, we are working on the biodegradation of plastics. Discovery, structure, mechanism, function, and protein/microbe engineering will provide advancements for the plastic issues.
2. Utilization of lignocellulosic biomass
“Lignin Is Garbage? No! It Natural resource.”
Lignin is an aromatic polymer that form key structural materials of vascular plants. Because the biomass of plants account for 82% in earth, lignin’s chemical composition up to 35% in wood plants make the material an unignorable resource with huge potential today. But degradation of lignocellulosic biomass is still tough, and scientists want to accelerate the decomposition of the rigid and complex polymer.
The known natural pathways of lignin degradation are not initiated by hydrolysis like other polymer degradation, but it is degraded by oxidases such as lignin peroxidase, manganese peroxidase, laccase, ETC. However, the depolymerization of lignin by those enzymes is not enough to be efficient, because of the repolymerization and enzyme damage by the radical species generated.
Our purpose is discovery of novel lignin depolymerizing enzyme in nature, and development of the enzyme though structure-based protein engineering. Also, we are interested in cellulose/xylose utilization by common microbes, such as E. coli.
3. Enzymes for biosynthesis of bioplastics
“A sustainable alternative to petroleum-based plastics: Polyhydroxyalkanoates”
Plastics have become an essential material in human life due to its properties, such as lightness, low price, easy to make desired articles, and resistance to biodegradation. However, due to the environmental issues and the limited petroleum resources, the environment-friendly and sustainable bioplastics have gained significant attention.
Polyhydroxyalkanoates (PHAs) are one of natural polyesters and synthesized by numerous microorganism for carbon and energy storage material. The first characterized and the best representative PHA biosynthetic pathway is that for the synthesis of poly(3-hydroxybutyrate) (PHB) comprising three crucial enzymes, acetyl-CoA acetyltransferase (β-ketothiolase; PhaA), acetoacetyl-CoA reductase (PhaB), and PHA synthase (PhaC). Despite of extensive studies on this pathway, the detailed molecular mechanisms of PHA biosynthesis have remained unclear due to the lack of structural information on PHA biosynthetic enzymes.
We focus on the structure-based molecular mechanisms of each enzyme as well as the overall mechanism of PHA biosynthesis and protein engineering for more efficient production of tailor-made PHAs for diverse industrial and medical applications.
4. Enzymes for biosynthesis of fuels
“How to make the renewable biofuels economical: produce more efficiently and more valuable biofuels for transportation”
The depletion of fossil-based fuels led to the development of alternative sources of energy to traditional fuels.
n-butanol is one of the most promising biofuel sources and contains various strength, such as high energy content, less corrosive nature, and less solubility in water, and easy to blend with gasoline or diesel fuels. Clostridia are the main fermentative organisms used for the production of biobutanol through the acetone-butanol-ethanol (ABE) fermentation pathway. Although, a large number of efforts have been made to improve n-butanol production in ABE fermentation, the final titer of n-butanol is limited.
The detailed understanding of the function and regulation of key enzymes involved in the n-butanol biosynthetic pathway might provide invaluable information to optimize heterologous metabolic pathways and maximize the n-butanol yield from engineered non-solventogenic microbes. We have performed structural and protein engineering studies on the crucial enzymes in n-butanol biosynthesis from C. acetobutylicum.
5. Efficient biosynthesis of amino acids
“How to make the renewable biofuels economical: produce more efficiently and more valuable biofuels for transportation”
Proteins are indispensable molecules in all life processes and are composed of 20 amino acids as a building block. Among the 20 amino acids, the essential amino acids can’t be synthesized in cells and must be taken in foods and supplementary materials. Due to the increase in global meat consumption, it is important to provide essential amino acids to livestock for their fast growth.
To date, amino acids have been produced by extraction from protein-hydrolysates, chemical synthesis, microbial processes (enzymatic synthesis and fermentation). Most of current industrial productions are based on fermentation by E. coli and C. glutamicum. Many studies on the improvement of amino acid productivity have been performed using metabolic engineering techniques and the productivity is maximized.
A new approach to enhance the amino acid productivity is required for further increase in amino acid productivity. Among 9 essential amino acids, we focus on three major feed additives, such as lysine, methionine, and valine. Our purpose is to develop the new strain with highly efficient amino acid productivity using structure-based protein engineering.
연구성과
Publications(최근 3년, 2020~2022)
- 2022년
Structural insight into a molecular mechanism of methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1
Seongmin Kim, Seul Hoo Lee, Il-Kwon Kim, Hogyun Seo, Kyoung-Jin Kim, Hoo Lee, Hogyun Seo, Kyung-Jin Kim
International Journal of Biological Macromolecules 6.953, 202 , 234-240 , 11.49
Structural and functional characterization of an auxiliary domain-containing PET hydrolase from Burkholderiales bacterium
Hye-Young Sagong, Seongmin Kim, Donghoon Lee, Hwaseok Hong, Seul, Hoo Lee, Hogyun Seo, Kyung-Jin Kim
Journal of Hazardous Materials 10.588, 3.47
- 2021년
Structural analysis of the peptidoglycan editing factor PdeF from Bacillus cereus ATCC 14579
Jihye Seok, Jiyeon Hong, Jiyoung Park, Kyung-Jin Kim
Biochemical and Biophysical Research Communications 3.575 , 583 , 43-48 , 34.46%
Crystal structure and molecular mechanism of phosphotransbutyrylase from Clostridium acetobutylicum.
Sangwoo Kim, Kyung-Jin Kim
Journal of Microbiology and Biotechnology 2.351, 31(10) , 1-9 , 70.61%
Crystal Structure and Functional Characterization of the Bifunctional N-(5′-Phosphoribosyl)anthranilate Isomerase-indole-3-glycerol-phosphate Synthase from Corynebacterium glutamicum
Woojin Park, Hyeoncheol Francis Son, Donghoon Lee, Il-Kwon Kim, Kyung-Jin Kim
Journal of Agricultural and Food Chemistry 5.279 , 69 , 12485-12493 , 6.63%
Purification, crystallization and X-ray crystallographic analysis of methylmalonyl- CoA epimerase from Metallosphaera sedula
Seongjoon Joo, Seul Hoo Lee, Donghoon Lee, Kyung-Jin Kim
BIODESIGN - , 9 , 32-35 , -
Cβ-Selective Aldol Addition of d-Threonine Aldolase by Spatial Constraint of Aldehyde Binding
Sung-Hyun Park, Hogyun Seo, Jihye Seok, Haseong Kim, Kil Koang Kwon, Soo-Jin Yeom, Seung-Goo Lee, Kyung-Jin Kim
ACS Catalysis 12.350, 11 , 6892-6899 , 7.233%
Implications for the PET decomposition mechanism through similarity and dissimilarity between PETases from Rhizobacter gummiphilus and Ideonella sakaiensis
Hye-Young Sagong, Hyeoncheol Francis Son, Hogyun Seo, Hwaseok, Hong, Donghoon Lee, Kyung-Jin Kim
Journal of Hazardous Materials 9.038 , 416 , - , 2.83%
Extra disulfide and ionic salt bridge improves the thermostability of lignin peroxidase H8 under acidic condition
Haewon Son, Hogyun Seo, Seunghyun Han, Suk Min Kim, Le Thanh Mai Pham, Mohd Faheem Khan, Ho Joon Sung, Sung-heuck Kang, Kyung-Jin Kim, Yong Hwan Kim
Enzyme and Microbial Technology 3.448 , 148 , - , 31.09%
Dual α-1,4- and β-1,4-Glycosidase Activities by the Novel Carbohydrate-Binding Module in α-l-Fucosidase from Vibrio sp. Strain EJY3
Hwaseok Hong, Do Hyoung Kim, Hogyun Seo, Kyoung Heon Kim, Kyung-Jin Kim
Journal of Agricultural and Food Chemistry 4.192 , 69 , 3380-3389 , 6.034%
Crystal Structure and Regiospecificity of Catechol O-Methyltransferase from Niastella koreensis
Seul Hoo Lee, Bongsang Kim, Kyung-Jin Kim
Journal of Agricultural and Food Chemistry 4.192 , 69 , 2531-2538 , 6.034%
Structural basis for nucleotide-independent regulation of acyl-CoA thioesterase from Bacillus cereus ATCC 14579
Jiyoung Park, Yeo-Jin Kim, Donghoon Lee, Kyung-Jin Kima
International Journal of Biological Macromolecules 5.162 , 170 , 390-396 , 9.551%
- 2020년
Structural and Functional Characterization of Cystathionine γ-lyase from Bacillus cereus ATCC 14579
Hye-Young Sagong, Bongsang Kim, Seongjoon Joo, Kyung-Jin Kim
Journal of Agricultural and Food Chemistry 4.192 , 68 , 15267-15274 , 6.034%
Crystal structure of an acetyl-CoA acetyltransferase from PHB producing bacterium Bacillus cereus ATCC 14579
Jiyeon Hong, Woojin Park, Hogyun Seo, Il-Kwon Kim, Kyung-Jin Kim
Biochemical and Biophysical Research Communications 2.985 , 533 , 442-448 , 35.915%
Metabolic engineering of Escherichia coli for production of non-natural acetins from glycerol
Bakht Zada, Seongjoon Joo, Chonglong Wang, Tenzin Tseten, Seong-Hee Jeong, Hogyun Seo, Jung-Hoon Sohn, Kyung-Jin Kim, Seon-Won Kim
Green Chemistry 9.480 , 22 , 7788-7802 , 3.659%
Structural bioinformatics-based protein engineering of thermo-stable PETase from Ideonella sakaiensis
Hyeoncheol Francis Son, Seongjoon Joo, Hogyun Seo, Hye-Young Sagong, Seul Hoo Lee, Hwaseok Hong, Kyung-Jin Kim
ISSN: 0141-0229 Enzyme and Microbial Technology 3.448 , 141 , 31.09%
High Galacto-Oligosaccharide Production and a Structural Model for Transgalactosylation of β-Galactosidase II from Bacillus circulans
Jae Youl Choi, Hwaseok Hong, Hogyun Seo, Jae Gu Pan, Eui Joong Kim, Pil Jae Maeng, Taek Ho Yang, Kyung-Jin Kim
Journal of Agricultural and Food Chemistry 4.192 , 68 (47) , 13806-13814 , 6.034%
Biochemical properties and crystal structure of isocitrate lyase from Bacillus cereus ATCC 14579
Seul Hoo Lee, Dongwoo Ki, Sangwoo Kim, Il-Kwon Kim, Kyung-Jin Kim
Biochemical and Biophysical Research Communications 2.985 , 533 , 1177-1183 , 35.915%
Structural basis for stereospecificity to d-amino acid of glycine oxidase from Bacillus cereus ATCC 14579
Jihye Seok, Yeo-Jin Kim, Il-Kwon Kim, Kyung-Jin Kim
Biochemical and Biophysical Research Communications 2.985 , 533 , 824-830 , 35.915%
Purification, crystallization and X-ray crystallographic analysis of glycine oxidase from Bacillus cereus ATCC 14579
Jihye Seok, Kyung-Jin Kim
Biodesign , 8 , 68-71
Biochemical properties and crystal structure of formate-tetrahydrofolate ligase from Methylobacterium extorquens CM4
Seongmin Kim, Seul Hoo Lee, Hogyun Seo, Kyung-Jin Kim
Biochemical and Biophysical Research Communications 2.705 , 528 , 426-431 , 37.67%
Microbial Polyhydroxyalkanoates and Nonnatural Polyesters
So Young Choi, In Jin Cho, Youngjoon Lee, Yeo-Jin Kim, Kyung-Jin Kim, Sang Yup Lee
Advanced Materials 25.809 , 1.01%
Enhanced succinic acid production by Mannheimia employing optimal malate dehydrogenase
Jung Ho Ahn, Hogyun Seo, Woojin Park, Jihye Seok, Jong An Lee, Won Jun Kim, Gi Bae Kim, Kyung-Jin Kim, Sang Yup Lee
Nature Communications 12.121 , 11 , 1970 , 7.24%
Decomposition of the PET Film by MHETase Using Exo-PETase Function
Hye-Young Sagong, Hogyun Seo, Taeho Kim, Hyeoncheol Francis Son, Seongjoon Joo, Seul Hoo Lee, Seongmin Kim, Jae-Sung Woo, Sung Yeon Hwang, Kyung-Jin Kim
ACS Catalysis 12.350 , 10 , 4805-4812 , 7.43%
Structural insight into bi-functional malonyl-CoA reductase
Hyeoncheol Francis Son, Sangwoo Kim, Hogyun Seo, Jiyeon Hong, Donghoon Lee, Kyeong Sik Jin, Sunghoon Park, Kyung-Jin Kim
Environmental Microbiology 5.147 , 15.79%
Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies
Hwaseok Hong, Hogyun Seo, Woojin Park, Kyung-Jin Kim
Environmental Microbiology 5.147 , 15.79%
Patents
아세틴 화합물의 생물학적 제조 방법
김선원, 바크자다, 김경진, 정성희 , 10-2019-0134943 , 10-2320656
고온에서 PET 분해 활성을 갖는 PETase 변이체
김경진 , 10-2020-0060246 , 10-2298651
말단을 가지는 폴리에틸렌 테레프탈레이트 고분자에 대한 외부 가수분해 활성을 가지는 MHETase 변이체
김경진 , 10-2020-0001693 , 10-2261596
ISPETASE VARIANTS
Kyung Jin Kim , 10-2019-0017256 , 10-2088340
재조합 PETase 생산 균주, 재조합 MHETase 생산 균주 및 이를 포함하는 PET 분해용 조성물
김경진 , 10-2018-0154759 , 10-2176506
고활성의 말산 탈수소효소가 도입된 숙신산 생성용 변이 미생물 및 이를 이용한 숙신산 제조방법
이상엽, 김경진, 안정호, 서호균, 이종언 , 10-2018-0120696 , 10-2129379
IsPETase 단백질 결정체의 제조 방법 및 IsPETase 변이체
김경진 , 10-2019-0017256 , 10-2088340
News
[매일신문] 경북대, CJ제일제당에 ‘PET 플라스틱 생분해’ 기술 이전
경북대학교(총장 홍원화)는 김경진 생명과학부 교수가 개발한 'PET 플라스틱 생분해' 관련 기술을 CJ제일제당(대표 최은석)에 이전하고, 최근 이와 관련된 기술이전 계약 및 공동연…_2021.10.15
[매일신문] 대구첨복재단-경북대 신약개발 연구협력
대구경북첨단의료산업진흥재단(이하 대구첨복재단)과 경북대가 신약개발연구에 힘을 모은다첨복재단 신약개발지원센터와 경북대 첨단복합 생명과학교육연구단은 지난 15일 혁신 신약개발분야 연구…_2021.06.26
[금강일보] 바이오촉매 기술 D-트레오닌 생산 기술 개발
2021.06.22
연구실 구성원
지도교수: 김경진 교수
Research Professor: 김상우
Researcher: 김일권
Ph.D course: 서호균, 주성준, 홍지연, 홍화석, 이동훈, 이슬후, 석지혜, 김성민, 박지영
Master course: 기동우, 이찬휘
Contact : kkim@knu.ac.kr
Homepage: https://webbuild1.knu.ac.kr/~protein/index.php
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