Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop

doi:10.1007/s11426-019-9623-0

	Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop
	Lu, Lining 1; Guo, Yu3 ; Wang, Tian 1; Liang, Lujun 1; Zhao, Suwen3 ; Wang, Feng 2; Liu, Lei 1
	2020-02
发表期刊	SCIENCE CHINA-CHEMISTRY (IF:10.4[JCR-2023],7.9[5-Year])
ISSN	1674-7291
EISSN	1869-1870
卷号	63 期号:2 页码:237-243
发表状态	已发表
DOI	10.1007/s11426-019-9623-0
摘要	MINDY-1 is a recently discovered new family of deubiquitinating enzymes (DUB), but one of its yeast homologs, YGL082W, does not show any DUB activity in vitro. Sequence alignment shows that YGL082W possesses the correct catalytic triad, and yet did not catalyze either the hydrolysis of di-ubiquitin, crosslinking with C-terminally propargylated ubiquitin, or hydrolysis of ubiquitin-7-amino-4-methylcoumarin. After obtaining a crystal structure of the catalytic domain of YGL082W, we identified an interesting difference between the catalytic center loop of YGL082W and that of its human homolog MINDY-1. Because the conformation of the catalytic center loop was previously reported to be important for the deubiquitination activity of MINDY-1, we hypothesized that Glu27 (instead of the corresponding Pro136 in MINDY-1) of the catalytic center loop of YGL082W may impair the conformational change and account for the lack of activity. This hypothesis was supported by homology modeling and molecular dynamics simulations, which showed that the Pro-to-Glu mutation (P136E mutation for MINDY-1) creates a hydrogen bond that inhibits the conformation change of the catalytic center loop of MINDY-1. Further experiments through site-directed mutation validated this hypothesis, showing that the P27E mutation caused MIY1 (a homologous active DUB from yeast) to lose activity.
关键词	deubiquitinating enzymes (DUB) enzymology X-ray crystal structure molecular dynamics
收录类别	SCI ; SCIE ; EI ; CSCD
语种	英语
WOS研究方向	Chemistry
WOS类目	Chemistry, Multidisciplinary
WOS记录号	WOS:000512035700015
出版者	SCIENCE PRESS
WOS关键词	CHEMICAL-SYNTHESIS ; ACTIVE-SITE ; SUBSTRATE-SPECIFICITY ; UBIQUITIN CHAINS ; PROTEINS ; LIGATION ; REVEALS ; INFLAMMATION ; MECHANISMS ; PROTEASE
原始文献类型	Article
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/114817
专题	生命科学与技术学院_硕士生 iHuman研究所_PI研究组_赵素文组
通讯作者	Zhao, Suwen; Wang, Feng; Liu, Lei
作者单位	1.Tsinghua Univ, Key Lab Bioorgan Phosphorus Chem & Chem Biol, State Key Lab Chem Oncogen Shenzhen,Minist Educ,D, Tsinghua Peking Ctr Life Sci,Ctr Synthet & Syst B, Beijing 100084, Peoples R China 2.Beijing Inst Technol, Sch Life Sci, Beijing 100081, Peoples R China 3.ShanghaiTech Univ, iHuman Inst, Sch Life Sci & Technol, Shanghai 201210, Peoples R China
通讯作者单位	iHuman研究所
推荐引用方式 GB/T 7714	Lu, Lining,Guo, Yu,Wang, Tian,et al. Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop[J]. SCIENCE CHINA-CHEMISTRY,2020,63(2):237-243.
APA	Lu, Lining.,Guo, Yu.,Wang, Tian.,Liang, Lujun.,Zhao, Suwen.,...&Liu, Lei.(2020).Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop.SCIENCE CHINA-CHEMISTRY,63(2),237-243.
MLA	Lu, Lining,et al."Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop".SCIENCE CHINA-CHEMISTRY 63.2(2020):237-243.