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Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5 '-monophosphatase
Yang, JS; Wang F(王飞); Zhou K(周柯); Gao ZQ(高增强); 刘鹏(多); Dong YH(董宇辉); Liu QS(刘全胜); Wang, F; Yang, D; Zhou, K; Liu, M; Gao, ZQ; Liu, P; Dong, YH; Zhang, JJ; Liu, QS
2018
Source PublicationBIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
ISSN0006-291X
EISSN1090-2104
Volume501Issue:3Pages:674-681
SubtypeArticle
AbstractHD-domain is a conserved domain, with the signature of histidine and aspartic (HD) residues doublets. HD-domain proteins may possess nucleotidase and phosphodiesterase activities, and they play important roles in signaling and nucleotide metabolism. In yeast, HD-domain proteins with nucleotidase activity remained unexplored. Here, we biochemically and structurally characterized two HD domain proteins YGK1 (YGL101W) and YB92 (YBR242W) from Saccharomyces cerevisiae as nucleoside 5'-monophosphatases, with substrate preference for deoxyribonucleoside 5'-monophosphatase over ribonucleoside 5'-monophosphatase. By determining the crystal structure of YGKI, we unveiled that YGKI structure resembled as the crystal structure of YfbR from E. coli. Size-exclusion chromatography and crosslinking studies suggested that YGKI and YB92 existed in the form of a dimer, respectively, which were consistent with structural observation of YGKI. Site-directed mutagenesis demonstrated that more extensive conserved residues near the divalent metal coordinating active site were essential for YGK1 activity than previous suggested. The metal coordinating His89 and Asp90, and the neighboring conserved Glu93, Glu114 and Glu145 were individually critical for catalysis. In addition, alignments suggested that three flexible loops with hydrophobic residues might be implicated in substrate selectivity to nucleoside moiety. Together, our comparative structural and mutational studies suggested that YGK1 and YB92 functioned as 5'-nucleotidases in S. cerevisiae. (C) 2018 Elsevier Inc. All rights reserved.
KeywordHD domain containing protein 5 ' nucleotidase Dimerization Nucleoside 5 ' Monophosphate
DOI10.1016/j.bbrc.2018.05.047
WOS KeywordESCHERICHIA-COLI ; 5'-NUCLEOTIDASES ; NUCLEOTIDASES ; PHOSPHOHYDROLASE ; PHOSPHATASE ; YJJG ; YFBR
Indexed BySCI ; MEDLINE
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biophysics
WOS SubjectBiochemistry & Molecular Biology ; Biophysics
WOS IDWOS:000436057500011
MedlineIDMEDLINE:29752939
Citation statistics
Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihep.ac.cn/handle/311005/287031
Collection多学科研究中心
实验物理中心
Affiliation中国科学院高能物理研究所
First Author AffilicationInstitute of High Energy
Recommended Citation
GB/T 7714
Yang, JS,Wang F,Zhou K,et al. Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5 '-monophosphatase[J]. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS,2018,501(3):674-681.
APA Yang, JS.,王飞.,周柯.,高增强.,刘鹏.,...&Liu, QS.(2018).Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5 '-monophosphatase.BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS,501(3),674-681.
MLA Yang, JS,et al."Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5 '-monophosphatase".BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 501.3(2018):674-681.
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