| 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
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| 2018 | |
| Source Publication | BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
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| ISSN | 0006-291X |
| EISSN | 1090-2104 |
| Volume | 501Issue:3Pages:674-681 |
| Subtype | Article |
| Abstract | HD-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. |
| Keyword | HD domain containing protein 5 ' nucleotidase Dimerization Nucleoside 5 ' Monophosphate |
| DOI | 10.1016/j.bbrc.2018.05.047 |
| WOS Keyword | ESCHERICHIA-COLI ; 5'-NUCLEOTIDASES ; NUCLEOTIDASES ; PHOSPHOHYDROLASE ; PHOSPHATASE ; YJJG ; YFBR |
| Indexed By | SCI ; MEDLINE |
| Language | 英语 |
| WOS Research Area | Biochemistry & Molecular Biology ; Biophysics |
| WOS Subject | Biochemistry & Molecular Biology ; Biophysics |
| WOS ID | WOS:000436057500011 |
| MedlineID | MEDLINE:29752939 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://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 Affilication | Institute 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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