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Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5'-monophosphatase.


Indexed by:Journal Papers

First Author:Yang, Jingsi

Correspondence Author:Dong, YH; Liu, QS (reprint author), Chinese Acad Sci, Multidiscipline Ctr, Inst High Energy Phys, Beijing 100049, Beijing, Peoples R China.

Co-authors:Liu, Quansheng,Wang, Fei,Yang, Dan,Zhou, Ke,Liu, Min,Gao, Zengqiang,Liu, Peng,Dong, Yuhui,Zhang, Jianjun

Date of Publication:2018-01-01

Journal:Biochemical and biophysical research communications

Included Journals:PubMed、SCIE



Page Number:674-681

ISSN No.:1090-2104

Key Words:HD domain containing protein; 5 ' nucleotidase; Dimerization; Nucleoside 5 '; Monophosphate

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 YGK1, we unveiled that YGK1 structure resembled as the crystal structure of YfbR from E.coli. Size-exclusion chromatography and crosslinking studies suggested that YGK1 and YB92 existed in the form of a dimer, respectively, which were consistent with structural observation of YGK1. 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. Copyright © 2018 Elsevier Inc. All rights reserved.

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