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

Biochemical and Biophysical Research Communications
Jingsi YangQuansheng Liu

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 ...Continue Reading

Citations

Feb 23, 2020·Plant Science : an International Journal of Experimental Plant Biology·Liangliang HuYuhong Li

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