5IHY

The crystal structure of Bacillus subtilis SeMet-YpgQ

5IHY の概要

• エントリーDOI: 10.2210/pdb5ihy/pdb
• 分子名称: Uncharacterized protein, NICKEL (II) ION (3 entities in total)
• 機能のキーワード: hd domain, hydrolase
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 47993.78

構造登録者

Jeon, Y.J.,Song, W.S.,Yoon, S.I. (登録日: 2016-03-01, 公開日: 2016-04-27, 最終更新日: 2024-11-20)

主引用文献

Jeon, Y.J.,Park, S.C.,Song, W.S.,Kim, O.H.,Oh, B.C.,Yoon, S.I.
Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase
J.Struct.Biol., 195:113-122, 2016

PubMed Abstract: The optimal balance of cellular nucleotides and the efficient elimination of non-canonical nucleotides are critical to avoiding erroneous mutation during DNA replication. One such mechanism involves the degradation of excessive or abnormal nucleotides by nucleotide-hydrolyzing enzymes. YpgQ contains the histidine-aspartate (HD) domain that is involved in the hydrolysis of nucleotides or nucleic acids, but the enzymatic activity and substrate specificity of YpgQ have never been characterized. Here, we unravel the catalytic activity and structural features of YpgQ to report the first Mn(2+)-dependent pyrophosphohydrolase that hydrolyzes (deoxy)ribonucleoside triphosphate [(d)NTP] to (deoxy)ribonucleoside monophosphate and pyrophosphate using the HD domain. YpgQ from Bacillus subtilis (bsYpgQ) displays a helical structure and assembles into a unique dimeric architecture that has not been observed in other HD domain-containing proteins. Each bsYpgQ monomer accommodates a metal ion and a nucleotide substrate in a cavity located between the N- and C-terminal lobes. The metal cofactor is coordinated by the canonical residues of the HD domain, namely, two histidine residues and two aspartate residues, and is positioned in close proximity to the β-phosphate group of the nucleotide, allowing us to propose a nucleophilic attack mechanism for the nucleotide hydrolysis reaction. YpgQ enzymes from other bacterial species also catalyze pyrophosphohydrolysis but exhibit different substrate specificity. Comparative structural and mutational studies demonstrated that residues outside the major substrate-binding site of bsYpgQ are responsible for the species-specific substrate preference. Taken together, our structural and biochemical analyses highlight the substrate-recognition mode and catalysis mechanism of YpgQ in pyrophosphohydrolysis.

PubMed: 27062940
DOI: 10.1016/j.jsb.2016.04.002

実験手法

X-RAY DIFFRACTION (2.5 Å)