5Y5Q

Crystal structure of the WSSV dUTPase D88N/R158E mutant in complex with dUTP

5Y5Q の概要

• エントリーDOI: 10.2210/pdb5y5q/pdb
• 分子名称: Wsv112, DEOXYURIDINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: dutpase, wssv, pyrophosphatase, dutp, viral protein
• 由来する生物種: White spot syndrome virus (isolate Shrimp/China/Tongan/1996) (WSSV)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 58477.89

構造登録者

Ma, Q.,Zang, K. (登録日: 2017-08-09, 公開日: 2017-12-06, 最終更新日: 2023-11-22)

主引用文献

Zang, K.,Li, F.,Ma, Q.
The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner.
J. Biol. Chem., 293:1088-1099, 2018

PubMed Abstract: dUTPases are essential enzymes for maintaining genome integrity and have recently been shown to play moonlighting roles when containing extra sequences. Interestingly, the trimeric dUTPase of white spot syndrome virus (wDUT) harbors a sequence insert at the position preceding the C-terminal catalytic motif V (pre-V insert), rarely seen in other dUTPases. However, whether this extra sequence endows wDUT with additional properties is unknown. Herein, we present the crystal structures of wDUT in both ligand-free and ligand-bound forms. We observed that the pre-V insert in wDUT forms an unusual β-hairpin structure in the domain-swapping region and thereby facilitates a unique orientation of the adjacent C-terminal segment, positioning the catalytic motif V onto the active site of its own subunit instead of a third subunit. Consequently, wDUT employs two-subunit active sites, unlike the widely accepted paradigm that the active site of trimeric dUTPase is contributed by all three subunits. According to results from local structural comparisons, the active-site configuration of wDUT is similar to that of known dUTPases. However, we also found that residues in the second-shell region of the active site are reconfigured in wDUT as an adaption to its unique C-terminal orientation. We also show that deletion of the pre-V insert significantly reduces wDUT's enzymatic activity and thermal stability. We hypothesize that this rare structural arrangement confers additional functionality to wDUT. In conclusion, our study expands the structural diversity in the conserved dUTPase family and illustrates how sequence insertion and amino acid substitution drive protein evolution cooperatively.

PubMed: 29187596
DOI: 10.1074/jbc.M117.815266

実験手法

X-RAY DIFFRACTION (1.56 Å)