9DFU

X-ray crystal structure of the second Viperin-like enzyme from T. virens variant F40H with bound CTP and SAM

9DFU の概要

• エントリーDOI: 10.2210/pdb9dfu/pdb
• 関連するPDBエントリー: 9DFN
• 分子名称: Radical SAM core domain-containing protein, CYTIDINE-5'-TRIPHOSPHATE, IRON/SULFUR CLUSTER, ... (6 entities in total)
• 機能のキーワード: viperin-like enzyme, ctp, sam, 4fe-4s cluster, ddhctp, antiviral protein
• 由来する生物種: Trichoderma virens
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38638.25

構造登録者

Lachowicz, J.C.,Bonanno, J.B.,Grove, T.L. (登録日: 2024-08-30, 公開日: 2025-02-19, 最終更新日: 2025-07-16)

主引用文献

Lachowicz, J.C.,Grudman, S.,Bonanno, J.B.,Fiser, A.,Grove, T.L.
Structural insights from active site variants and beta-8 loop interactions in viperin-like enzymes.
Structure, 33:1263-, 2025

PubMed Abstract: Viperin and viperin-like enzymes (VLEs) are members of the radical SAM superfamily that perform radical-mediated dehydrations on nucleoside triphosphates to yield 3'-deoxy-3',4'-didehydronucleoside triphosphates (ddhNTPs). Interestingly, viperin and VLEs demonstrate species-dependent substrate selectivity. Some fungal species have a second VLE and, while most viperin and VLEs contain an NΦHXCXCXCF motif, these secondary VLEs are catalytically hindered by a histidine to phenylalanine substitution, an NΦFXCXCXCF motif (NΦF). Herein, we utilize a combination of bioinformatics, enzymology, and X-ray crystallography to demonstrate that NΦF VLEs likely utilize CTP as a substrate. Based on these observations, we demonstrate that the β-8 loop in TvVip1 can be engineered with the β-8 loop from a CTP-selective viperin (Mus musculus) to "swap" substrate selectivity from UTP to CTP. These results provide insight into the determinants of substrate selectivity exhibited by VLEs and introduce a potential route for engineering viperin and VLEs to form alternative ddhNTPs.

PubMed: 40373765
DOI: 10.1016/j.str.2025.04.009

実験手法

X-RAY DIFFRACTION (2.3 Å)