9DFU

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

Summary for 9DFU

• Entry DOI: 10.2210/pdb9dfu/pdb
• Related: 9DFN
• Descriptor: Radical SAM core domain-containing protein, CYTIDINE-5'-TRIPHOSPHATE, IRON/SULFUR CLUSTER, ... (6 entities in total)
• Functional Keywords: viperin-like enzyme, ctp, sam, 4fe-4s cluster, ddhctp, antiviral protein
• Biological source: Trichoderma virens
• Total number of polymer chains: 1
• Total formula weight: 38638.25

Authors

Lachowicz, J.C.,Bonanno, J.B.,Grove, T.L. (deposition date: 2024-08-30, release date: 2025-02-19, Last modification date: 2025-05-28)

Primary citation

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, 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

Experimental method

X-RAY DIFFRACTION (2.3 Å)