9DFW
X-ray crystal structure of an engineered Viperin-like enzyme from T. virens with bound CTP and SAM
Summary for 9DFW
| Entry DOI | 10.2210/pdb9dfw/pdb |
| Related | 9DFN 9DFU |
| Descriptor | Radical SAM core domain-containing protein, IRON/SULFUR CLUSTER, S-ADENOSYLMETHIONINE, ... (8 entities in total) |
| Functional Keywords | engineered viperin-like enzyme, viperin-like enzyme, ctp, sam, 4fe-4s cluster, ddhctp, antiviral protein |
| Biological source | Trichoderma virens |
| Total number of polymer chains | 3 |
| Total formula weight | 113448.66 |
| Authors | Lachowicz, J.C.,Bonanno, J.B.,Grove, T.L. (deposition date: 2024-08-30, release date: 2025-02-12, 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 Cited by 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: 40373765DOI: 10.1016/j.str.2025.04.009 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.677 Å) |
Structure validation
Download full validation report
