6KZ6

Crystal structure of ASFV dUTPase

Summary for 6KZ6

• Entry DOI: 10.2210/pdb6kz6/pdb
• Descriptor: E165R, 2'-DEOXYURIDINE 5'-MONOPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: homotrimer, dutpase, dump, viral protein, hydrolase
• Biological source: African swine fever virus (ASFV)
• Total number of polymer chains: 3
• Total formula weight: 62737.21

Authors

Guo, Y.,Chen, C.,Li, G.B.,Cao, L.,Wang, C.W. (deposition date: 2019-09-23, release date: 2019-11-13, Last modification date: 2024-03-27)

Primary citation

Li, G.,Wang, C.,Yang, M.,Cao, L.,Fu, D.,Liu, X.,Sun, D.,Chen, C.,Wang, Y.,Jia, Z.,Yang, C.,Guo, Y.,Rao, Z.
Structural Insight into African Swine Fever Virus dUTPase Reveals a Novel Folding Pattern in the dUTPase Family.
J.Virol., 94:-, 2020

PubMed Abstract: The African swine fever virus (ASFV) is the deadly pathogen of African swine fever (ASF) that induces high mortality, approaching 100% in domestic pigs, causes enormous losses to the global pig industry, and threatens food security. Currently, there is no effective treatment or preventive countermeasure. dUTPases (deoxyuridine 5'-triphosphate pyrophosphatases) are ubiquitous enzymes that are essential for the hydrolysis of dUTP and prevent the misincorporation of dUTP into newly synthesized DNA. Here, we present the crystal structures of the ASFV dUTPase in complex with the product dUMP and cofactor Mg at a resolution of 2.2 Å. We observed that a unique "turning point" at G125 plays an unexpected critical role in the swapping region of the C-terminal segment, which is further stabilized by the interactions of the last C-terminal β strand with the β1 and β2 strands, thereby positioning the catalytic motif 5 into the active site of its own subunit instead of into a third subunit. Therefore, the ASFV dUTPase employs a novel two-subunit active site that is different than the classic trimeric dUTPase active site, which is composed of all three subunits. Meanwhile, further results confirmed that the configuration of motifs 1 to 5 has high structural homology with and a catalytic mechanism similar to that of the known trimeric dUTPases. In general, our study expands the information not only on the structural diversity of the conserved dUTPase family but also on the details needed to utilize this dUTPase as a novel target in the treatment of ASF. African swine fever virus (AFSV), a large enveloped double-stranded DNA virus, causes a deadly infection in domestic pigs. In addition to Africa, Europe, and South America, countries in Asia, such as China, Vietnam, and Mongolia, have suffered the hazards posed by ASFV outbreaks in recent years. Until now, there has been no vaccine for protection from ASFV infection or effective treatments to cure ASF. Here, we solved the crystal structure of the ASFV dUTPase-dUMP-Mg complex. The ASFV dUTPase displays a noncanonical folding pattern that differs from that of the classic homotrimeric dUTPase, in which the active site is composed of two subunits. In addition, several nonconserved residues within the 3-fold axis channel play a vital role in ASFV dUTPase homotrimer stability. Our finding on these unique structural features of the ASFV dUTPase could be explored for the design of potential specific inhibitors that target this unique enzyme.

PubMed: 31748385
DOI: 10.1128/JVI.01698-19

Experimental method

X-RAY DIFFRACTION (2.187 Å)