4r8s

From Proteopedia

Dengue serotype 3 methyltransferase bound to Sinefungin

PDB ID 4r8s

Drag the structure with the mouse to rotate

Structural highlights

4r8s is a 2 chain structure with sequence from Dengue virus 3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.48Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C1KBQ3_9FLAV Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).[SAAS:SAAS026470_004_099774]

Publication Abstract from PubMed

Flavivirus methyltransferase is a genetically-validated antiviral target. Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. This raises a possibility that SAM is an integral structural component required for the folding of dengue virus (DENV) methyltransferase. Here we exclude this possibility by solving the crystal structure of DENV methyltransferase without SAM. The SAM ligand was removed from the enzyme through a urea-mediated denaturation-and-renaturation protocol. The crystal structure of the SAM-depleted enzyme exhibits a vacant SAM-binding pocket, with a conformation identical to that of the SAM-enzyme co-crystal structure. Functionally, equivalent enzymatic activities (N-7 methylation, 2'-O methylation, and GMP-enzyme complex formation) were detected for the SAM-depleted and SAM-containing recombinant proteins. These results clearly indicate that the SAM molecule is not an essential component for the correct folding of DENV methyltransferase. Furthermore, the results imply a potential antiviral approach to search for inhibitors that can bind to the SAM-binding pocket and compete against SAM binding. To demonstrate this potential, we have soaked crystals of DENV methyltransferase without a bound SAM with the natural product Sinefungin and show that preformed crystals are capable of binding ligands in this pocket.

Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine.,Noble CG, Li SH, Dong H, Chew SH, Shi PY Antiviral Res. 2014 Sep 19;111C:78-81. doi: 10.1016/j.antiviral.2014.09.003. PMID:25241250^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Noble CG, Li SH, Dong H, Chew SH, Shi PY. Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine. Antiviral Res. 2014 Sep 19;111C:78-81. doi: 10.1016/j.antiviral.2014.09.003. PMID:25241250 doi:http://dx.doi.org/10.1016/j.antiviral.2014.09.003