8h0m

From Proteopedia

Crystal structure of VioD

Structural highlights

8h0m is a 1 chain structure with sequence from Duganella sp. ZLP-XI. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.702Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A024AX32_9BURK

Publication Abstract from PubMed

Violacein is a pigment synthesized by gram-negative bacteria with various biological activities such as antimicrobial, antiviral, and anticancer activities. VioD is a key oxygenase converting protodeoxyviolaceinic acid to protoviolaceinic acid in violacein biosynthesis. To elucidate the catalytic mechanism of VioD, here, we resolved two crystal structures of VioD, a binary complex structure containing VioD and a FAD and a ternary complex structure composed of VioD, a FAD and a 2-ethyl-1-hexanol (EHN). Structural analysis revealed a deep funnel like binding pocket with wide entrance, this pocket is positively charged. The EHN is located at the deep bottom of the binding pocket near isoalloxazine ring. Further docking simulation help us to propose the mechanism of the hydroxylation of the substrate catalyzed by VioD. Bioinformatic analysis suggested and emphasized the importance of the conserved residues involved in substrate binding. Our results provide a structural basis for the catalytic mechanism of VioD.

Structural basis for substrate binding and catalytic mechanism of the key enzyme VioD in the violacein synthesis pathway.,Xu M, Xu D, Gao M, Zhuang X, Wang W, Sun B, Ran T Proteins. 2023 Mar 4. doi: 10.1002/prot.26484. PMID:36869636^[1]

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

References

↑ Xu M, Xu D, Gao M, Zhuang X, Wang W, Sun B, Ran T. Structural basis for substrate binding and catalytic mechanism of the key enzyme VioD in the violacein synthesis pathway. Proteins. 2023 Mar 4. PMID:36869636 doi:10.1002/prot.26484