6KQW

Crystal structure of Yijc from B. subtilis

Summary for 6KQW

• Entry DOI: 10.2210/pdb6kqw/pdb
• Descriptor: Uncharacterized UDP-glucosyltransferase YjiC, CITRIC ACID (3 entities in total)
• Functional Keywords: prenyltransferase, transferase
• Biological source: Bacillus subtilis subsp. subtilis str. 168
• Total number of polymer chains: 1
• Total formula weight: 43935.14

Authors

Hu, Y.M.,Dai, L.H.,Huang, J.W.,Liu, W.D.,Chen, C.C.,Guo, R.T. (deposition date: 2019-08-20, release date: 2020-09-30, Last modification date: 2023-11-22)

Primary citation

Dai, L.H.,Qin, L.,Hu, Y.M.,Huang, J.W.,Hu, Z.,Min, J.,Sun, Y.,Guo, R.T.
Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity.
Biochem.Biophys.Res.Commun., 534:73-78, 2021

PubMed Abstract: Glycosylation catalyzed by uridine diphosphate-dependent glycosyltransferases (UGT) contributes to the chemical and functional diversity of a number of natural products. Bacillus subtilis Bs-YjiC is a robust and versatile UGT that holds potentials in the biosynthesis of unnatural bioactive ginsenosides. To understand the molecular mechanism underlying the substrate promiscuity of Bs-YjiC, we solved crystal structures of Bs-YjiC and its binary complex with uridine diphosphate (UDP) at resolution of 2.18 Å and 2.44 Å, respectively. Bs-YjiC adopts the classical GT-B fold containing the N-terminal and C-terminal domains that accommodate the sugar acceptor and UDP-glucose, respectively. Molecular docking indicates that the spacious sugar-acceptor binding pocket of Bs-YjiC might be responsible for its broad substrate spectrum and unique glycosylation patterns toward protopanaxadiol-(PPD) and PPD-type ginsenosides. Our study reveals the structural basis for the aglycone promiscuity of Bs-YjiC and will facilitate the protein engineering of Bs-YjiC to synthesize novel bioactive glycosylated compounds.

PubMed: 33310191
DOI: 10.1016/j.bbrc.2020.11.104

Experimental method

X-RAY DIFFRACTION (2.18 Å)