6kqw

Crystal structure of Yijc from B. subtilisCrystal structure of Yijc from B. subtilis

Structural highlights

6kqw is a 1 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.18Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NDPGT_BACSU Glycosyltransferase that can glycosylate a wide range of substrates, including various flavonoids, phenyl ketones, curcuminoid, lignins, zingerone, triterpenes, stilbene and anthraquinone, using UDP-glucose or ADP-glucose as sugar donor (PubMed:28315700, PubMed:33152360). It also exhibits O-, N- and S-glycosylation activities towards simple aromatics (PubMed:28315700). In vivo, the broad acceptor tolerance of YjiC might function as a detoxification agent against exogenous xenobiotics to make the strain adaptable to the changeable environment (Probable).^[1] ^[2] ^[3]

Publication Abstract from PubMed

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 A and 2.44 A, 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.

Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity.,Dai L, Qin L, Hu Y, Huang JW, Hu Z, Min J, Sun Y, Guo RT Biochem Biophys Res Commun. 2021 Jan 1;534:73-78. doi:, 10.1016/j.bbrc.2020.11.104. Epub 2020 Dec 10. PMID:33310191^[4]

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

References

↑ Dai L, Li J, Yao P, Zhu Y, Men Y, Zeng Y, Yang J, Sun Y. Exploiting the aglycon promiscuity of glycosyltransferase Bs-YjiC from Bacillus subtilis and its application in synthesis of glycosides. J Biotechnol. 2017 Apr 20;248:69-76. PMID:28315700 doi:10.1016/j.jbiotec.2017.03.009
↑ Liu B, Zhao C, Xiang Q, Zhao N, Luo Y, Bao R. Structural and biochemical studies of the glycosyltransferase Bs-YjiC from Bacillus subtilis. Int J Biol Macromol. 2021 Jan 1;166:806-817. doi: 10.1016/j.ijbiomac.2020.10.238., Epub 2020 Nov 2. PMID:33152360 doi:http://dx.doi.org/10.1016/j.ijbiomac.2020.10.238
↑ Dai L, Li J, Yao P, Zhu Y, Men Y, Zeng Y, Yang J, Sun Y. Exploiting the aglycon promiscuity of glycosyltransferase Bs-YjiC from Bacillus subtilis and its application in synthesis of glycosides. J Biotechnol. 2017 Apr 20;248:69-76. PMID:28315700 doi:10.1016/j.jbiotec.2017.03.009
↑ Dai L, Qin L, Hu Y, Huang JW, Hu Z, Min J, Sun Y, Guo RT. Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity. Biochem Biophys Res Commun. 2021 Jan 1;534:73-78. doi:, 10.1016/j.bbrc.2020.11.104. Epub 2020 Dec 10. PMID:33310191 doi:http://dx.doi.org/10.1016/j.bbrc.2020.11.104

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OCA

[1] Dai L, Li J, Yao P, Zhu Y, Men Y, Zeng Y, Yang J, Sun Y. Exploiting the aglycon promiscuity of glycosyltransferase Bs-YjiC from Bacillus subtilis and its application in synthesis of glycosides. J Biotechnol. 2017 Apr 20;248:69-76. PMID:28315700 doi:10.1016/j.jbiotec.2017.03.009

[2] Liu B, Zhao C, Xiang Q, Zhao N, Luo Y, Bao R. Structural and biochemical studies of the glycosyltransferase Bs-YjiC from Bacillus subtilis. Int J Biol Macromol. 2021 Jan 1;166:806-817. doi: 10.1016/j.ijbiomac.2020.10.238., Epub 2020 Nov 2. PMID:33152360 doi:http://dx.doi.org/10.1016/j.ijbiomac.2020.10.238

[3] Dai L, Li J, Yao P, Zhu Y, Men Y, Zeng Y, Yang J, Sun Y. Exploiting the aglycon promiscuity of glycosyltransferase Bs-YjiC from Bacillus subtilis and its application in synthesis of glycosides. J Biotechnol. 2017 Apr 20;248:69-76. PMID:28315700 doi:10.1016/j.jbiotec.2017.03.009

[4] Dai L, Qin L, Hu Y, Huang JW, Hu Z, Min J, Sun Y, Guo RT. Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity. Biochem Biophys Res Commun. 2021 Jan 1;534:73-78. doi:, 10.1016/j.bbrc.2020.11.104. Epub 2020 Dec 10. PMID:33310191 doi:http://dx.doi.org/10.1016/j.bbrc.2020.11.104

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