6kqw: Difference between revisions

Latest revision as of 10:40, 22 November 2023

Crystal 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:	CIT
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:https://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:https://dx.doi.org/10.1016/j.bbrc.2020.11.104

Proteopedia Page Contributors and Editors (what is this?)

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:https://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:https://dx.doi.org/10.1016/j.bbrc.2020.11.104

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[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='6kqw' size='340' side='right'caption='[[6kqw]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6kqw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KQW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6kqw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KQW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.18&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yjiC, BSU12220 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6kqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kqw OCA], [https://pdbe.org/6kqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kqw RCSB], [https://www.ebi.ac.uk/pdbsum/6kqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kqw ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDPGT_BACSU 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).<ref>PMID:28315700</ref> <ref>PMID:33152360</ref> <ref>PMID:28315700</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
 [[Category: Large Structures]]
-[[Category: Chen, C C]]
+[[Category: Chen CC]]
-[[Category: Dai, L H]]
+[[Category: Dai LH]]
-[[Category: Guo, R T]]
+[[Category: Guo RT]]
-[[Category: Hu, Y M]]
+[[Category: Hu YM]]
-[[Category: Huang, J W]]
+[[Category: Huang JW]]
-[[Category: Liu, W D]]
+[[Category: Liu WD]]
-[[Category: Prenyltransferase]]
-[[Category: Transferase]]

6kqw: Difference between revisions

Latest revision as of 10:40, 22 November 2023

Crystal structure of Yijc from B. subtilis

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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