6kqx

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Yijc from B. subtilis in complex with UDP

Structural highlights

6kqx 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 2.44Å
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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6kqx"

@@ Line 3: / Line 3: @@
 <StructureSection load='6kqx' size='340' side='right'caption='[[6kqx]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6kqx]] 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=6KQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KQX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6kqx]] 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=6KQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KQX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 2.44&#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=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=6kqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kqx OCA], [https://pdbe.org/6kqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kqx RCSB], [https://www.ebi.ac.uk/pdbsum/6kqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kqx 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]]

6kqx

From Proteopedia

Current revision

Crystal structure of Yijc from B. subtilis in complex with UDP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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