9wvy: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 9wvy is ~~ON HOLD~~

==NDP-4-keto-6-deoxyglucose-3-dehydratase KsgR in complex with PMP and AKG==

== Structural highlights ==

<table><tr><td colspan='2'>[[9wvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces Streptomyces]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9WVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9WVY FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</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=9wvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9wvy OCA], [https://pdbe.org/9wvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9wvy RCSB], [https://www.ebi.ac.uk/pdbsum/9wvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9wvy ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A0K1H368_9ACTN A0A0K1H368_9ACTN]

== Publication Abstract from PubMed ==

Kasugamine (2,4-diamino-2,3,4,6-tetradeoxy-d-mannose, 1) is a rare multideoxy diamino-sugar forming the core skeleton of the commercial aminoglycoside antibiotic Kasugamycin (KSG, 2), an agricultural fungicide that has been used against rice blast disease for more than 60 years. Despite the reported biosynthetic gene cluster (BGC) for 2, the enzymatic logic leading to the formation of 1 remained unclear. Here, we report the biosynthetic mechanism of 1. Five enzymes horizontal line KsgQ, KsgB, KsgD, KsgR, and KsgC horizontal line can biochemically convert uridine diphosphate-N-acetyl-d-glucosamine (UDP-GlcNAc, 4) to generate the sugar donor 6, which is incorporated into 2, as confirmed by stable isotope-labeled feeding experiments. KsgB is characterized as the first enzyme catalyzing the deacetylation of uridine diphosphate-N-acetyl-d-mannosamine (UDP-ManNAc, 5), while KsgR represents the first UDP-sugar 3-dehydrase catalyzing the C-3 deoxygenation of the KsgD product (8) via the cofactors pyridoxal-5'-phosphate (PLP) and l-glutamic acid (l-Glu), and employs a ColD-like catalytic mechanism, as shown by crystallographic analysis, molecular docking, and site-directed mutagenesis. Our findings unravel the biosynthetic mysteries of 1, highlight the intriguing strategies for biosynthesizing diamino-sugars in nature, and provide some evidence for further completely uncovering the biosynthetic logic of 2.

~~Authors:~~ Chen, Y~~.L.~~, Mei, K.R.

Characterization of UDP-Sugar 3-Dehydrase KsgR in the Biosynthesis of a Distinctive Multideoxy Diamino-Sugar Kasugamine of Kasugamycin.,Li Y, Chen Y, Shi J, Wu J, Wang Y, Ren J, Li Y, Zhou J, Gao Q, Mei K, Guo Z J Am Chem Soc. 2026 May 13;148(18):19205-19213. doi: 10.1021/jacs.6c03331. Epub , 2026 May 3. PMID:42076866<ref>PMID:42076866</ref>

~~Description: NDP~~-4-~~keto-6-deoxyglucose-3-dehydratase KasR in complex with PMP and Glutamic acid~~

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

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Mei, K.R~~]]

[[Category: Chen~~, Y.L~~]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Streptomyces]]

[[Category: Chen YL]]

[[Category: Mei KR]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9wvy is ON HOLD
+==NDP-4-keto-6-deoxyglucose-3-dehydratase KsgR in complex with PMP and AKG==
+<StructureSection load='9wvy' size='340' side='right'caption='[[9wvy]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9wvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces Streptomyces]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9WVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9WVY FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</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=9wvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9wvy OCA], [https://pdbe.org/9wvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9wvy RCSB], [https://www.ebi.ac.uk/pdbsum/9wvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9wvy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A0K1H368_9ACTN A0A0K1H368_9ACTN]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Kasugamine (2,4-diamino-2,3,4,6-tetradeoxy-d-mannose, 1) is a rare multideoxy diamino-sugar forming the core skeleton of the commercial aminoglycoside antibiotic Kasugamycin (KSG, 2), an agricultural fungicide that has been used against rice blast disease for more than 60 years. Despite the reported biosynthetic gene cluster (BGC) for 2, the enzymatic logic leading to the formation of 1 remained unclear. Here, we report the biosynthetic mechanism of 1. Five enzymes horizontal line KsgQ, KsgB, KsgD, KsgR, and KsgC horizontal line can biochemically convert uridine diphosphate-N-acetyl-d-glucosamine (UDP-GlcNAc, 4) to generate the sugar donor 6, which is incorporated into 2, as confirmed by stable isotope-labeled feeding experiments. KsgB is characterized as the first enzyme catalyzing the deacetylation of uridine diphosphate-N-acetyl-d-mannosamine (UDP-ManNAc, 5), while KsgR represents the first UDP-sugar 3-dehydrase catalyzing the C-3 deoxygenation of the KsgD product (8) via the cofactors pyridoxal-5'-phosphate (PLP) and l-glutamic acid (l-Glu), and employs a ColD-like catalytic mechanism, as shown by crystallographic analysis, molecular docking, and site-directed mutagenesis. Our findings unravel the biosynthetic mysteries of 1, highlight the intriguing strategies for biosynthesizing diamino-sugars in nature, and provide some evidence for further completely uncovering the biosynthetic logic of 2.
-Authors: Chen, Y.L., Mei, K.R.
+Characterization of UDP-Sugar 3-Dehydrase KsgR in the Biosynthesis of a Distinctive Multideoxy Diamino-Sugar Kasugamine of Kasugamycin.,Li Y, Chen Y, Shi J, Wu J, Wang Y, Ren J, Li Y, Zhou J, Gao Q, Mei K, Guo Z J Am Chem Soc. 2026 May 13;148(18):19205-19213. doi: 10.1021/jacs.6c03331. Epub , 2026 May 3. PMID:42076866<ref>PMID:42076866</ref>
-Description: NDP-4-keto-6-deoxyglucose-3-dehydratase KasR in complex with PMP and Glutamic acid
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Mei, K.R]]
+<div class="pdbe-citations 9wvy" style="background-color:#fffaf0;"></div>
-[[Category: Chen, Y.L]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Streptomyces]]
+[[Category: Chen YL]]
+[[Category: Mei KR]]