7cl5: Difference between revisions

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-'''Unreleased structure'''
-The entry 7cl5 is ON HOLD  until Paper Publication
+==The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine==
+<StructureSection load='7cl5' size='340' side='right'caption='[[7cl5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7cl5]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_kanamyceticus Streptomyces kanamyceticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CL5 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9CS:(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL+2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE'>9CS</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</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=7cl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cl5 OCA], [https://pdbe.org/7cl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cl5 RCSB], [https://www.ebi.ac.uk/pdbsum/7cl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cl5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KANJ_STRKN KANJ_STRKN] Mediates the conversion of kanamycin B into 2'-dehydrokanamycin A during the transformation of kanamycin B to kanamycin A.<ref>PMID:22374809</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Kanamycin A is the major 2-deoxystreptamine (2DOS)-containing aminoglycoside antibiotic produced by Streptomyces kanamyceticus. The 2DOS moiety is linked with 6-amino-6-deoxy-d-glucose (6ADG) at O-4 and 3-amino-3-deoxy-d-glucose at O-6. Because the 6ADG moiety is derived from d-glucosamine (GlcN), deamination at C-2 and introduction of C-6-NH2 are required in the biosynthesis. A dehydrogenase KanQ and an aminotransferase KanB are presumed to be responsible for the introduction of C-6-NH2, although the substrates have not been identified. Here, we examined the substrate specificity of KanQ to better understand the biosynthetic pathway. It was found that KanQ oxidized kanamycin C more efficiently than the 3''-deamino derivative. Furthermore, substrate specificity of an oxygenase KanJ, which is responsible for deamination at C-2 of the GlcN moiety, was examined, and the crystal structure of KanJ was determined. It was found that C-6-NH2 is important for substrate recognition by KanJ. Thus, the modification of the GlcN moiety occurs after pseudotrisaccharide formation, followed by the introduction of C-6-NH2 by KanQ/KanB and deamination at C-2 by KanJ.
-Authors:
+Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.,Eguchi T, Kudo F, Kitayama Y, Miyanaga A, Numakura M Chembiochem. 2021 Jan 5. doi: 10.1002/cbic.202000839. PMID:33403742<ref>PMID:33403742</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7cl5" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Streptomyces kanamyceticus]]
+[[Category: Eguchi T]]
+[[Category: Kitayama Y]]
+[[Category: Kudo F]]
+[[Category: Miyanaga A]]