View source for 6jw8


==The crystal structure of KanD2 in complex with NADH and 3"-deamino-3"-hydroxykanamycin B==
<StructureSection load='6jw8' size='340' side='right'caption='[[6jw8]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6jw8]] is a 2 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=6JW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JW8 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CK0:(2S,3R,4S,5S,6R)-2-[(1S,2S,3R,4S,6R)-3-[(2R,3R,4R,5S,6R)-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-4,6-bis(azanyl)-2-oxidanyl-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol'>CK0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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=6jw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jw8 OCA], [https://pdbe.org/6jw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jw8 RCSB], [https://www.ebi.ac.uk/pdbsum/6jw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jw8 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q6L737_STRKN Q6L737_STRKN] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Kanosamine (3-amino-3-deoxy-d-glucose) is a characteristic sugar unit found in kanamycins, a group of aminoglycoside antibiotics. The kanosamine moiety originates from d-glucose in kanamycin biosynthesis. However, the timing of the replacement of the 3-OH group of the d-glucose-derived biosynthetic intermediate with the amino group is elusive. Comparison of biosynthetic gene clusters for related aminoglycoside antibiotics suggests that the nicotinamide adenine dinucleotide (NAD(+))-dependent dehydrogenase KanD2 and the pyridoxal 5'-phosphate (PLP)-dependent aminotransferase KanS2 are responsible for the introduction of the amino group at the C3 position of kanosamine. In this study, we demonstrated that KanD2 and KanS2 convert kanamycin A, B, and C to the corresponding 3''-deamino-3''-hydroxykanamycins (3''-hks) in the presence of PLP, 2-oxoglutarate, and NADH via a reverse reaction in the pathway. Furthermore, we observed that all of the 3''-hks are oxidized by KanD2 with NAD(+), but d-glucose, UDP-d-glucose, d-glucose 6-phosphate, and d-glucose 1-phosphate are not. Crystal structure analysis of KanD2 complexed with 3''-hkB and NADH illustrated the selective recognition of pseudotrisaccharides, especially the d-glucose moiety with 2-deoxystreptamine, by a combination of hydrogen bonds and CH-pi interactions. Overall, it was clarified that the kanosamine moiety of kanamycins is constructed after the glucosylation of the pseudodisaccharide biosynthetic intermediates in kanamycin biosynthesis.

Biochemical and Structural Analysis of a Dehydrogenase, KanD2, and an Aminotransferase, KanS2, That Are Responsible for the Construction of the Kanosamine Moiety in Kanamycin Biosynthesis.,Kudo F, Kitayama Y, Miyanaga A, Hirayama A, Eguchi T Biochemistry. 2020 Apr 6. doi: 10.1021/acs.biochem.0c00204. PMID:32237736<ref>PMID:32237736</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6jw8" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptomyces kanamyceticus]]
[[Category: Eguchi T]]
[[Category: Hirayama A]]
[[Category: Kitayama Y]]
[[Category: Kudo F]]
[[Category: Miyanaga A]]