7cl5: Difference between revisions
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The | ==The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine== | ||
<StructureSection load='7cl5' size='340' side='right'caption='[[7cl5]], [[Resolution|resolution]] 2.50Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7cl5]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1441 As 4.1441]. 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 [http://proteopedia.org/fgij/fg.htm?mol=7CL5 FirstGlance]. <br> | |||
</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kanJ, kacB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1967 AS 4.1441])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.37 1.14.11.37] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7cl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cl5 OCA], [http://pdbe.org/7cl5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cl5 RCSB], [http://www.ebi.ac.uk/pdbsum/7cl5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cl5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 7cl5" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: As 4 1441]] | |||
[[Category: Large Structures]] | |||
[[Category: Oxidoreductase]] | |||
[[Category: Eguchi, T]] | |||
[[Category: Kitayama, Y]] | |||
[[Category: Kudo, F]] | |||
[[Category: Miyanaga, A]] | |||
[[Category: Dioxygenase]] | |||
[[Category: Kanamycin biosynthesis]] | |||
Revision as of 08:54, 20 January 2021
The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycineThe crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine
Structural highlights
Function[KANJ_STRKN] Mediates the conversion of kanamycin B into 2'-dehydrokanamycin A during the transformation of kanamycin B to kanamycin A.[1] Publication Abstract from PubMedKanamycin 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. 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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